甜瓜属Ty1-copia类逆转座子分析及其对异源四倍体遗传变异的影响研究
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摘要
逆转座子广泛分布于植物界,是转座元件中数量最多的一类。Tyl-copia类逆转座子是植物中研究较为深入的一类,其以RNA为中介,采用“复制-粘贴”的方式进行转座,对植物基因组大小、结构、进化等都有重要影响。异源多倍化是物种形成的重要过程,在许多物种起源过程中起着重要作用。新形成的异源多倍体经历着巨大的“基因组”冲击,能够激活逆转座子的表达,而逆转座子的转录又会反过来影响异源多倍体的遗传及表观遗传变异。因此,本研究以甜瓜属野生酸黄瓜Cucumis hystrix(2n=2x=24)为材料,研究了Tyl-copia类逆转座子的异质性、拷贝数、基因组以及染色体分布；随后基于本实验室新合成的甜瓜属异源四倍体C. hytivus (2n=4x=38),研究了异源多倍化对逆转座子转录活性的影响；最后研究了逆转座子对异源四倍体早期世代遗传和表观遗传变异的影响,探索其遗传及表观遗传变异的相关机制。
1.甜瓜属Tyl-copia类逆转座子分离、分布及遗传多样性分析
利用兼并引物从甜瓜属栽培黄瓜基因组中扩增Tyl-copia类逆转座子逆转录酶的保守片段。扩增产物经回收测序后,共获得17条逆转录酶基因序列。序列分析表明,这些序列的长度为207bp-266bp,同源性范围为44.1%-98.1%,表现出高度的异质性。在这17条序列中,有10条是完整的,可能具有潜在的转录活性,其余7条为不完整序列,发生了移框突变和/或终止密码子突变。聚类分析显示这些序列可以分成4个家族,与来自其它作物的逆转录酶基因表现出较高的同源性。
另外从甜瓜属野生酸黄瓜中克隆了24个高度异质的Tyl-copia类逆转座子逆转录酶基因序列。Southern杂交分析表明该逆转座子以多拷贝形式存在于酸黄瓜基因组。斑点杂交分析表明其拷贝数大约为5460,约占基因组总量的8.5%。聚类分析显示这些序列可分为5个家族,与其它作物中的逆转录酶序列存在高度同源性。荧光原位杂交(Fluorescence in situ hybridization, FISH)揭示Tyl-copia类逆转座子存在于酸黄瓜所有染色体,并在末端异染色质区成簇状分布。
2.-甜瓜属异源多倍化对Tyl-copia类逆转座子转录活性的影响
为了研究甜瓜属异源多倍化对新合成异源四倍体中TyI-copia类逆转座子转录活性的影响,利用RT-PCR从异源四倍体C. hytivus及其二倍体亲本(C. hystrix和Csativus)中扩增逆转录酶基因。结果仅在异源四倍体中获得了目的片段,回收测序后共获得18个高度异质的序列。有义突变和无义突变分析暗示这些逆转座子序列主要受净化选择影响。RT-PCR和gPCR分析验证了逆转录酶基因在甜瓜属异源四倍体早期四个世代中的表达,证实这些逆转座子的活性是由异源多倍化造成的。
3.逆转座子对甜瓜属异源四倍体早期世代基因组变异的影响
为了检测逆转座子对甜瓜属异源四倍体基因组变异的影响,本文以野生酸黄瓜C. hystrix与栽培黄瓜C. sativus的正反交种间杂种F1、异源四倍体C. hytivus早期世代(C. hystrix作母本)及其二倍体亲本为材料进行SSAP分析。结果发现正反交F1及异源四倍体均发生广泛的序列变异,包括亲本条带的丢失和新增条带的出现,正反交条带丢失数和新增条带数基本没有差异。无论是条带丢失还是增加,均主要发生在F1、S1和S2代,因此推测异源四倍体早期基因组变异是一个快速的过程。
同时利用基于逆转座子的分子标记IRAP和REMAP以及微卫星标记ISSR等,研究甜瓜属新合成异源四倍体早期世代的基因组变异。结果共检测出28个变异条带,包括24个亲本丢失条带和4个新增条带,表明基因组变异主要表现为亲本序列丢失。在这24个丢失序列中,18个是酸黄瓜特异序列,4个是栽培黄瓜特异序列,另2个是双亲共有序列,暗示序列丢失可能与亲本基因组的组成相关。而且大部分变异出现在S1代,并能在随后三个世代(S2-S4)中稳定遗传,表明基因组变异是一个快速的过程,促进异源四倍体稳定形成。
进一步对发生变异的序列进行回收测序,共获得11个序列。比对分析显示变异序列在编码区和非编码区都有出现,表明逆转座子随机插入基因组中。随后利用荧光原位杂交技术研究变异序列的染色体分布,结果显示FISH信号倾向分布于着丝粒区和端粒区,表明这些区域可能是基因组变异的热点区域。
4.逆转座子对甜瓜属异源四倍体早期世代表观遗传变异的影响
利用荧光原位杂交技术研究了LTR逆转座子在甜瓜属新合成异源四倍体Chytivus的染色体分布,结果揭示LTR逆转座子分布于C. hytivus所有染色体,并在末端区域呈簇状聚集,在大部分染色体仅在一个末端聚集,而少数在两个末端都有聚集,表明逆转座子在异源四倍体中具有高拷贝数和不均匀分布等特点。
利用cDNA-SSAP技术研究逆转座子对甜瓜属异源四倍体早期世代表观遗传变异的影响,结果显示异源四倍体早期世代发生了广泛的表观遗传变异,主要表现为基因沉默和基因激活。对发生变异的序列进行回收测序,共获得20个序列,包括12个基因沉默和8个基因激活。序列分析表明这些沉默/激活基因包括已知基因和未知基因,进一步RT-PCR和gPCR分析验证了上述结果。基因沉默和激活主要发生在异源四倍体的早期世代,并能在随后世代稳定遗传,暗示逆转座子通过对其邻近基因的表达造成干扰,从而有助于新合成异源四倍体的快速稳定。
Retrotransposons are the most abundant and widespread class of transposable elements (TEs) in plant kingdom. Tyl-copia-like retrotransposon is one of the most deeply studied types, which transpose through a RNA intermediate by a "copy-paste" mechanism. They play an important role in plant genome size, structure, evolution, and so on. Allopolyploidy is a prominent process for plant speciation, and plays a significant role in the origin of many species. Newly formed allopolyploid experiences a huge "genomic shock", which can activate the expression of retrotransposons. In contrast, the transcription of retrotransposons can affect genetic and epigenetic changes of allopolyploid. Therefore, in this work, we studied the heterogeneity, copy numbers, genomic and chromosomal distribution of Tyl-copia retrotransposons in Cucumis hystrix (2n=2x=24), a wild species of Cucumis. And then researched the effect of allopolyploidization on transcriptional activation of retrotransposons in the newly formed allotetraploid C. hytivus (2n=4x=38). Finally, the effect of retrotransposons on genetic and epigenetic changes in early generations of Cucumis allotetraploid was investigated to explore the genetic and epigenetic mechanisms.
1. The isolation, distribution and genetic diversity analysis of Tyl-copia retrotransposons in Cucumis
The reverse transcriptase sequences of Tyl-copia retrotransposons were isolated from genome of Cucumis sativus using degenerate oligonucleotide primers. The amplified production was recovered and sequenced,17 different sequences of reverse transcriptase were obtained. These sequences showed high heterogeneity with length varied from 207bp-266bp and homology ranged from 44.1%-98.1%. Among them,10 were intact with potential transcriptional activity, whereas the remaining sequences had a stop codon, a frameshift, or both. Phylogenetic analysis showed that these sequences were divided into four families and had high homology with other species.
In addition,24 highly heterogeneous reverse transcriptase sequences of Tyl-copia retrotransposon were isolated from C. hystrix. Southern hybridization analysis showed that retrotransposons existed in C. hystrix by high copies. Southern dot-blot analysis revealed that the copy number was about 5460, which constituted approximately 8.5% of the C hystrix genome. Phylogenetic analysis showed that these sequences were divided into 5 families and had high homology with other species. Fluorescence in situ hybridization (FISH) revealed the retrotransposons of this kind were widely dispersed over all the chromosomes with clusters in terminal heterochromatin regions.
2. The influence of allopolyploidization on expression of Tyl-copia retrotransposons in Cucumis
To investigate the effect of allopolyploidy on the expression of Tyl-copia retrotransposons in Cucumis newly synthesized allotetraploid, C. hytivus, RT-PCR strategy was carried out to amplify reverse transcriptase (RT) genes from C. hytivus and its diploid parents (C hystrix and C. sativus). Only the allotetraploid yielded the expected product. When recovered and sequenced,18 unique clones with significantly high heterogeneity were obtained. The synonymous (dS) and nonsynonymous (dN) substitution analysis suggested that the RT sequences had been under purifying selection. RT-PCR and gPCR analysis of the cloned reverse transcriptase in the first four generations of Cucumis allotetraploid further proved that the activation of retrotransposons was induced by allopolyploidization.
3. Effect of retrotransposons on genomic changes in early generations of Cucumis allotetraploid
In order to study the genetic variation of early generations of Cucumis allotetraploid, genomic DNAs from the reciprocal F1 hybrids of C. hystrix and C. sativus, early generations of the newly synthesized allotetraploid and their diploid parents were used for SSAP (Sequence specific amplification polymorphism) analysis. The results showed that loss of parental fragments and gaining of novel fragments were detected in the reciprocal F1 hybrids and allotetraploid of interspecific hybridization. No significant differences with regards to the number of fragments lost or gained between reciprocal crosses were noted. Both loss and gaining of fragments are mainly occurred in F1, S1 and S2 generations, indicating the variation in early generations is a rapid process.
In the meantime, two retrotransposon-based markers IRAP (Inter-retrotransposon amplified polymorphism) and REMAP (Retrotransposon-microsatellite amplified polymorphism) and a microsatellite-based marker ISSR (Inter-simple sequence repeat) were employed to investigate genomic changes in early generations of C. hytivus. Twenty-eight fragments were examined, included 24 loss of parent fragment and 4 gaining of novel fragment, suggesting that sequence loss is a relatively frequent event. Among the 24 lost fragments,18 were of C. hystrix origin,4 were C. sativus-specific, and the remaining 2 were shared by both species, implying that fragment loss may be correlated with the genomic constitution of diploid parents. Moreover, most changes were observed in the S1 generation and stably inherited in the subsequent three generations (S2-S4), indicating that genomic changes were rapid driving force for the stabilization of allotetraploid.
Further, the altered DNA fragments were recovered and sequenced, and finally 11 sequences were obtained. Sequence analysis showed that genomic changes in the allotetraploid occurred in both coding and non-coding regions, which might suggest that retrotransposons inserted in genome randomly. Subsequently, FISH analysis revealed a unique chromosomal distribution of altered fragments, where the preferential FISH signals occurred in the centromeric and telomeric regions, implying that these regions were the possible hotspots for genomic changes.
4. Effect of retrotransposons on epigenetic changes in early generations of Cucumis allotetraploid
FISH technique was employed to study the chromosomal distribution of LTR retrotransposons in Cucumis allotetraploid. The result revealed that LTR retrotransposons distributed throughout all the chromosomes, with clusters on terminal regions. Most chromosomes showed clusters only on one terminal whereas a few had clusters on both terminals, indicating their high copy numbers and uneven distribution in C. hytivus.
cDNA-SSAP strategy was used to investigate the effect of retrotransposons on epigenetic changes in the first four generations of newly formed Cucumis allotetraploid. Extensive epigenetic changes were detected, including gene silencing and gene activation. The transcripts that exhibited gene expression alteration were recovered and sequenced, and 20 sequences were obtained, containing 12 gene silencing and 8 gene activation. Sequence analysis showed that the silenced/activated genes consisted of known and unknown genes. Further RT-PCR and gPCR analysis validated the above result. Both gene silencing and activation mainly occurred in early generations of the allotetraploid, and could be stably inherited in subsequent generations. These results implied the transcriptional interference of retrotransposons on their adjacent genes, which contributed to the stabilization of newly formed allotetraploid.
1.甜瓜属Tyl-copia类逆转座子分离、分布及遗传多样性分析
利用兼并引物从甜瓜属栽培黄瓜基因组中扩增Tyl-copia类逆转座子逆转录酶的保守片段。扩增产物经回收测序后,共获得17条逆转录酶基因序列。序列分析表明,这些序列的长度为207bp-266bp,同源性范围为44.1%-98.1%,表现出高度的异质性。在这17条序列中,有10条是完整的,可能具有潜在的转录活性,其余7条为不完整序列,发生了移框突变和/或终止密码子突变。聚类分析显示这些序列可以分成4个家族,与来自其它作物的逆转录酶基因表现出较高的同源性。
另外从甜瓜属野生酸黄瓜中克隆了24个高度异质的Tyl-copia类逆转座子逆转录酶基因序列。Southern杂交分析表明该逆转座子以多拷贝形式存在于酸黄瓜基因组。斑点杂交分析表明其拷贝数大约为5460,约占基因组总量的8.5%。聚类分析显示这些序列可分为5个家族,与其它作物中的逆转录酶序列存在高度同源性。荧光原位杂交(Fluorescence in situ hybridization, FISH)揭示Tyl-copia类逆转座子存在于酸黄瓜所有染色体,并在末端异染色质区成簇状分布。
2.-甜瓜属异源多倍化对Tyl-copia类逆转座子转录活性的影响
为了研究甜瓜属异源多倍化对新合成异源四倍体中TyI-copia类逆转座子转录活性的影响,利用RT-PCR从异源四倍体C. hytivus及其二倍体亲本(C. hystrix和Csativus)中扩增逆转录酶基因。结果仅在异源四倍体中获得了目的片段,回收测序后共获得18个高度异质的序列。有义突变和无义突变分析暗示这些逆转座子序列主要受净化选择影响。RT-PCR和gPCR分析验证了逆转录酶基因在甜瓜属异源四倍体早期四个世代中的表达,证实这些逆转座子的活性是由异源多倍化造成的。
3.逆转座子对甜瓜属异源四倍体早期世代基因组变异的影响
为了检测逆转座子对甜瓜属异源四倍体基因组变异的影响,本文以野生酸黄瓜C. hystrix与栽培黄瓜C. sativus的正反交种间杂种F1、异源四倍体C. hytivus早期世代(C. hystrix作母本)及其二倍体亲本为材料进行SSAP分析。结果发现正反交F1及异源四倍体均发生广泛的序列变异,包括亲本条带的丢失和新增条带的出现,正反交条带丢失数和新增条带数基本没有差异。无论是条带丢失还是增加,均主要发生在F1、S1和S2代,因此推测异源四倍体早期基因组变异是一个快速的过程。
同时利用基于逆转座子的分子标记IRAP和REMAP以及微卫星标记ISSR等,研究甜瓜属新合成异源四倍体早期世代的基因组变异。结果共检测出28个变异条带,包括24个亲本丢失条带和4个新增条带,表明基因组变异主要表现为亲本序列丢失。在这24个丢失序列中,18个是酸黄瓜特异序列,4个是栽培黄瓜特异序列,另2个是双亲共有序列,暗示序列丢失可能与亲本基因组的组成相关。而且大部分变异出现在S1代,并能在随后三个世代(S2-S4)中稳定遗传,表明基因组变异是一个快速的过程,促进异源四倍体稳定形成。
进一步对发生变异的序列进行回收测序,共获得11个序列。比对分析显示变异序列在编码区和非编码区都有出现,表明逆转座子随机插入基因组中。随后利用荧光原位杂交技术研究变异序列的染色体分布,结果显示FISH信号倾向分布于着丝粒区和端粒区,表明这些区域可能是基因组变异的热点区域。
4.逆转座子对甜瓜属异源四倍体早期世代表观遗传变异的影响
利用荧光原位杂交技术研究了LTR逆转座子在甜瓜属新合成异源四倍体Chytivus的染色体分布,结果揭示LTR逆转座子分布于C. hytivus所有染色体,并在末端区域呈簇状聚集,在大部分染色体仅在一个末端聚集,而少数在两个末端都有聚集,表明逆转座子在异源四倍体中具有高拷贝数和不均匀分布等特点。
利用cDNA-SSAP技术研究逆转座子对甜瓜属异源四倍体早期世代表观遗传变异的影响,结果显示异源四倍体早期世代发生了广泛的表观遗传变异,主要表现为基因沉默和基因激活。对发生变异的序列进行回收测序,共获得20个序列,包括12个基因沉默和8个基因激活。序列分析表明这些沉默/激活基因包括已知基因和未知基因,进一步RT-PCR和gPCR分析验证了上述结果。基因沉默和激活主要发生在异源四倍体的早期世代,并能在随后世代稳定遗传,暗示逆转座子通过对其邻近基因的表达造成干扰,从而有助于新合成异源四倍体的快速稳定。
Retrotransposons are the most abundant and widespread class of transposable elements (TEs) in plant kingdom. Tyl-copia-like retrotransposon is one of the most deeply studied types, which transpose through a RNA intermediate by a "copy-paste" mechanism. They play an important role in plant genome size, structure, evolution, and so on. Allopolyploidy is a prominent process for plant speciation, and plays a significant role in the origin of many species. Newly formed allopolyploid experiences a huge "genomic shock", which can activate the expression of retrotransposons. In contrast, the transcription of retrotransposons can affect genetic and epigenetic changes of allopolyploid. Therefore, in this work, we studied the heterogeneity, copy numbers, genomic and chromosomal distribution of Tyl-copia retrotransposons in Cucumis hystrix (2n=2x=24), a wild species of Cucumis. And then researched the effect of allopolyploidization on transcriptional activation of retrotransposons in the newly formed allotetraploid C. hytivus (2n=4x=38). Finally, the effect of retrotransposons on genetic and epigenetic changes in early generations of Cucumis allotetraploid was investigated to explore the genetic and epigenetic mechanisms.
1. The isolation, distribution and genetic diversity analysis of Tyl-copia retrotransposons in Cucumis
The reverse transcriptase sequences of Tyl-copia retrotransposons were isolated from genome of Cucumis sativus using degenerate oligonucleotide primers. The amplified production was recovered and sequenced,17 different sequences of reverse transcriptase were obtained. These sequences showed high heterogeneity with length varied from 207bp-266bp and homology ranged from 44.1%-98.1%. Among them,10 were intact with potential transcriptional activity, whereas the remaining sequences had a stop codon, a frameshift, or both. Phylogenetic analysis showed that these sequences were divided into four families and had high homology with other species.
In addition,24 highly heterogeneous reverse transcriptase sequences of Tyl-copia retrotransposon were isolated from C. hystrix. Southern hybridization analysis showed that retrotransposons existed in C. hystrix by high copies. Southern dot-blot analysis revealed that the copy number was about 5460, which constituted approximately 8.5% of the C hystrix genome. Phylogenetic analysis showed that these sequences were divided into 5 families and had high homology with other species. Fluorescence in situ hybridization (FISH) revealed the retrotransposons of this kind were widely dispersed over all the chromosomes with clusters in terminal heterochromatin regions.
2. The influence of allopolyploidization on expression of Tyl-copia retrotransposons in Cucumis
To investigate the effect of allopolyploidy on the expression of Tyl-copia retrotransposons in Cucumis newly synthesized allotetraploid, C. hytivus, RT-PCR strategy was carried out to amplify reverse transcriptase (RT) genes from C. hytivus and its diploid parents (C hystrix and C. sativus). Only the allotetraploid yielded the expected product. When recovered and sequenced,18 unique clones with significantly high heterogeneity were obtained. The synonymous (dS) and nonsynonymous (dN) substitution analysis suggested that the RT sequences had been under purifying selection. RT-PCR and gPCR analysis of the cloned reverse transcriptase in the first four generations of Cucumis allotetraploid further proved that the activation of retrotransposons was induced by allopolyploidization.
3. Effect of retrotransposons on genomic changes in early generations of Cucumis allotetraploid
In order to study the genetic variation of early generations of Cucumis allotetraploid, genomic DNAs from the reciprocal F1 hybrids of C. hystrix and C. sativus, early generations of the newly synthesized allotetraploid and their diploid parents were used for SSAP (Sequence specific amplification polymorphism) analysis. The results showed that loss of parental fragments and gaining of novel fragments were detected in the reciprocal F1 hybrids and allotetraploid of interspecific hybridization. No significant differences with regards to the number of fragments lost or gained between reciprocal crosses were noted. Both loss and gaining of fragments are mainly occurred in F1, S1 and S2 generations, indicating the variation in early generations is a rapid process.
In the meantime, two retrotransposon-based markers IRAP (Inter-retrotransposon amplified polymorphism) and REMAP (Retrotransposon-microsatellite amplified polymorphism) and a microsatellite-based marker ISSR (Inter-simple sequence repeat) were employed to investigate genomic changes in early generations of C. hytivus. Twenty-eight fragments were examined, included 24 loss of parent fragment and 4 gaining of novel fragment, suggesting that sequence loss is a relatively frequent event. Among the 24 lost fragments,18 were of C. hystrix origin,4 were C. sativus-specific, and the remaining 2 were shared by both species, implying that fragment loss may be correlated with the genomic constitution of diploid parents. Moreover, most changes were observed in the S1 generation and stably inherited in the subsequent three generations (S2-S4), indicating that genomic changes were rapid driving force for the stabilization of allotetraploid.
Further, the altered DNA fragments were recovered and sequenced, and finally 11 sequences were obtained. Sequence analysis showed that genomic changes in the allotetraploid occurred in both coding and non-coding regions, which might suggest that retrotransposons inserted in genome randomly. Subsequently, FISH analysis revealed a unique chromosomal distribution of altered fragments, where the preferential FISH signals occurred in the centromeric and telomeric regions, implying that these regions were the possible hotspots for genomic changes.
4. Effect of retrotransposons on epigenetic changes in early generations of Cucumis allotetraploid
FISH technique was employed to study the chromosomal distribution of LTR retrotransposons in Cucumis allotetraploid. The result revealed that LTR retrotransposons distributed throughout all the chromosomes, with clusters on terminal regions. Most chromosomes showed clusters only on one terminal whereas a few had clusters on both terminals, indicating their high copy numbers and uneven distribution in C. hytivus.
cDNA-SSAP strategy was used to investigate the effect of retrotransposons on epigenetic changes in the first four generations of newly formed Cucumis allotetraploid. Extensive epigenetic changes were detected, including gene silencing and gene activation. The transcripts that exhibited gene expression alteration were recovered and sequenced, and 20 sequences were obtained, containing 12 gene silencing and 8 gene activation. Sequence analysis showed that the silenced/activated genes consisted of known and unknown genes. Further RT-PCR and gPCR analysis validated the above result. Both gene silencing and activation mainly occurred in early generations of the allotetraploid, and could be stably inherited in subsequent generations. These results implied the transcriptional interference of retrotransposons on their adjacent genes, which contributed to the stabilization of newly formed allotetraploid.
引文
1. 陈劲枫,钱春桃,林茂松,等.甜瓜属植物种间杂交研究进展[J].植物学通报,2004,21(1)：1-8.
2. 陈劲枫,任刚,余纪柱,等.甜瓜属远缘杂种回交自交群体的过氧化物酶同工酶分析[J].武汉植物学研究,2002,20(5)：333-337.
3. 陈龙正.甜瓜属人工异源双二倍体Cucumis hytivus早期世代遗传与表观遗传变化[D].南京农业大学博士学位论文,2008.
4. 程治军,秦瑞珍,张欣,等.多倍体化引起植物表型突变的分子机理研究[J].作物学报,2005,31(7)：940-943.
5. 关和新,陆普媛.植物人工异源多倍体的遗传及后遗传变化[J].中国生物工程杂志,2003,23(9)：34-39.
6. 郭军洋,陈劲枫Cucumis hytivus染色体组间交换重组及其对雄配子育性的影响[J].武汉植物学研究,2005,23(2)：107-110.
7. 郭军洋,陈劲枫,罗向东,等Cucumis属双二倍体种小孢子发生和雄配子体发育的细胞学研究[J].西北植物学报,2005,25(1)：0022-0026.
8. 何予卿,孙梅,朱英国,等.Copia类型反转录转座子在籽粒苋中的表现[J].遗传学报,2002,29(5)：461-466.
9. 李再云,华玉伟,葛贤宏,等.植物远源杂交中的染色体行为及其遗传与进化意义[J].遗传,2005,27(2)：315-324.
10.刘爱华,王建波.序列消除与异源多倍体植物基因组的进化[J].武汉植物学研究,2004,22(2)：158-162.
11.卢圣栋.现代分子生物学技术[M].北京：高等教育出版社.1993.
12.钱春桃,陈劲枫,庄飞云,等.甜瓜属远源杂交回交自交群体的过氧化物酶同工酶分析[J].武汉植物学研究,2002,20(5)：333-337.
13.任刚.甜瓜属种间杂交新种(Cucumis hytivus Chen & Kirkbride)的遗传特性、同工酶标记及其分类地位研究[D].南京农业大学硕士论文,2003.
14.韦杰.柑橘反转录转座子基因的特征分析及其相关分子标记的开发.华中农业大学博士学位论文,2007.
15.吴刚.crylAB基因在转基因水稻中的遗传、表达与沉默[D].浙江大学博士学位论文,2000.
16.杨继.植物多倍体基因组的形成与进化[J].植物分类学报,2001,39(4)：357-371.
17.张晓青,陈劲枫,雷春,等.不同倍性黄瓜遗传差异的AFLP分析[J].西北植物学报,2006,26(11)：2265-2269.
18.朱玉贤,李毅.现代分子生物学[M].北京：高等教育出版社,1997,pp：305-314.
19.庄飞云,陈劲枫,钱春桃等.甜瓜属人工异源双二倍体(Cucumis hytivus)染色体组间重组的细胞学及分子标记研究[J].中国农业科学,2005,38(3)：582-588.
20.庄飞云,陈劲枫,钱春桃,等.甜瓜属种间杂交及其后代对低温的适应性反应[J].南京农业大学学报,2002,25(2)：27-30.
21. Adams KL, Cronn R, Percifield R, et al. Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing [J]. Proceedings of the National Academy of Sciences of the United States of America,2003,100(8):4649-4654.
22. Adams KL, Percifield R, Wendel JF. Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid [J]. Genetics,2004,168(4):2217-2226.
23. Adams KL and Wendel JF. Exploring the genomic mysteries of polyploidy in cotton [J]. Biological Journal of the Linnean Society,2004,82:573-581.
24. Adams KL, Wendel JF. Novel patterns of gene expression in polyploid plants [J]. Trends in Genetics,2005,21(10):539-543.
25. Alix K, Ryder CD, Moore J, et al. The genomic organization of retrotransposons in Brassica oleracea [J]. Plant Molecular Biology,2005,59(6):839-851.
26. Anne R, Benoit P, Philippe F, et al. Whole genome surveys of rice, maize and sorghum reveal multiple horizontal transfers of the LTR-retrotransposon Route66 in Poaceae [J]. BMC Evolutionary Biology,2009,9(58):1-10.
27. Arnold ML. Natural hybridization and the evolution of domesticated, pest and disease organisms [J]. Molecular Ecology,2004,13(5):997-1007.
28. Arumuganathan K, Earle ED. Nuclear DNA content of some important plant species [J]. Plant Molecular Biology Reporter,1991,9(3):208-219.
29. Axelesson T, Bowman CM, Sharpe AG, et al. Amphidiploid Brassica juncea contains conserved progenitor genomes [J]. Genome,2000,43(4):679-688.
30. Bao WK, Yan YR. Octoploid triticale in China. Advance in science of China [J]. Biology,1993,3: 55-76.
31. Baumel A, Ainouche M, Kalendar R, et al. Retrotransposons and genomic stability in populations of the young allopolyploid species Spartina anglica C.E. Hubbard (Poaceae) [J]. Molecular Biology and Evolution,2002,19(8):1218-1227.
32. Beaulieu J, Jean M, Belzile F. The allotetraploid Arabidopsis thaliana-Arabidopsis lyrata subsp petraea as an alternative model system for the study of polyploidy in plants [J]. Molecular Genetics and Genomics,2009,281(4):421-435.
33. Beguiristain T, Grandbastien MA, Puigdomenech P, et al. Three Tntl subfamilies show different stress-associated patterns of expression in tobacco. Consequences for retrotransposon control and evolution in plants [J], Plant Physiology,2001,127(1):212-221.
34. Belyayev A, Raskina O, Nevo E. Chromosomal distribution of reverse transcriptase-containing retroelements in two Triticeae species [J]. Chromosome Research,2001,9(2):129-136.
35. Belyayev A, Raskina O, Nevo E. Variability of the chromosomal distribution of Ty3-gypsy retrotransposons in the populations of two wild Triticeae species [J]. Cytogenetic and Genome Research,2005,109(1-3):43-49.
36. Bennetzen JL. The contributions of retroelements to plant genome organization, function and evolution [J]. Trends in Microbiology,1996,4(9):347-353.
37. Bennetzen JL. Transposable element contributions to plant gene and genome evolution [J]. Plant Molecular Biology,2000,42(1):251-269.
38. Bento M, Pereira HS, Rocheta M, et al. Polyploidization as a retraction force in plant genome evolution:sequence rearrangements in Triticale [J]. PLoS ONE,2008,1(e1402):1-8.
39. Berenyi M, Gichuki ST, Schmidt J, et al. Tyl-copia retrotransposon-based S-SAP (sequence-specific amplified polymorphism) for genetic analysis of sweetpotato [J]. Theoretical and Applied Genetics,2002,105(6-7):862-869.
40. Bernet GP, Asins MJ. Identification and genomic distribution of gypsy like retrotransposons in Citrus and Poncirus [J]. Theoretical and Applied Genetics,2003,108(1):121-130.
41. Bevan M, Bancroft I, Bent E, et al. Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana [J]. Nature,1998,391(6666):485-488.
42. Boeke JD, Corces VG. Transcription and reverse transcription of retrotransposons [J]. Annual Review in Microbiology,1989,43:403-434.
43. Boyko E, Kalendar R, Korzun V, et al. A high-density cytogenetic map of the Aegilops tauschii genome incorporating retrotransposons and defense-related genes:insights into cereal chromosome structure and function [J]. Plant Molecular Biology,2002,48(5-6):767-789.
44. Brandes A, Heslop-Harrison JS, Kamm A, et al. Comparative analysis of the chromosomal and genomic organization of Tyl-copia-like retrotransposons in pteridophytes, gymnosperms and angiosperms [J]. Plant Molecular Biology,1997,33(1):11-21.
45. Bureau TE, White SE, Wessler S. Transduction of a cellular gene by a plant retroelement [J]. Cell, 1994,77(4):479-480.
46. Burow MD, Simpson CE, Starr JL, et al. Transmission genetics of chromatin from a synthetic amphidiploids to cultivated peanut (Arachis hypogaea L.):broadening the gene pool of a monophyletic polyploid species [J]. Genetics,2001,159(2):823-837.
47. Casacuberta JM, Santiago N. Plant LTR-retrotransposons and MITE:control of transposition and impact on the evolution of plant genes and genomes [J]. Gene,2003,311(5):1-11.
48. Chavanne F, Zhang DX, Liaud MF, et al. Structure and evolution of Cyclop:a novel giant retrotransposon of the Ty3/Gypsy family highly amplified in pea and other legume species [J]. Plant Molecular Biology,1998,37(2):363-375.
49. Chen JF, Adelberg JW, Staub JE, et al. A new synthetic amphidiploid in Cucumis from a C. sativus x C. hystrix F1 interspecific hybrid. In:J. McCreight (ed):Cucurbitaceae'98-Evaluation and enhancement of Cucurbit germplasm. ASHS Press, Alexandria, Va. USA,1998, pp:336-339.
50. Chen JF, Isshiki S, Tashiro Y, et al. Biochemical affinities between Cucumis hystrix Charkr. and two cultivated Cucumis species (C. sativus L. and C melo L.) based on isozyme analysis [J]. Euphytica, 1997a,97:139-141.
51. Chen JF, Isshiki S, Tashiro Y, et al. Studies on a wild cucumber from China(Cucumis hystrix Chakr.). I. Genetic distances between C. hystrix and two cultivated Cucumis species (C. sativus L. and C. melo L.) based on isozyme analysis [J]. Journal of Japan Society for Horticulture Science, 1995,64(2):264-265.
52. Chen JF, Kirkbride JH. A new synthetic species Cucumis(Cucurbitaceae) from interspecific hybridization and chromosome doubling [J]. Brittonia,2000,52(4):315-319.
53. Chen JF, Moriarty G, Jahn M. Some disease resistance tests in Cucumis hystrix and its progenies from interspecific hybridization with cucumber [J]. Proceeding of 8th RUCARPIA Meeting on Cucubit Genetics and Breeding,2004,189-196.
54. Chen JF, Luo XD, Qian CT, et al. Cucumis monosomic alien addition lines:morphological, cytological, and genotypic analyses [J]. Theoretical and Applied Genetics,2004,108(7): 1343-1348.
55. Chen JF, Staub JE, Adelberg J, et al. Synthesis and preliminary characterization of a new species (amphidiploid) in Cucumis [J]. Euphytica,2002,123(3):315-322.
56. Chen JF, Staub JE, Jiang JM. A reevaluation of karyotype in cucumber(Cucumis sativus L.) [J]. Genetic Resources and Crop Evolution,1998,45(4):301-305.
57. Chen JF, Staub JE, Qian CT, et al. Reproduction and cytogenetic characterization of interspecific hybrids from Cucumis hystrix Chakr. x Cucumis sativus L. [J]. Theoretical and Applied Genetics, 2003,106(4):688-695.
58. Chen JF, Staub JE, Tashiro Y, et al. Successful interspecific hybridization between Cucumis sativus L. and C. hystrix Chakr. [J]. Euphytica,1997b,96(3):413-419.
59. Chen JF, Zhang SL, Zhang XG. The Xishuangbanna gourd (Cucumis sativus var. xishuangbanna Qi et Yuan), a traditionally cultivated plant of the Hanai people, Xishuangbanna, Yunan, China [J]. Cucurbit Genetics Cooperative Report,1994,17:18-20.
60. Chen LZ, Lou QF, Zhuang Y, et al. Cytological diploidization and rapid genome changes of the newly synthesized allotetraploids Cucumis x hytivus [J]. Planta,2007,225(3):603-614.
61. Chen LZ, Chen JF. Changes of cytosine methylation induced by wide hybridization and allopolyploidy in Cucumis [J]. Genome,2008,51(10):789-799.
62. Chen M, SanMiguel P, Bennetzen JL. Sequence organization and conservation in sh2/al-homologous regions of sorghum and rice [J]. Genetics,1998,148(1):435-443.
63. Chen Q, Armstrong K. Genomic in situ hybridization in Avena sativa [J]. Genome,1994,37(4): 607-612.
64. Chen ZJ, Comai L, Pikaard SC. Gene dosage and stochastic effects determine the severity and direction of uniparental ribosomal RNA gene silencing (nucleolar dominance) in Arabidopsis allopolyploids [J]. Proceedings of the National Academy of Sciences of the United States of America, 1998,95(25):14891-14896.
65. Chen ZJ, Ni Z. Mechanisms of genomic rearrangements and gene expression changes in plant polyploids [J]. BioEssays,2006,28(3):240-252.
66. Chen ZJ, Pikaard CS. Epigenetic silencing of RNA polymerase I transcription:a role for DNA methylation and histone modification in nucleolar dominance [J]. Genes & Development,1997a, 11(16):2124-2136.
67. Chen ZJ, Pikaard CS. Transcriptional analysis of nucleolar dominance in polyploid plants:biased expression/silencing of progenitor rRNA genes is developmentally regulated in Brassica [J]. Proceedings of the National Academy of Sciences of the United States of America,1997b,94(7): 3442-3447.
68. Comai L. Genetic and epigenetic interactions in allopolyploid plants [J]. Plant Molecular Biology, 2000,43(2-3):387-399.
69. Comai L, Tyagi AP, Winter K, et al. Phenotypic instability and rapid gene silencing in newly formed Arabidopsis allotetraploids [J]. Plant Cell,2000,12(9):1551-1568.
70. Contento A, Heslop-Harrison JS, Schwarzacher T. Diversity of a major repetitive DNA sequence in diploid and polyploid Triticeae [J]. Cytogenetic and Genome Research,2005,109(1-3):34-42.
71. Dixit A, Ma KH, Yu JW, et al. Reverse transcriptase domain sequences from Mungbean (Vigna radiate) LTR retrotransposons:sequence characterization and phylogenetic analysis [J]. Plant Cell Reports,2006,25(2):100-111.
72. Dolezel J, Greihuber J, Lucretti S, et al. Plant genome size estimation by flow cytometry: inter-laboratory comparison [J]. Annals of Botany (London),1998,82(suppl 1):17-26.
73. Doolittle RF, Feng DF, Johnson MS, et al. Origins and evolutionary relationships of retroviruses [J]. The Quarterly Review of Biology,1989,64(1):1-30.
74. Drouin G, Dover GA. A plant processed pseudogene [J]. Nature,1987,328:557-558.
75. Ellis THN, Poyser SJ, Knox MR, et al. Polymorphism of insertion sites of Tyl-copia class retrotransposons and its use for linkage and diversity analysis in pea [J]. Molecular and General Genetics,1998,260(1):9-19.
76. Fedoroff N. Transposons and genome evolution in plants [J]. Proceedings of the National Academy of Sciences of the United States of America,2000,97(13):7002-7007.
77. Feldman M, Levy AA. Allopolyploidy-a shaping force in the evolution of wheat genomes [J]. Cytogenetic and Genome Research,2005,109(1-3):250-258.
78. Feldman M, Liu B, Segal G, et al. Rapid elimination of low-copy DNA sequences in polyploid wheat:a possible mechanism for differentiation of homoeologous chromosomes [J]. Genetics,1997, 147(3):1381-1387.
79. Feng Q, Zhang Y, Hao P, et al. Sequence and analysis of rice chromosome 4 [J]. Nature,2002, 420(6913):316-320.
80. Feschotte C, Jiang N, Wessler SR. Plant transposable elements:where genetics meets genomics [J]. Nature Reviews Genetics,2002,3(5):329-341.
81. Finnegan EJ, Kovac KA. Plant DNA methyltransferases [J]. Plant Molecular Biology,2000, 43(2-3):189-201.
82. Flavell AJ, Dunbar E, Anderson R, et al. Tyl-copia group retrotransposons are ubiquitous and heterogeneous in higher plants [J]. Nucleic Acids Research,1992a,20(14):3639-3644.
83. Flavell AJ, Knox MR, Pearce SR, et al. Retrotransposon-based insertion polymorphisms (RBIP) for high throughput marker analysis [J]. Plant Journal,1998,16(5):643-650.
84. Flavell AJ, Smith DB, Kumar A. Extreme heterogeneity of Tyl-copia group retrotransposons in plants [J]. Molecular and General Genetics,1992b,231(2):233-242.
85. Flavell RB. Repetitive DNA and chromosome evolution in plants [J]. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences,1986,312(1154):227-242.
86. Frieman M, Chen ZJ, Saez-Vasquez J, et al. RNA polymerase I transcription in a Brassica interspecific hybrid and its progenitors:tests of transcription factor involvement in nucleolar dominance [J]. Genetics,1999,152(1):451-460.
87. Friesen N, Brandes A, Heslop-Harrison JS. Diversity, origin, and distribution of retrotransposons (gypsy and copia) in conifers [J]. Molecular Biology and Evolution,2001,18(7):1176-1188.
88. Fortune PM, Roulin A, Panaud O. Horizontal transfer of transposable elements in plants [J]. Communicative and Integrative Biology,2008,1(1):74-77.
89. Fu X, Kohli A, Twyman RM, et al. Alternative silencing effect involve distinct types of non-spreading cytosine methylation at a three-gene, single copy transgenic locus in rice [J]. Molecular and General Genetics,2000,263(1):106-118.
90. Galitski T, Saldanha AJ, Styles CA, et al. Ploidy regulation of gene expression [J]. Science,1999, 285(5425):251-254.
91. Garber K, Bilic I, Pusch O, et al. The Tpv2 family of retrotransposons of Phaseolus vulgaris structure, integration characteristics, and use for genotype classification [J]. Plant Molecular Biology,1999,39(4):797-807.
92. Goldman N, Yang Z. A codon-based model of nucleotide substitution for protein-coding DNA sequences [J]. Molecular Biology and Evolution,1994,11(5):725-736.
93. Grandbastein MA. Activation of plant retrotransposons under stress conditions [J]. Trends in Plant Science,1998,3(5):181-187.
94. Grandbastien MA. Retroelements in high plants [J]. Trends in Genetics,1992,8(3):103-108.
95. Grandbastien MA, Lucas H, Morel JB, et al. The expression of the tobacco Tntl retrotransposon is linked to plant defense responses [J]. Genetica,1997,100(1-3):241-252.
96. Grandbastien MA, Spielmann A, Caboche M. Tntl, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics [J]. Nature,1989,337(6205):377-380.
97. Gribbon BM, Pearce SR, Kalendar R, et al. Phylogeny and transpositional activity of Tyl-copia group retrotransposons in cereal genomes [J]. Molecular and General Genetics,1999,261(6): 883-891.
98. Guo M, Birchler JA. Trans-acting dosage effects on the expression of model gene system in maize aneuploids [J]. Science,1994,266(5193):1999-2002.
99. Hamilton A, Voinnet O, Chappell L, et al. Two classes of short interfering RNA in RNA silencing [J]. The EMBO Journal,2002,21(17):4671-4679.
100. Han YH, Zhang ZH, Liu JH, et al. Distribution of the tandem repeat sequences and karyotyping in cucumber (Cucumis sativus L.) by fluorescence in situ hybridization [J]. Cytogenetic Genome Research,2008,122(1):80-88.
101. Hanson RE, Zhao XP, Islam-Faridi MN, et al. Evolution of interspersed repetitive elements in Gossypium (Malvaceae) [J]. American Journal of Botany,1998,85:1364-1368.
102. He P, Friebe BR, Gill BS, et al. Allopolyploidy alters gene expression in the highly stable hexaploid wheat [J]. Plant Molecular Biology,2003,52(2):401-414.
103. Heslop-Harrison JS, Brandes A, Taketa S, et al. The chromosomal distributions of Ty1-copia group retrotransposable elements in higher plants and their implications for genome evolution [J]. Genetica,1997,100(1-3):197-204.
104. Hill P, Burford D, Martin DMA, et al. Retrotransposon populations of Vicia species with varying genome size [J]. Molecular Genetics and Genomics,2005,273(5):209-216.
105. Hirochika H. Retrotransposons of rice:their regulation and use for genome analysis [J]. Plant Molecular Biology,1997,35(1-2):231-240.
106. Hirochika H, Fukuchi A, Kikuchi F. Retrotransposon families in rice [J]. Molecular and General Genetics,1992,233(1-2):209-216.
107. Hirochika H, Otsuki H, Yoshikawa M, et al. Autonomous transposition of the tobacco retrotransposon Ttol in rice [J]. Plant Cell,1996,8(4):725-734.
108. Hori Y, Fujimoto R, Sato Y, et al. A novel wx mutation caused by insertion of a retrotransposon-like sequence in a glutinous cultivar of rice(Oryza sativa) [J]. Theoretical and Applied Genetics,2007, 115(2):217-224.
109. Houchins K, O' Dell M, Flavell RB, et al. Cytosine methylation and nucleolar dominance in cereal hybrids [J]. Molecular and General Genetics,1997,255(3):294-301.
110. Hysing SC, Sall T, Nybom H, et al. Temporal diversity changes among 198 Nordic bread wheat landraces and cultivars detected by retrotransposon-based S-SAP analysis [J]. Plant Genetic Resources:Characterization and Utilization,2008,6(2):113-125.
111. Jiang B, Lou QF, Wang D, et al. Allopolyploidization induced the activation of Ty1-copia retrotransposons in Cucumis hytivus, a newly formed Cucumis allotetraploid [J]. Botanical Studies, 2011, (in press).
112. Jiang B, Wu ZM, Lou QF, et al. Genetic diversity of Ty1-copia retrotransposons in a wild species of Cucumis (C. hystrix) [J]. Scientia Horticulturae,2010,127(1):46-53.
113. Jiang JM, Gill BS, Wang GL, et al. Metaphase and interphase fluorescence in situ hybridization mapping of the rice genome with bacterial artificial chromosomes [J]. Proceedings of the National Academy of Sciences of the United States of America,1995,92(10):4487-4491.
114. Jin YK, Bennetzen JL. Integration and nonrandom mutation of a plasma membrane proton ATPase gene fragment within the Bsl retroelement of maize [J]. Plant Cell,1994,6(8):1177-1186.
115. Jones AL, Thomas CL, Maule AJ. De novo methylation and co-suppression induced by a cytoplasmically replicating plant RNA virus [J]. The EMBO Journal,1998,17(21):6385-6393.
116. Josefsson C, Dilkes B, Comai L. Parent-dependent loss of gene silencing during interspecies hybridization [J]. Current Biology,2006,16(13):1322-1328.
117. Kakutani T, Jeddeloh JA, Flowers SK, et al. Developmental abnormalities and epimutations associated with DNA hypomethylation mutations [J]. Proceedings of the National Academy of Sciences of the United States of America,1996,93(22):12406-12411.
118.Kalendar R, Grob T, Regina M, et al. IRAP and REMAP:two new retrotransposon-based DNA fingerprinting techniques [J]. Theoretical and Applied Genetics,1999,98(5):704-711.
119. Kalendar R, Tanskanen J, Immonen S, et al. Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence [J]. Proceedings of the National Academy of Sciences of the United States of America,2000,97(12): 6603-6607.
120. Kashkush K, Feldman M, Levy AA. Gene loss, silencing and activation in a newly synthesized wheat allotetraploid [J]. Genetics,2002,160(4):1651-1659.
121. Kashkush K, Feldman M, Levy AA. Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat [J]. Nature Genetics,2003,33(1):102-106.
122. Katsiotis A, Schmidt T, Heslop-Harrison JS. Chromosomal and genomic organization of Tyl-copia-like retrotransposon sequences in the genus Avena [J]. Genome,1995,39(2):410-417.
123. Kenton A, Parokonny AS, Gleba YY, et al. Characterization of the Nicotiana tabacum L. genome by molecular cytogenetics [J]. Molecular and General Genetics,1993,240(2):159-169.
124. Kenward KD, Bai D, Ban MR, et al. Isolation and characterization of Tnd-1, a retrotransposon marker linked to black root rot resistance in tobacco [J]. Theoretical and Applied Genetics,1999, 98(3-4):387-395.
125. Kidwell MG, Lisch DR. Transposable elements and host genome evolution [J]. Trends in Ecology & Evolution,2000,15(3):95-99.
126. Kimura Y, Tosa Y, Shimada S, et al. OARE-1, a Tyl-copia retrotransposon in oat activated by abiotic and biotic stresses [J]. Plant and Cell Physiology,2001,42(12):1345-1354.
127. Kirkbride JH. Biosystematic monograph of the genus Cucumis (Cucurbitaceae):botanical identification of cucumbers and melons [M]. Parkway Publishers, Boone, North Carolina,1993, pp: 84-88.
128. Kobayashi S, Goto-Yamamoto N, Hirochika H. Retrotransposon-induced mutations in grape skin color [J]. Science,2004,304(5673):982.
129. Konieczny A, Voytas DF, Cumings MP, et al. A superfamily of Arabidopsis thaliana retrotransposons [J]. Genetics,1991,127:801-809.
130. Kraitshtein Z, Yaakow B, Khasdan V, et al. Genetic and epigenetic dynamics of a retrotransposon after allopolyploidization of wheat [J]. Genetics,2010,186(3):801-812.
131. Kumar A. The adventures of the Tyl-copia group of retrotransposons in plants [J]. Trends in Genetics,1996,12(2):41-43.
132. Kumar A. The evolution of plant retroviruses:moving to greener pasture [J]. Trends in Plant Science,1998,3(10):371-374.
133. Kumar A, Bennetzen JL. Plant retrotransposons [J]. Annual Review of Genetics,1999,33:479-532.
134. Kumar A, Hirochika H. Applications of retrotransposons as genetic tools in plant biology [J]. Trends in Plant Science,2001,6(3):127-134.
135. Kumar A, Pearce SR, McLean K, et al. The Tyl-copia group of retrotransposons in plants:genomic organization, evolution and use as molecular markers [J]. Genetica,1997,100(1-3):205-217.
136. Kumekawa N, Ohtsubo E, Ohtsubo H. Identification and phylogenetic analysis of gypsy-type retrotransposons in the plant kingdom [J]. Genes & Genetic Systems,1999,74(6):299-307.
137. Kunze R, Saedler H, Lonnig WE. Plant transposable elements [J]. Advances in Botanical Research, 1997,27:331-470.
138. Lee HS, Chen ZJ. Protein-coding genes are epigenetically regulated in Arabidopsis polyploid [J]. Proceedings of the National Academy of Sciences of the United States of America,2001,98(12): 6753-6758.
139. Leitch AR, Leitch IJ. Genomic plasticity and the diversity of polyploid plants [J]. Science,2008, 320(5875):481-483.
140. Leitch IJ, Bennett MD. Polyploidy in angiosperms [J]. Trends in Plant Science,1997,2(12): 470-476.
141. Leitch IJ, Bennett MD. Genome downsizing in polyploid plants [J]. Biological Journal of the Linnean Society,2004,82:651-663.
142. Leprince AS, Grandbastien MA, Meyer C. Retrotransposons of the TntlB family are mobile in Nicotiana plumbaginifolia and can induce alternative splicing of the host gene upon insertion [J]. Plant Molecular Biology,2001,47(4):533-541.
143. Levy A A, Feldman M. The impact of polyploidy on grass genome evolution [J]. Plant Physiology, 2002,130(4):1587-1593.
144. Lewis MS, Pikaard CS. Restricted chromosomal silencing in nucleolar dominance [J]. Proceedings of the National Academy of Sciences of the United States of America,2001,98(25):14536-14540.
145. Lim JK, Simmons MJ. Gross chromosome rearrangements mediated by transposable elements in Drosophila melanogaster [J]. BioEssays,1994,16(4):269-275.
146. Liu B, Brubaker CL, Mergeai G, et al. Polyploid formation in cotton is not accompanied by rapid genomic changes [J]. Genome,2001,44(3):321-330.
147. Liu B, Segal G, Vega JM. Isolation and characterization of chromosome-specific DNA sequences from a chromosome arm genomic library of common wheat [J]. Plant Journal,1997,11(5): 959-965.
148. Liu B, Vega JM, Segal G, et al. Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops. Ⅰ. Changes in low-copy noncoding DNA sequences [J]. Genome,1998a,41: 272-277.
149. Liu B, Vega JM, Feldman M. Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops. Ⅱ. Changes in low-copy coding DNA sequences [J]. Genome,1998b,41(4):535-542.
150. Liu B, Wendel JF. Non-Mendelian phenomena in allopolyploid genome evolution [J]. Current Genomics,2002,3(6):489-505.
151. Liu B, Wendel JF. Retrotransposon activation followed by rapid repression in introgressed rice plants [J]. Genome,2000,43(5):874-880.
152. Liu ZL, Han FP, Tan M, et al. Activation of a rice endogenous retrotransposon Tos17 in tissue culture is accompanied by cytosine demethylation and causes heritable alteration in methylation pattern of flanking genomic regions [J]. Theoretical and Applied Genetics,2004,109(1):200-209.
153. Liu ZL, Wang YM, Shen Y, et al. Extensive alterations in DNA methylation and transcription in rice caused by introgression from Zizania latifolia [J]. Plant Molecular Biology,2004,54(4):571-582.
154. Lippman Z, Gendrel AV, Black M, et al. Role of transposable elements in heterochromatin and epigenetic control [J]. Nature,2004,430(6998):471-476.
155. Llaca V, Messing J. Amplicons of maize zein genes are conserved within genic but expanded and constricted in intergenic regions [J]. Plant Journal,1998,15(2):211-220.
156. Loguercio LL, Wilkins TA. Structural analysis of a hmg-coA-reductase pseudogene:insights into evolutionary processes affecting the hmgr gene family in allotetraploid cotton (Gossypium hirsutum L.) [J]. Current Genetics,1998,34(4):241-249.
157. Lonning WE, Saedler H. Chromosome rearrangements and transposable elements [J]. Annual Review of Genetics,2002,36:389-410.
158. Lou QF, Chen JF. Ty1-copia retrotransposon-based SSAP marker development and its potential in the genetic study of cucurbits [J]. Genome,2007,50(9):802-810.
159. Lundin M, Nehlin JO, Ronne H. Importance of a flanking AT-rich region in target site recognition by the GC box-binding zinc finger protein MIG1 [J]. Molecular and Cellular Biology,1994,14(3): 1979-1985.
160. Ma Y, Sun HY, Zhao G, et al. Isolation and characterization of genomic retrotransposon sequences from octoploid strawberry (Fragaria×ananassa Duch.) [J]. Plant Cell Reports,2008,27(3): 499-507.
161. MacRae AF. A pentamer-repeat-containing DNA sequence in Texas bluebonnet (Lupinus texensis Hook.) [J]. Genome,1998,41(4):553-559.
162. Madlung A, Masuelli RW, Watson B, et al. Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids [J]. Plant Physiology,2002,129(2): 733-746.
163. Madlung A, Tyagi AP, Watson B, et al. Genomic changes in synthetic Arabidopsis polyploids [J]. Plant Journal,2005,41(2):221-230.
164. Manninen O, Kalendar R, Robinson J, et al. Application of BARE-1 retrotransposon markers to the mapping of a major resistance gene for net blotch in barley [J]. Molecular and General Genetics, 2000,264(3):325-334.
165. Marillonnet S, Wessler SR. Retrotransposon insertion into the maize waxy gene results in tissue-specific RNA processing [J]. Plant Cell,1997,9(6):967-978.
166. Martienssen RA, Colot V. DNA methylation and epigenetic inheritance in plants and filamentous fungi [J]. Science,2001,293(5532):1070-1074.
167. Masterson J. Stomatal size in fossil plants:evidence for polyploidy in majority of angiosperms [J]. Science,1994,264(5157):421-424.
168. Matzke MA, Matzke AJ. Epigenetic silencing of plant transgenes as a consequence of diverse cellular defence responses [J]. Cellular and Molecular Life Sciences,1998,54(1):94-103.
169. McClintock B. The origin and behavior of mutable loci in maize [J]. Proceedings of the National Academy of Sciences of the United States of America,1950,36(6):344-355.
170. McClintock B. The significance of responses of the genome to challenge [J]. Science,1984, 226(4676):792-801.
171. Messing J, Bharti AK, Karlowski WM, et al. Sequence composition and genome organization of maize [J]. Proceedings of the National Academy of Sciences of the United States of America,2004, 101(40):14349-14354.
172. Mhiri C, De Wit PJ, Grandbastien MA. Activation of the promoter of the Tntl retrotransposon in tomato after inoculation with the fungal pathogen Cladosporium fulvum [J]. Molecular Plant-Mcrobe Interactions,1999,12(7):592-603.
173. Michaud EJ, Van Vugt MJ, Bultman SJ, et al. Differential expression of a new dominant agouti allele (Aiapy) is correlated with methylation state and is influenced by parental lineage [J]. Genes & Development,1994,8(12):1463-1472.
174. Miller JT, Dong F, Jackson SA, et al. Retrotransposon-related DNA sequences in the centromeres of grass chromosomes [J]. Genetics,1998,150(4):1615-1623.
175. Mittelsten SO, Jakovleva L, Afsar K, et al. A Change of ploidy can modify epigenetic silencing [J]. Proceedings of the National Academy of Sciences of the United States of America,1996,93(14): 7114-7119.
176. Miyata T, Yasunaga T. Molecular evolution of mRNA:A method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application [J]. Journal of Molecular Evolution,1980,16(1):23-36.
177. Mizuuchi K. Transpositional recombination:mechanistic insights from studies of Mu and other elements [J]. Annual Review of Biochemistry,1992,61:1011-1051.
178. Mochida K, Yamazaki Y, Ogihara Y. Discrimination of homoeologous gene expression in hexaploid wheat by SNP analysis of contigs grouped from a large number of expressed sequence tags [J]. Molecular Genetics and Genomics,2003,270(5):371-377.
179. Moore G, Lucas H, Batty N, et al. A family of retrotransposons and associated genomic variation in wheat [J]. Genomics,1991,10(2):461-468.
180. Murray HG, Thompson WF. Rapid isolation of higher weight DNA [J]. Nucleic Acids Research, 1980,8(19):4321-4326.
181. Nakatsuka A, Iwami N, Matsumoto S, et al. Tyl-copia group retrotransposons in persimmon (Diospyros kaki Thumb.) [J]. Genes & Genetic Systems,2002,77(2):131-136.
182. Newell-Price J, Clark AJL, King P. DNA methylation and silencing of gene expression [J]. Trends in Endocrinology and Metabolism,2000,11(4):142-148.
183. Okamoto H, Hirochika H. Efficient insertion mutagenesis of Arabidopsis by tissue culture-induced activation of the tobacco retrotransposon Ttol[J]. Plant Journal,2000,23(2):291-304.
184. Osborn TC, Pires JC, Birchler JA, et al. Understanding mechanisms of novel gene expression in polyploids [J]. Trends in Genetics,2003,19(3):141-147.
185. Ostertag EM, Kazazian HH. Biology of mammalian LI retrotransposons [J]. Annual Review of Genetics,2001,35:501-538.
186. Ozkan H, Levy AA, Feldman M. Allopolyploid-induced rapid genome evolution in the wheat (Aegilops-Triticum) group [J]. Plant Cell,2001,13(8):1735-1747.
187. Panstruga R, Buschges R, Piffanelli P, et al. A contiguous 60 kb genomic stretch from barley reveals molecular evidence for gene islands in a monocot genome [J]. Nucleic Acids Research,1998,26(4): 1056-1062.
188. Pardue ML, Danilevskaya ON, Traverse KL, et al. Evolutionary links between telomeres and transposable elements [J]. Genetica,1997,100(1-3):73-84.
189. Pearce SR, Harrison G, Li D, et al. The Tyl-copia group retrotransposons in Vicia species:copy number, sequence heterogeneity and chromosomal localisation [J]. Molecular and General Genetics, 1996b,250(3):305-315.
190. Pearce SR, Knox M, Ellis THN, et al. Pea Tyl-copia group retrotransposons:transpositional activity and use as markers to study genetic diversity in Pisum [J]. Molecular and General Genetics, 2000,263(6):898-907.
191. Pearce SR, Kumar A, Flavell AJ. Activation of the Tyl-copia group retrotransposons of potato (Solatium tuberosum) during protoplast isolation [J]. Plant Cell Reports,1996c,15(12):949-953.
192. Pearce SR, Pich U, Harrison G, et al. The Tyl-copia group retrotransposons of Allium cepa are distributed throughout the chromosomes but are enriched in the terminal heterochromatin [J]. Chromosome Research,1996a,4(5):357-364.
193. Petit M, Guidat C, Daniel J, et al. Mobilization of retrotransposons in synthetic allotetraploid tobacco [J]. New Phytologist,2010,186(1):135-147.
194. Porceddu A, Albertini E, Barcaccia G, et al. Development of S-SAP markers based on an LTR-like sequence from Medicago sativa L. [J]. Molecular Genetics and Genomics,2002,267(1):107-114.
195. Presting GG, Malysheva L, Fuchs J, et al. A TY3/gypsy retrotransposon-like sequence localizes to the centromeric region of cereal chromosomes [J]. Plant Journal,1998,16(6):721-728.
196. Ramallo E, Kalendar R, Schulman AH, et al. Reme 1, a Copia retrotransposon in melon, is transcriptionally induced by UV light [J]. Plant Molecular Biology,2008,66(1-2):137-150.
197. Reinisch AJ, Dong JM, Brubaker CL, et al. A detailed RFLP map of cotton, Gossypium hirsutum x Gossypium barbadense:chromosome organization and evolution in a disomic polyploid genome [J]. Genetics,1994,138(3):829-847.
198. Rich SM, Ayala FJ. The recent origin of allelic variation in antigenic determinants of Plasmodium falciparum [J]. Genetics,1998,150(1):515-517.
199. Richter TE, Ronald PC. The evolution of disease resistance genes [J]. Plant Molecular Biology, 2000,42(1):195-204.
200. Rieseberg LH, Van Fossen C, Desrochers AM. Hybrid speciation accompanied by genomic reorganization in wild sunflowers [J]. Nature,1995,375:313-316.
201. Roelofs D, Van Velzen J, Kuperus P, et al. Molecular evidence for an extinct parent of the tetraploid species Microseris acuminate and M. campestris (Asteraceae, Lactuceae) [J].6Molecular Ecology, 1997,6(7):641-649.
202. Rogers SA, Pauls KP. Tyl-copia-like retrotransposons of tomato (Lycopersicon esculentum Mill.) [J]. Genome,2000,43(5):887-894.
203. Roulin A, Piegu B, Wing RA, et al. Evidence of multiple horizontal transfers of the terminal repeat retrotransposon.RIREI within the genus Oryza [J]. Plant Journal,2008,53(6):950-959.
204. Ruas CF, Weiss-Schneeweiss H, Stuessy TF, et al. Characterization, genomic organization and chromosomal distribution of Tyl-copia retrotransposons in species of Hypochaeris (Asteraceae) [J]. Gene,2008,412(1-2):39-49.
205. Sakamoto K, Ohmido N, Fukui K, et al. Site-specific accumulation of a LINE-like retrotransposon in a sex chromosome of the dioecious plant Cannabis sativa [J]. Plant Molecular Biology,2000, 44(6):723-732.
206. Saitou N, Nei M. The neighbor-joining method:A new method for reconstructing phylogenetic trees [J]. Plant Molecular Biology,1987,44(6):406-425.
207. Sandhu D, Gill KS. Gene-containing regions of wheat and the other grass genomes [J]. Plant Physiology,2002,128(3):803-811.
208. SanMiguel P, Bennetzen JL. Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons [J]. Annals of Botany,1998,82:37-44.
209. SanMiguel P, Tikhonov A, Jin YK, et al. Nested retrotransposons in the intergenic regions of the maize genome [J]. Science,1996,274(5288):765-768.
210. Santini S, Cavallini A, Natali L, et al. Tyl-copia-like and Ty3-gypsy-like DNA sequence in Helianthus species [J]. Chromosoma,2002,111(3):192-200.
211. Schmidt HA, Strimmer K, Vingron M, et al. TREE-PUZZLE:maximum likelihood phylogenetic analysis using quartets and parallel computing [J]. Bioinformatics,2002,18(3):502-504.
212. Schranz ME, Osborn TC. Novel flowering time variation in the resynthesized polyploid Brassica napus [J]. Journal of Heredity,2000,91(3):242-246.
213. Shaked H, Kashkush K, Ozakan H, et al. Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat [J]. Plant Cell,2001,13(8):1749-1759.
214. Guo HS, Lopez-Moya JJ, Garcia JA. Mitotic stability of infection-induced resistance to plum pox potyvirus associated with transgene silencing and DNA methylation [J]. Molecular Plant-Microbe Interactions,1999,12(2):103-111.
215. Shan XH, Liu ZL, Dong ZY, et al. Mobilization of the active MITE transposons mPing and Pong in rice by introgression from wild rice (Zizania latifolia Griseb.) [J].7Molecular Biology and Evolution, 2005,22(4):976-990.
216. Shepherd NS, Schwarz-Sommer Z, Vel Spalve JB, et al. Similarity of the Cinl repetitive family of Zea mays to eukaryotic transposable elements [J]. Nature,1984,307(5947):185-187.
217. Silva JC, Loreto EL, Clark JB. Factors that affect the horizontal transfer of transposable elements [J]. Current Issues in Molecular Biology,2004,6(1):57-71.
218. Slokin RK, Martienssen R. Transposable elements and the epigenetic regulation of the genome [J]. Nature Review Genetics,2007,8(4):272-285.
219. Soltis PS. Ancient and recent polyploidy in angiosperms [J]. New Phytologist,2005,166(1):5-8.
220. Song K, Lu P, Tang K, et al. Rapid genome changes in synthetic polyploids of Brassica and its implications for polyploid evolution [J]. Proceedings of the National Academy of Sciences of the United States of America,1995,92(17):7719-7723.
221.Staton SE. Visualizing changes in the genomic organization of retrotransposons in Helianthus hybrid species [M]. Master Dissertation of Miami University,2008.
222. Steinhauer DA, Holland JJ. Direct method for quantitation of extreme polymerase error frequencies at selected single base sites in viral RNA [J]. Journal of Virology,1986,57(1):219-228.
223. Stergiou G, Katsiotis A, Hagidimitriou M et al. Genomic and chromosomal organization of Tyl-copia-like sequences in Olea europaea and evolutionary relationships of Olea retroelements [J]. Theoretical and Applied Genetics,2002,104(6-7):926-933.
224. Suoniemi A, Tanskanen J, Schulman AH. Gypsy-like retrotransposons are widespread in the plant kingdom [J]. Plant Journal,1998,13(5):699-705.
225. Tam SM, Mhiri C, Vogelaar A, et al. Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotransposon-based SSAP, AFLP and SSR [J]. Theoretical and Applied Genetics,2005,110(5):819-831.
226. Tamura K, Dudley J, Nei M, et al. MEGA 4:molecular evolutionary genetics analysis (MEGA) software version 4.0 [J]. Molecular Biology and Evolution,2007,24(8):1596-1599.
227. Tang YM, Ma YZ, Li LC, et al. Identification and characterization of reverse transcriptase domain of transcriptionally active retrotransposons in wheat genomes [J]. Journal of Integrative Plant Biology,2005,47(5):604-612.
228. Tapia G, Verdugo I, Yanez M, et al. Involvement of ethylene in stress-induced expression of the TLCl.1 retrotransposon from Lycopersicon chilense Dun. [J]. Plant Physiology,2005,138(4): 2075-2086.
229. Thompson JD, Higgins DG, Gibson TJ. Clustal W:improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice [J]. Nucleic Acids Research,1994,22(22):4673-4680.
230. Tikhonov AP, SanMiguel PJ, Nakajima Y, et al. Colinearity and its exceptions in orthologous adh regions of maize and sorghum [J]. Proceedings of the National Academy of Sciences of the United States of America,1999,96(13):7409-7414.
231. Vershinin AV, Ellis THN. Heterogeneity of the internal structure of PDR1, a family of Tyl-copia-like retrotransposons in pea [J]. Molecular and General Genetics,1999,262(45): 703-713.
232. Vicient CM, Schulman AH. Copia-like retrotransposons in the rice genome:few and assorted [J]. Genome letters,2002,1(1):35-47.
233. Vicient CM, Suoniemi A, Anamthawat-Jonsson K, et al. Retrotransposon BARE-1 and its role in genome evolution in the genus Hordeum [J]. Plant Cell,1999,11(9):1769-1784.
234. Volkov RA, Borisjuk NV, Panchuk Ⅱ, et al. Elimination and rearrangement of parental rDNA in the allotetraploid Nicotiana tabacum [J]. Molecular Biology and Evolution,1999,16(3):311-320.
235. Voytas DF, Cummings MP, Konieczny A, et al. Copia-Iike retrotransposon are ubiquitous among plants [J]. Proceedings of the National Academy of Sciences of the United States of America,1992, 89(15):7124-7128.
236. Waugh R, McLean K, Flavell S, et al. Genetic distribution of Bare-1-Iike retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP) [J]. Molecular and General Genetics,1997,253(6):687-694.
237. Wendel JF. Genome evolution in polyploids [J]. Plant Molecular Biology,2000,42:225-249.
238. Wendel JF, Schnabel A, Seelanan T. Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium) [J]. Proceedings of the National Academy of Sciences of the United States of America,1995,92(1):280-284.
239. White SE, Habera LF, Wessler SR. Retrotransposons in the flanking regions of normal plant genes: a role for copia-Iike elements in the evolution of gene structure and expression [J]. Proceedings of the National Academy of Sciences of the United States of America,1994,91(25):11792-11796.
240. Williamson VM. Transposable elements in yeast [J]. International Review of Cytology,1983,83: 1-25.
241. Wright DA, Ke N, Smalle J, et al. Multiple non-LTR retrotransposons in the genome of Arabidopsis thaliana [J]. Genetics,1996,142(2):569-578.
242. Wu R, Guo WL, Wang XR, et al. Unintended consequence of plant transformation:biolistic transformation caused transpositional activation of an endogenous retrotransposon Tosl7 in rice ssp. japonica cv. Matsumae [J]. Plant Cell Reports,2009,28(7):1043-1051.
243. Yanez M, Verdugo I, Rodriguez M, et al. High heterogeneous families of Tyl-copia retrotransposons in the Lycopersicon chilense genome [J]. Gene,1998,222(2):223-228.
244. Yang Z. Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A [J]. Journal of Molecular Evolution,2000,51 (5):423-432.
245. Yao JL, Dong YH, Morris BAM. Parthenocarpic apple fruit production conferred by transposon insertion mutations in a MADS-box transcription factor [J]. Proceedings of the National Academy of Sciences of the United States of America,2001,98(3):1306-1311.
246. Yu GX, Wise RP. An anchored AFLP-and retrotransposon-based map of diploid,Avena [J]. Genome, 2000,43(5):736-749.
247. Zhang D, Sang T. Physical mapping of ribosomal RNA genes in peonies (Paeonia; Paeoniaceae) by fluorescent in situ hybridization:implications for phylogeny and concerted evolution [J]. American Journal of Botany,1999,86(5):735-740.
248. Zhao XP, Si Y, Hanson R, et al. Dispersed repetitive DNA has spread to new genomes since polyploid formation in cotton [J]. Genome Research,1998,8(5):479-492.
249. Zhong CX, Marshall JB, Topp C, et al. Centromeric retroelements and satellites interact with maize kinetochore protein CENH3 [J]. Plant Cell,2002,14(11):2825-2836.
250. Zhuang Y, Chen JF. Changes of gene expression in early generations of the synthetic allotetraploid Cucumis x hytivus Chen et Kirkbride [J]. Genetic Resources and Crop Evolution,2009,56(8): 1071-1076.
251. Zhuang FY, Chen JF, Staub JE, et al. Assessment of genetic relationships among Cucumis spp. by SSR and RAPD marker analysis [J]. Plant Breeding,2004,123(2):167-172.
2. 陈劲枫,任刚,余纪柱,等.甜瓜属远缘杂种回交自交群体的过氧化物酶同工酶分析[J].武汉植物学研究,2002,20(5)：333-337.
3. 陈龙正.甜瓜属人工异源双二倍体Cucumis hytivus早期世代遗传与表观遗传变化[D].南京农业大学博士学位论文,2008.
4. 程治军,秦瑞珍,张欣,等.多倍体化引起植物表型突变的分子机理研究[J].作物学报,2005,31(7)：940-943.
5. 关和新,陆普媛.植物人工异源多倍体的遗传及后遗传变化[J].中国生物工程杂志,2003,23(9)：34-39.
6. 郭军洋,陈劲枫Cucumis hytivus染色体组间交换重组及其对雄配子育性的影响[J].武汉植物学研究,2005,23(2)：107-110.
7. 郭军洋,陈劲枫,罗向东,等Cucumis属双二倍体种小孢子发生和雄配子体发育的细胞学研究[J].西北植物学报,2005,25(1)：0022-0026.
8. 何予卿,孙梅,朱英国,等.Copia类型反转录转座子在籽粒苋中的表现[J].遗传学报,2002,29(5)：461-466.
9. 李再云,华玉伟,葛贤宏,等.植物远源杂交中的染色体行为及其遗传与进化意义[J].遗传,2005,27(2)：315-324.
10.刘爱华,王建波.序列消除与异源多倍体植物基因组的进化[J].武汉植物学研究,2004,22(2)：158-162.
11.卢圣栋.现代分子生物学技术[M].北京：高等教育出版社.1993.
12.钱春桃,陈劲枫,庄飞云,等.甜瓜属远源杂交回交自交群体的过氧化物酶同工酶分析[J].武汉植物学研究,2002,20(5)：333-337.
13.任刚.甜瓜属种间杂交新种(Cucumis hytivus Chen & Kirkbride)的遗传特性、同工酶标记及其分类地位研究[D].南京农业大学硕士论文,2003.
14.韦杰.柑橘反转录转座子基因的特征分析及其相关分子标记的开发.华中农业大学博士学位论文,2007.
15.吴刚.crylAB基因在转基因水稻中的遗传、表达与沉默[D].浙江大学博士学位论文,2000.
16.杨继.植物多倍体基因组的形成与进化[J].植物分类学报,2001,39(4)：357-371.
17.张晓青,陈劲枫,雷春,等.不同倍性黄瓜遗传差异的AFLP分析[J].西北植物学报,2006,26(11)：2265-2269.
18.朱玉贤,李毅.现代分子生物学[M].北京：高等教育出版社,1997,pp：305-314.
19.庄飞云,陈劲枫,钱春桃等.甜瓜属人工异源双二倍体(Cucumis hytivus)染色体组间重组的细胞学及分子标记研究[J].中国农业科学,2005,38(3)：582-588.
20.庄飞云,陈劲枫,钱春桃,等.甜瓜属种间杂交及其后代对低温的适应性反应[J].南京农业大学学报,2002,25(2)：27-30.
21. Adams KL, Cronn R, Percifield R, et al. Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing [J]. Proceedings of the National Academy of Sciences of the United States of America,2003,100(8):4649-4654.
22. Adams KL, Percifield R, Wendel JF. Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid [J]. Genetics,2004,168(4):2217-2226.
23. Adams KL and Wendel JF. Exploring the genomic mysteries of polyploidy in cotton [J]. Biological Journal of the Linnean Society,2004,82:573-581.
24. Adams KL, Wendel JF. Novel patterns of gene expression in polyploid plants [J]. Trends in Genetics,2005,21(10):539-543.
25. Alix K, Ryder CD, Moore J, et al. The genomic organization of retrotransposons in Brassica oleracea [J]. Plant Molecular Biology,2005,59(6):839-851.
26. Anne R, Benoit P, Philippe F, et al. Whole genome surveys of rice, maize and sorghum reveal multiple horizontal transfers of the LTR-retrotransposon Route66 in Poaceae [J]. BMC Evolutionary Biology,2009,9(58):1-10.
27. Arnold ML. Natural hybridization and the evolution of domesticated, pest and disease organisms [J]. Molecular Ecology,2004,13(5):997-1007.
28. Arumuganathan K, Earle ED. Nuclear DNA content of some important plant species [J]. Plant Molecular Biology Reporter,1991,9(3):208-219.
29. Axelesson T, Bowman CM, Sharpe AG, et al. Amphidiploid Brassica juncea contains conserved progenitor genomes [J]. Genome,2000,43(4):679-688.
30. Bao WK, Yan YR. Octoploid triticale in China. Advance in science of China [J]. Biology,1993,3: 55-76.
31. Baumel A, Ainouche M, Kalendar R, et al. Retrotransposons and genomic stability in populations of the young allopolyploid species Spartina anglica C.E. Hubbard (Poaceae) [J]. Molecular Biology and Evolution,2002,19(8):1218-1227.
32. Beaulieu J, Jean M, Belzile F. The allotetraploid Arabidopsis thaliana-Arabidopsis lyrata subsp petraea as an alternative model system for the study of polyploidy in plants [J]. Molecular Genetics and Genomics,2009,281(4):421-435.
33. Beguiristain T, Grandbastien MA, Puigdomenech P, et al. Three Tntl subfamilies show different stress-associated patterns of expression in tobacco. Consequences for retrotransposon control and evolution in plants [J], Plant Physiology,2001,127(1):212-221.
34. Belyayev A, Raskina O, Nevo E. Chromosomal distribution of reverse transcriptase-containing retroelements in two Triticeae species [J]. Chromosome Research,2001,9(2):129-136.
35. Belyayev A, Raskina O, Nevo E. Variability of the chromosomal distribution of Ty3-gypsy retrotransposons in the populations of two wild Triticeae species [J]. Cytogenetic and Genome Research,2005,109(1-3):43-49.
36. Bennetzen JL. The contributions of retroelements to plant genome organization, function and evolution [J]. Trends in Microbiology,1996,4(9):347-353.
37. Bennetzen JL. Transposable element contributions to plant gene and genome evolution [J]. Plant Molecular Biology,2000,42(1):251-269.
38. Bento M, Pereira HS, Rocheta M, et al. Polyploidization as a retraction force in plant genome evolution:sequence rearrangements in Triticale [J]. PLoS ONE,2008,1(e1402):1-8.
39. Berenyi M, Gichuki ST, Schmidt J, et al. Tyl-copia retrotransposon-based S-SAP (sequence-specific amplified polymorphism) for genetic analysis of sweetpotato [J]. Theoretical and Applied Genetics,2002,105(6-7):862-869.
40. Bernet GP, Asins MJ. Identification and genomic distribution of gypsy like retrotransposons in Citrus and Poncirus [J]. Theoretical and Applied Genetics,2003,108(1):121-130.
41. Bevan M, Bancroft I, Bent E, et al. Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana [J]. Nature,1998,391(6666):485-488.
42. Boeke JD, Corces VG. Transcription and reverse transcription of retrotransposons [J]. Annual Review in Microbiology,1989,43:403-434.
43. Boyko E, Kalendar R, Korzun V, et al. A high-density cytogenetic map of the Aegilops tauschii genome incorporating retrotransposons and defense-related genes:insights into cereal chromosome structure and function [J]. Plant Molecular Biology,2002,48(5-6):767-789.
44. Brandes A, Heslop-Harrison JS, Kamm A, et al. Comparative analysis of the chromosomal and genomic organization of Tyl-copia-like retrotransposons in pteridophytes, gymnosperms and angiosperms [J]. Plant Molecular Biology,1997,33(1):11-21.
45. Bureau TE, White SE, Wessler S. Transduction of a cellular gene by a plant retroelement [J]. Cell, 1994,77(4):479-480.
46. Burow MD, Simpson CE, Starr JL, et al. Transmission genetics of chromatin from a synthetic amphidiploids to cultivated peanut (Arachis hypogaea L.):broadening the gene pool of a monophyletic polyploid species [J]. Genetics,2001,159(2):823-837.
47. Casacuberta JM, Santiago N. Plant LTR-retrotransposons and MITE:control of transposition and impact on the evolution of plant genes and genomes [J]. Gene,2003,311(5):1-11.
48. Chavanne F, Zhang DX, Liaud MF, et al. Structure and evolution of Cyclop:a novel giant retrotransposon of the Ty3/Gypsy family highly amplified in pea and other legume species [J]. Plant Molecular Biology,1998,37(2):363-375.
49. Chen JF, Adelberg JW, Staub JE, et al. A new synthetic amphidiploid in Cucumis from a C. sativus x C. hystrix F1 interspecific hybrid. In:J. McCreight (ed):Cucurbitaceae'98-Evaluation and enhancement of Cucurbit germplasm. ASHS Press, Alexandria, Va. USA,1998, pp:336-339.
50. Chen JF, Isshiki S, Tashiro Y, et al. Biochemical affinities between Cucumis hystrix Charkr. and two cultivated Cucumis species (C. sativus L. and C melo L.) based on isozyme analysis [J]. Euphytica, 1997a,97:139-141.
51. Chen JF, Isshiki S, Tashiro Y, et al. Studies on a wild cucumber from China(Cucumis hystrix Chakr.). I. Genetic distances between C. hystrix and two cultivated Cucumis species (C. sativus L. and C. melo L.) based on isozyme analysis [J]. Journal of Japan Society for Horticulture Science, 1995,64(2):264-265.
52. Chen JF, Kirkbride JH. A new synthetic species Cucumis(Cucurbitaceae) from interspecific hybridization and chromosome doubling [J]. Brittonia,2000,52(4):315-319.
53. Chen JF, Moriarty G, Jahn M. Some disease resistance tests in Cucumis hystrix and its progenies from interspecific hybridization with cucumber [J]. Proceeding of 8th RUCARPIA Meeting on Cucubit Genetics and Breeding,2004,189-196.
54. Chen JF, Luo XD, Qian CT, et al. Cucumis monosomic alien addition lines:morphological, cytological, and genotypic analyses [J]. Theoretical and Applied Genetics,2004,108(7): 1343-1348.
55. Chen JF, Staub JE, Adelberg J, et al. Synthesis and preliminary characterization of a new species (amphidiploid) in Cucumis [J]. Euphytica,2002,123(3):315-322.
56. Chen JF, Staub JE, Jiang JM. A reevaluation of karyotype in cucumber(Cucumis sativus L.) [J]. Genetic Resources and Crop Evolution,1998,45(4):301-305.
57. Chen JF, Staub JE, Qian CT, et al. Reproduction and cytogenetic characterization of interspecific hybrids from Cucumis hystrix Chakr. x Cucumis sativus L. [J]. Theoretical and Applied Genetics, 2003,106(4):688-695.
58. Chen JF, Staub JE, Tashiro Y, et al. Successful interspecific hybridization between Cucumis sativus L. and C. hystrix Chakr. [J]. Euphytica,1997b,96(3):413-419.
59. Chen JF, Zhang SL, Zhang XG. The Xishuangbanna gourd (Cucumis sativus var. xishuangbanna Qi et Yuan), a traditionally cultivated plant of the Hanai people, Xishuangbanna, Yunan, China [J]. Cucurbit Genetics Cooperative Report,1994,17:18-20.
60. Chen LZ, Lou QF, Zhuang Y, et al. Cytological diploidization and rapid genome changes of the newly synthesized allotetraploids Cucumis x hytivus [J]. Planta,2007,225(3):603-614.
61. Chen LZ, Chen JF. Changes of cytosine methylation induced by wide hybridization and allopolyploidy in Cucumis [J]. Genome,2008,51(10):789-799.
62. Chen M, SanMiguel P, Bennetzen JL. Sequence organization and conservation in sh2/al-homologous regions of sorghum and rice [J]. Genetics,1998,148(1):435-443.
63. Chen Q, Armstrong K. Genomic in situ hybridization in Avena sativa [J]. Genome,1994,37(4): 607-612.
64. Chen ZJ, Comai L, Pikaard SC. Gene dosage and stochastic effects determine the severity and direction of uniparental ribosomal RNA gene silencing (nucleolar dominance) in Arabidopsis allopolyploids [J]. Proceedings of the National Academy of Sciences of the United States of America, 1998,95(25):14891-14896.
65. Chen ZJ, Ni Z. Mechanisms of genomic rearrangements and gene expression changes in plant polyploids [J]. BioEssays,2006,28(3):240-252.
66. Chen ZJ, Pikaard CS. Epigenetic silencing of RNA polymerase I transcription:a role for DNA methylation and histone modification in nucleolar dominance [J]. Genes & Development,1997a, 11(16):2124-2136.
67. Chen ZJ, Pikaard CS. Transcriptional analysis of nucleolar dominance in polyploid plants:biased expression/silencing of progenitor rRNA genes is developmentally regulated in Brassica [J]. Proceedings of the National Academy of Sciences of the United States of America,1997b,94(7): 3442-3447.
68. Comai L. Genetic and epigenetic interactions in allopolyploid plants [J]. Plant Molecular Biology, 2000,43(2-3):387-399.
69. Comai L, Tyagi AP, Winter K, et al. Phenotypic instability and rapid gene silencing in newly formed Arabidopsis allotetraploids [J]. Plant Cell,2000,12(9):1551-1568.
70. Contento A, Heslop-Harrison JS, Schwarzacher T. Diversity of a major repetitive DNA sequence in diploid and polyploid Triticeae [J]. Cytogenetic and Genome Research,2005,109(1-3):34-42.
71. Dixit A, Ma KH, Yu JW, et al. Reverse transcriptase domain sequences from Mungbean (Vigna radiate) LTR retrotransposons:sequence characterization and phylogenetic analysis [J]. Plant Cell Reports,2006,25(2):100-111.
72. Dolezel J, Greihuber J, Lucretti S, et al. Plant genome size estimation by flow cytometry: inter-laboratory comparison [J]. Annals of Botany (London),1998,82(suppl 1):17-26.
73. Doolittle RF, Feng DF, Johnson MS, et al. Origins and evolutionary relationships of retroviruses [J]. The Quarterly Review of Biology,1989,64(1):1-30.
74. Drouin G, Dover GA. A plant processed pseudogene [J]. Nature,1987,328:557-558.
75. Ellis THN, Poyser SJ, Knox MR, et al. Polymorphism of insertion sites of Tyl-copia class retrotransposons and its use for linkage and diversity analysis in pea [J]. Molecular and General Genetics,1998,260(1):9-19.
76. Fedoroff N. Transposons and genome evolution in plants [J]. Proceedings of the National Academy of Sciences of the United States of America,2000,97(13):7002-7007.
77. Feldman M, Levy AA. Allopolyploidy-a shaping force in the evolution of wheat genomes [J]. Cytogenetic and Genome Research,2005,109(1-3):250-258.
78. Feldman M, Liu B, Segal G, et al. Rapid elimination of low-copy DNA sequences in polyploid wheat:a possible mechanism for differentiation of homoeologous chromosomes [J]. Genetics,1997, 147(3):1381-1387.
79. Feng Q, Zhang Y, Hao P, et al. Sequence and analysis of rice chromosome 4 [J]. Nature,2002, 420(6913):316-320.
80. Feschotte C, Jiang N, Wessler SR. Plant transposable elements:where genetics meets genomics [J]. Nature Reviews Genetics,2002,3(5):329-341.
81. Finnegan EJ, Kovac KA. Plant DNA methyltransferases [J]. Plant Molecular Biology,2000, 43(2-3):189-201.
82. Flavell AJ, Dunbar E, Anderson R, et al. Tyl-copia group retrotransposons are ubiquitous and heterogeneous in higher plants [J]. Nucleic Acids Research,1992a,20(14):3639-3644.
83. Flavell AJ, Knox MR, Pearce SR, et al. Retrotransposon-based insertion polymorphisms (RBIP) for high throughput marker analysis [J]. Plant Journal,1998,16(5):643-650.
84. Flavell AJ, Smith DB, Kumar A. Extreme heterogeneity of Tyl-copia group retrotransposons in plants [J]. Molecular and General Genetics,1992b,231(2):233-242.
85. Flavell RB. Repetitive DNA and chromosome evolution in plants [J]. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences,1986,312(1154):227-242.
86. Frieman M, Chen ZJ, Saez-Vasquez J, et al. RNA polymerase I transcription in a Brassica interspecific hybrid and its progenitors:tests of transcription factor involvement in nucleolar dominance [J]. Genetics,1999,152(1):451-460.
87. Friesen N, Brandes A, Heslop-Harrison JS. Diversity, origin, and distribution of retrotransposons (gypsy and copia) in conifers [J]. Molecular Biology and Evolution,2001,18(7):1176-1188.
88. Fortune PM, Roulin A, Panaud O. Horizontal transfer of transposable elements in plants [J]. Communicative and Integrative Biology,2008,1(1):74-77.
89. Fu X, Kohli A, Twyman RM, et al. Alternative silencing effect involve distinct types of non-spreading cytosine methylation at a three-gene, single copy transgenic locus in rice [J]. Molecular and General Genetics,2000,263(1):106-118.
90. Galitski T, Saldanha AJ, Styles CA, et al. Ploidy regulation of gene expression [J]. Science,1999, 285(5425):251-254.
91. Garber K, Bilic I, Pusch O, et al. The Tpv2 family of retrotransposons of Phaseolus vulgaris structure, integration characteristics, and use for genotype classification [J]. Plant Molecular Biology,1999,39(4):797-807.
92. Goldman N, Yang Z. A codon-based model of nucleotide substitution for protein-coding DNA sequences [J]. Molecular Biology and Evolution,1994,11(5):725-736.
93. Grandbastein MA. Activation of plant retrotransposons under stress conditions [J]. Trends in Plant Science,1998,3(5):181-187.
94. Grandbastien MA. Retroelements in high plants [J]. Trends in Genetics,1992,8(3):103-108.
95. Grandbastien MA, Lucas H, Morel JB, et al. The expression of the tobacco Tntl retrotransposon is linked to plant defense responses [J]. Genetica,1997,100(1-3):241-252.
96. Grandbastien MA, Spielmann A, Caboche M. Tntl, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics [J]. Nature,1989,337(6205):377-380.
97. Gribbon BM, Pearce SR, Kalendar R, et al. Phylogeny and transpositional activity of Tyl-copia group retrotransposons in cereal genomes [J]. Molecular and General Genetics,1999,261(6): 883-891.
98. Guo M, Birchler JA. Trans-acting dosage effects on the expression of model gene system in maize aneuploids [J]. Science,1994,266(5193):1999-2002.
99. Hamilton A, Voinnet O, Chappell L, et al. Two classes of short interfering RNA in RNA silencing [J]. The EMBO Journal,2002,21(17):4671-4679.
100. Han YH, Zhang ZH, Liu JH, et al. Distribution of the tandem repeat sequences and karyotyping in cucumber (Cucumis sativus L.) by fluorescence in situ hybridization [J]. Cytogenetic Genome Research,2008,122(1):80-88.
101. Hanson RE, Zhao XP, Islam-Faridi MN, et al. Evolution of interspersed repetitive elements in Gossypium (Malvaceae) [J]. American Journal of Botany,1998,85:1364-1368.
102. He P, Friebe BR, Gill BS, et al. Allopolyploidy alters gene expression in the highly stable hexaploid wheat [J]. Plant Molecular Biology,2003,52(2):401-414.
103. Heslop-Harrison JS, Brandes A, Taketa S, et al. The chromosomal distributions of Ty1-copia group retrotransposable elements in higher plants and their implications for genome evolution [J]. Genetica,1997,100(1-3):197-204.
104. Hill P, Burford D, Martin DMA, et al. Retrotransposon populations of Vicia species with varying genome size [J]. Molecular Genetics and Genomics,2005,273(5):209-216.
105. Hirochika H. Retrotransposons of rice:their regulation and use for genome analysis [J]. Plant Molecular Biology,1997,35(1-2):231-240.
106. Hirochika H, Fukuchi A, Kikuchi F. Retrotransposon families in rice [J]. Molecular and General Genetics,1992,233(1-2):209-216.
107. Hirochika H, Otsuki H, Yoshikawa M, et al. Autonomous transposition of the tobacco retrotransposon Ttol in rice [J]. Plant Cell,1996,8(4):725-734.
108. Hori Y, Fujimoto R, Sato Y, et al. A novel wx mutation caused by insertion of a retrotransposon-like sequence in a glutinous cultivar of rice(Oryza sativa) [J]. Theoretical and Applied Genetics,2007, 115(2):217-224.
109. Houchins K, O' Dell M, Flavell RB, et al. Cytosine methylation and nucleolar dominance in cereal hybrids [J]. Molecular and General Genetics,1997,255(3):294-301.
110. Hysing SC, Sall T, Nybom H, et al. Temporal diversity changes among 198 Nordic bread wheat landraces and cultivars detected by retrotransposon-based S-SAP analysis [J]. Plant Genetic Resources:Characterization and Utilization,2008,6(2):113-125.
111. Jiang B, Lou QF, Wang D, et al. Allopolyploidization induced the activation of Ty1-copia retrotransposons in Cucumis hytivus, a newly formed Cucumis allotetraploid [J]. Botanical Studies, 2011, (in press).
112. Jiang B, Wu ZM, Lou QF, et al. Genetic diversity of Ty1-copia retrotransposons in a wild species of Cucumis (C. hystrix) [J]. Scientia Horticulturae,2010,127(1):46-53.
113. Jiang JM, Gill BS, Wang GL, et al. Metaphase and interphase fluorescence in situ hybridization mapping of the rice genome with bacterial artificial chromosomes [J]. Proceedings of the National Academy of Sciences of the United States of America,1995,92(10):4487-4491.
114. Jin YK, Bennetzen JL. Integration and nonrandom mutation of a plasma membrane proton ATPase gene fragment within the Bsl retroelement of maize [J]. Plant Cell,1994,6(8):1177-1186.
115. Jones AL, Thomas CL, Maule AJ. De novo methylation and co-suppression induced by a cytoplasmically replicating plant RNA virus [J]. The EMBO Journal,1998,17(21):6385-6393.
116. Josefsson C, Dilkes B, Comai L. Parent-dependent loss of gene silencing during interspecies hybridization [J]. Current Biology,2006,16(13):1322-1328.
117. Kakutani T, Jeddeloh JA, Flowers SK, et al. Developmental abnormalities and epimutations associated with DNA hypomethylation mutations [J]. Proceedings of the National Academy of Sciences of the United States of America,1996,93(22):12406-12411.
118.Kalendar R, Grob T, Regina M, et al. IRAP and REMAP:two new retrotransposon-based DNA fingerprinting techniques [J]. Theoretical and Applied Genetics,1999,98(5):704-711.
119. Kalendar R, Tanskanen J, Immonen S, et al. Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence [J]. Proceedings of the National Academy of Sciences of the United States of America,2000,97(12): 6603-6607.
120. Kashkush K, Feldman M, Levy AA. Gene loss, silencing and activation in a newly synthesized wheat allotetraploid [J]. Genetics,2002,160(4):1651-1659.
121. Kashkush K, Feldman M, Levy AA. Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat [J]. Nature Genetics,2003,33(1):102-106.
122. Katsiotis A, Schmidt T, Heslop-Harrison JS. Chromosomal and genomic organization of Tyl-copia-like retrotransposon sequences in the genus Avena [J]. Genome,1995,39(2):410-417.
123. Kenton A, Parokonny AS, Gleba YY, et al. Characterization of the Nicotiana tabacum L. genome by molecular cytogenetics [J]. Molecular and General Genetics,1993,240(2):159-169.
124. Kenward KD, Bai D, Ban MR, et al. Isolation and characterization of Tnd-1, a retrotransposon marker linked to black root rot resistance in tobacco [J]. Theoretical and Applied Genetics,1999, 98(3-4):387-395.
125. Kidwell MG, Lisch DR. Transposable elements and host genome evolution [J]. Trends in Ecology & Evolution,2000,15(3):95-99.
126. Kimura Y, Tosa Y, Shimada S, et al. OARE-1, a Tyl-copia retrotransposon in oat activated by abiotic and biotic stresses [J]. Plant and Cell Physiology,2001,42(12):1345-1354.
127. Kirkbride JH. Biosystematic monograph of the genus Cucumis (Cucurbitaceae):botanical identification of cucumbers and melons [M]. Parkway Publishers, Boone, North Carolina,1993, pp: 84-88.
128. Kobayashi S, Goto-Yamamoto N, Hirochika H. Retrotransposon-induced mutations in grape skin color [J]. Science,2004,304(5673):982.
129. Konieczny A, Voytas DF, Cumings MP, et al. A superfamily of Arabidopsis thaliana retrotransposons [J]. Genetics,1991,127:801-809.
130. Kraitshtein Z, Yaakow B, Khasdan V, et al. Genetic and epigenetic dynamics of a retrotransposon after allopolyploidization of wheat [J]. Genetics,2010,186(3):801-812.
131. Kumar A. The adventures of the Tyl-copia group of retrotransposons in plants [J]. Trends in Genetics,1996,12(2):41-43.
132. Kumar A. The evolution of plant retroviruses:moving to greener pasture [J]. Trends in Plant Science,1998,3(10):371-374.
133. Kumar A, Bennetzen JL. Plant retrotransposons [J]. Annual Review of Genetics,1999,33:479-532.
134. Kumar A, Hirochika H. Applications of retrotransposons as genetic tools in plant biology [J]. Trends in Plant Science,2001,6(3):127-134.
135. Kumar A, Pearce SR, McLean K, et al. The Tyl-copia group of retrotransposons in plants:genomic organization, evolution and use as molecular markers [J]. Genetica,1997,100(1-3):205-217.
136. Kumekawa N, Ohtsubo E, Ohtsubo H. Identification and phylogenetic analysis of gypsy-type retrotransposons in the plant kingdom [J]. Genes & Genetic Systems,1999,74(6):299-307.
137. Kunze R, Saedler H, Lonnig WE. Plant transposable elements [J]. Advances in Botanical Research, 1997,27:331-470.
138. Lee HS, Chen ZJ. Protein-coding genes are epigenetically regulated in Arabidopsis polyploid [J]. Proceedings of the National Academy of Sciences of the United States of America,2001,98(12): 6753-6758.
139. Leitch AR, Leitch IJ. Genomic plasticity and the diversity of polyploid plants [J]. Science,2008, 320(5875):481-483.
140. Leitch IJ, Bennett MD. Polyploidy in angiosperms [J]. Trends in Plant Science,1997,2(12): 470-476.
141. Leitch IJ, Bennett MD. Genome downsizing in polyploid plants [J]. Biological Journal of the Linnean Society,2004,82:651-663.
142. Leprince AS, Grandbastien MA, Meyer C. Retrotransposons of the TntlB family are mobile in Nicotiana plumbaginifolia and can induce alternative splicing of the host gene upon insertion [J]. Plant Molecular Biology,2001,47(4):533-541.
143. Levy A A, Feldman M. The impact of polyploidy on grass genome evolution [J]. Plant Physiology, 2002,130(4):1587-1593.
144. Lewis MS, Pikaard CS. Restricted chromosomal silencing in nucleolar dominance [J]. Proceedings of the National Academy of Sciences of the United States of America,2001,98(25):14536-14540.
145. Lim JK, Simmons MJ. Gross chromosome rearrangements mediated by transposable elements in Drosophila melanogaster [J]. BioEssays,1994,16(4):269-275.
146. Liu B, Brubaker CL, Mergeai G, et al. Polyploid formation in cotton is not accompanied by rapid genomic changes [J]. Genome,2001,44(3):321-330.
147. Liu B, Segal G, Vega JM. Isolation and characterization of chromosome-specific DNA sequences from a chromosome arm genomic library of common wheat [J]. Plant Journal,1997,11(5): 959-965.
148. Liu B, Vega JM, Segal G, et al. Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops. Ⅰ. Changes in low-copy noncoding DNA sequences [J]. Genome,1998a,41: 272-277.
149. Liu B, Vega JM, Feldman M. Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops. Ⅱ. Changes in low-copy coding DNA sequences [J]. Genome,1998b,41(4):535-542.
150. Liu B, Wendel JF. Non-Mendelian phenomena in allopolyploid genome evolution [J]. Current Genomics,2002,3(6):489-505.
151. Liu B, Wendel JF. Retrotransposon activation followed by rapid repression in introgressed rice plants [J]. Genome,2000,43(5):874-880.
152. Liu ZL, Han FP, Tan M, et al. Activation of a rice endogenous retrotransposon Tos17 in tissue culture is accompanied by cytosine demethylation and causes heritable alteration in methylation pattern of flanking genomic regions [J]. Theoretical and Applied Genetics,2004,109(1):200-209.
153. Liu ZL, Wang YM, Shen Y, et al. Extensive alterations in DNA methylation and transcription in rice caused by introgression from Zizania latifolia [J]. Plant Molecular Biology,2004,54(4):571-582.
154. Lippman Z, Gendrel AV, Black M, et al. Role of transposable elements in heterochromatin and epigenetic control [J]. Nature,2004,430(6998):471-476.
155. Llaca V, Messing J. Amplicons of maize zein genes are conserved within genic but expanded and constricted in intergenic regions [J]. Plant Journal,1998,15(2):211-220.
156. Loguercio LL, Wilkins TA. Structural analysis of a hmg-coA-reductase pseudogene:insights into evolutionary processes affecting the hmgr gene family in allotetraploid cotton (Gossypium hirsutum L.) [J]. Current Genetics,1998,34(4):241-249.
157. Lonning WE, Saedler H. Chromosome rearrangements and transposable elements [J]. Annual Review of Genetics,2002,36:389-410.
158. Lou QF, Chen JF. Ty1-copia retrotransposon-based SSAP marker development and its potential in the genetic study of cucurbits [J]. Genome,2007,50(9):802-810.
159. Lundin M, Nehlin JO, Ronne H. Importance of a flanking AT-rich region in target site recognition by the GC box-binding zinc finger protein MIG1 [J]. Molecular and Cellular Biology,1994,14(3): 1979-1985.
160. Ma Y, Sun HY, Zhao G, et al. Isolation and characterization of genomic retrotransposon sequences from octoploid strawberry (Fragaria×ananassa Duch.) [J]. Plant Cell Reports,2008,27(3): 499-507.
161. MacRae AF. A pentamer-repeat-containing DNA sequence in Texas bluebonnet (Lupinus texensis Hook.) [J]. Genome,1998,41(4):553-559.
162. Madlung A, Masuelli RW, Watson B, et al. Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids [J]. Plant Physiology,2002,129(2): 733-746.
163. Madlung A, Tyagi AP, Watson B, et al. Genomic changes in synthetic Arabidopsis polyploids [J]. Plant Journal,2005,41(2):221-230.
164. Manninen O, Kalendar R, Robinson J, et al. Application of BARE-1 retrotransposon markers to the mapping of a major resistance gene for net blotch in barley [J]. Molecular and General Genetics, 2000,264(3):325-334.
165. Marillonnet S, Wessler SR. Retrotransposon insertion into the maize waxy gene results in tissue-specific RNA processing [J]. Plant Cell,1997,9(6):967-978.
166. Martienssen RA, Colot V. DNA methylation and epigenetic inheritance in plants and filamentous fungi [J]. Science,2001,293(5532):1070-1074.
167. Masterson J. Stomatal size in fossil plants:evidence for polyploidy in majority of angiosperms [J]. Science,1994,264(5157):421-424.
168. Matzke MA, Matzke AJ. Epigenetic silencing of plant transgenes as a consequence of diverse cellular defence responses [J]. Cellular and Molecular Life Sciences,1998,54(1):94-103.
169. McClintock B. The origin and behavior of mutable loci in maize [J]. Proceedings of the National Academy of Sciences of the United States of America,1950,36(6):344-355.
170. McClintock B. The significance of responses of the genome to challenge [J]. Science,1984, 226(4676):792-801.
171. Messing J, Bharti AK, Karlowski WM, et al. Sequence composition and genome organization of maize [J]. Proceedings of the National Academy of Sciences of the United States of America,2004, 101(40):14349-14354.
172. Mhiri C, De Wit PJ, Grandbastien MA. Activation of the promoter of the Tntl retrotransposon in tomato after inoculation with the fungal pathogen Cladosporium fulvum [J]. Molecular Plant-Mcrobe Interactions,1999,12(7):592-603.
173. Michaud EJ, Van Vugt MJ, Bultman SJ, et al. Differential expression of a new dominant agouti allele (Aiapy) is correlated with methylation state and is influenced by parental lineage [J]. Genes & Development,1994,8(12):1463-1472.
174. Miller JT, Dong F, Jackson SA, et al. Retrotransposon-related DNA sequences in the centromeres of grass chromosomes [J]. Genetics,1998,150(4):1615-1623.
175. Mittelsten SO, Jakovleva L, Afsar K, et al. A Change of ploidy can modify epigenetic silencing [J]. Proceedings of the National Academy of Sciences of the United States of America,1996,93(14): 7114-7119.
176. Miyata T, Yasunaga T. Molecular evolution of mRNA:A method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application [J]. Journal of Molecular Evolution,1980,16(1):23-36.
177. Mizuuchi K. Transpositional recombination:mechanistic insights from studies of Mu and other elements [J]. Annual Review of Biochemistry,1992,61:1011-1051.
178. Mochida K, Yamazaki Y, Ogihara Y. Discrimination of homoeologous gene expression in hexaploid wheat by SNP analysis of contigs grouped from a large number of expressed sequence tags [J]. Molecular Genetics and Genomics,2003,270(5):371-377.
179. Moore G, Lucas H, Batty N, et al. A family of retrotransposons and associated genomic variation in wheat [J]. Genomics,1991,10(2):461-468.
180. Murray HG, Thompson WF. Rapid isolation of higher weight DNA [J]. Nucleic Acids Research, 1980,8(19):4321-4326.
181. Nakatsuka A, Iwami N, Matsumoto S, et al. Tyl-copia group retrotransposons in persimmon (Diospyros kaki Thumb.) [J]. Genes & Genetic Systems,2002,77(2):131-136.
182. Newell-Price J, Clark AJL, King P. DNA methylation and silencing of gene expression [J]. Trends in Endocrinology and Metabolism,2000,11(4):142-148.
183. Okamoto H, Hirochika H. Efficient insertion mutagenesis of Arabidopsis by tissue culture-induced activation of the tobacco retrotransposon Ttol[J]. Plant Journal,2000,23(2):291-304.
184. Osborn TC, Pires JC, Birchler JA, et al. Understanding mechanisms of novel gene expression in polyploids [J]. Trends in Genetics,2003,19(3):141-147.
185. Ostertag EM, Kazazian HH. Biology of mammalian LI retrotransposons [J]. Annual Review of Genetics,2001,35:501-538.
186. Ozkan H, Levy AA, Feldman M. Allopolyploid-induced rapid genome evolution in the wheat (Aegilops-Triticum) group [J]. Plant Cell,2001,13(8):1735-1747.
187. Panstruga R, Buschges R, Piffanelli P, et al. A contiguous 60 kb genomic stretch from barley reveals molecular evidence for gene islands in a monocot genome [J]. Nucleic Acids Research,1998,26(4): 1056-1062.
188. Pardue ML, Danilevskaya ON, Traverse KL, et al. Evolutionary links between telomeres and transposable elements [J]. Genetica,1997,100(1-3):73-84.
189. Pearce SR, Harrison G, Li D, et al. The Tyl-copia group retrotransposons in Vicia species:copy number, sequence heterogeneity and chromosomal localisation [J]. Molecular and General Genetics, 1996b,250(3):305-315.
190. Pearce SR, Knox M, Ellis THN, et al. Pea Tyl-copia group retrotransposons:transpositional activity and use as markers to study genetic diversity in Pisum [J]. Molecular and General Genetics, 2000,263(6):898-907.
191. Pearce SR, Kumar A, Flavell AJ. Activation of the Tyl-copia group retrotransposons of potato (Solatium tuberosum) during protoplast isolation [J]. Plant Cell Reports,1996c,15(12):949-953.
192. Pearce SR, Pich U, Harrison G, et al. The Tyl-copia group retrotransposons of Allium cepa are distributed throughout the chromosomes but are enriched in the terminal heterochromatin [J]. Chromosome Research,1996a,4(5):357-364.
193. Petit M, Guidat C, Daniel J, et al. Mobilization of retrotransposons in synthetic allotetraploid tobacco [J]. New Phytologist,2010,186(1):135-147.
194. Porceddu A, Albertini E, Barcaccia G, et al. Development of S-SAP markers based on an LTR-like sequence from Medicago sativa L. [J]. Molecular Genetics and Genomics,2002,267(1):107-114.
195. Presting GG, Malysheva L, Fuchs J, et al. A TY3/gypsy retrotransposon-like sequence localizes to the centromeric region of cereal chromosomes [J]. Plant Journal,1998,16(6):721-728.
196. Ramallo E, Kalendar R, Schulman AH, et al. Reme 1, a Copia retrotransposon in melon, is transcriptionally induced by UV light [J]. Plant Molecular Biology,2008,66(1-2):137-150.
197. Reinisch AJ, Dong JM, Brubaker CL, et al. A detailed RFLP map of cotton, Gossypium hirsutum x Gossypium barbadense:chromosome organization and evolution in a disomic polyploid genome [J]. Genetics,1994,138(3):829-847.
198. Rich SM, Ayala FJ. The recent origin of allelic variation in antigenic determinants of Plasmodium falciparum [J]. Genetics,1998,150(1):515-517.
199. Richter TE, Ronald PC. The evolution of disease resistance genes [J]. Plant Molecular Biology, 2000,42(1):195-204.
200. Rieseberg LH, Van Fossen C, Desrochers AM. Hybrid speciation accompanied by genomic reorganization in wild sunflowers [J]. Nature,1995,375:313-316.
201. Roelofs D, Van Velzen J, Kuperus P, et al. Molecular evidence for an extinct parent of the tetraploid species Microseris acuminate and M. campestris (Asteraceae, Lactuceae) [J].6Molecular Ecology, 1997,6(7):641-649.
202. Rogers SA, Pauls KP. Tyl-copia-like retrotransposons of tomato (Lycopersicon esculentum Mill.) [J]. Genome,2000,43(5):887-894.
203. Roulin A, Piegu B, Wing RA, et al. Evidence of multiple horizontal transfers of the terminal repeat retrotransposon.RIREI within the genus Oryza [J]. Plant Journal,2008,53(6):950-959.
204. Ruas CF, Weiss-Schneeweiss H, Stuessy TF, et al. Characterization, genomic organization and chromosomal distribution of Tyl-copia retrotransposons in species of Hypochaeris (Asteraceae) [J]. Gene,2008,412(1-2):39-49.
205. Sakamoto K, Ohmido N, Fukui K, et al. Site-specific accumulation of a LINE-like retrotransposon in a sex chromosome of the dioecious plant Cannabis sativa [J]. Plant Molecular Biology,2000, 44(6):723-732.
206. Saitou N, Nei M. The neighbor-joining method:A new method for reconstructing phylogenetic trees [J]. Plant Molecular Biology,1987,44(6):406-425.
207. Sandhu D, Gill KS. Gene-containing regions of wheat and the other grass genomes [J]. Plant Physiology,2002,128(3):803-811.
208. SanMiguel P, Bennetzen JL. Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons [J]. Annals of Botany,1998,82:37-44.
209. SanMiguel P, Tikhonov A, Jin YK, et al. Nested retrotransposons in the intergenic regions of the maize genome [J]. Science,1996,274(5288):765-768.
210. Santini S, Cavallini A, Natali L, et al. Tyl-copia-like and Ty3-gypsy-like DNA sequence in Helianthus species [J]. Chromosoma,2002,111(3):192-200.
211. Schmidt HA, Strimmer K, Vingron M, et al. TREE-PUZZLE:maximum likelihood phylogenetic analysis using quartets and parallel computing [J]. Bioinformatics,2002,18(3):502-504.
212. Schranz ME, Osborn TC. Novel flowering time variation in the resynthesized polyploid Brassica napus [J]. Journal of Heredity,2000,91(3):242-246.
213. Shaked H, Kashkush K, Ozakan H, et al. Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat [J]. Plant Cell,2001,13(8):1749-1759.
214. Guo HS, Lopez-Moya JJ, Garcia JA. Mitotic stability of infection-induced resistance to plum pox potyvirus associated with transgene silencing and DNA methylation [J]. Molecular Plant-Microbe Interactions,1999,12(2):103-111.
215. Shan XH, Liu ZL, Dong ZY, et al. Mobilization of the active MITE transposons mPing and Pong in rice by introgression from wild rice (Zizania latifolia Griseb.) [J].7Molecular Biology and Evolution, 2005,22(4):976-990.
216. Shepherd NS, Schwarz-Sommer Z, Vel Spalve JB, et al. Similarity of the Cinl repetitive family of Zea mays to eukaryotic transposable elements [J]. Nature,1984,307(5947):185-187.
217. Silva JC, Loreto EL, Clark JB. Factors that affect the horizontal transfer of transposable elements [J]. Current Issues in Molecular Biology,2004,6(1):57-71.
218. Slokin RK, Martienssen R. Transposable elements and the epigenetic regulation of the genome [J]. Nature Review Genetics,2007,8(4):272-285.
219. Soltis PS. Ancient and recent polyploidy in angiosperms [J]. New Phytologist,2005,166(1):5-8.
220. Song K, Lu P, Tang K, et al. Rapid genome changes in synthetic polyploids of Brassica and its implications for polyploid evolution [J]. Proceedings of the National Academy of Sciences of the United States of America,1995,92(17):7719-7723.
221.Staton SE. Visualizing changes in the genomic organization of retrotransposons in Helianthus hybrid species [M]. Master Dissertation of Miami University,2008.
222. Steinhauer DA, Holland JJ. Direct method for quantitation of extreme polymerase error frequencies at selected single base sites in viral RNA [J]. Journal of Virology,1986,57(1):219-228.
223. Stergiou G, Katsiotis A, Hagidimitriou M et al. Genomic and chromosomal organization of Tyl-copia-like sequences in Olea europaea and evolutionary relationships of Olea retroelements [J]. Theoretical and Applied Genetics,2002,104(6-7):926-933.
224. Suoniemi A, Tanskanen J, Schulman AH. Gypsy-like retrotransposons are widespread in the plant kingdom [J]. Plant Journal,1998,13(5):699-705.
225. Tam SM, Mhiri C, Vogelaar A, et al. Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotransposon-based SSAP, AFLP and SSR [J]. Theoretical and Applied Genetics,2005,110(5):819-831.
226. Tamura K, Dudley J, Nei M, et al. MEGA 4:molecular evolutionary genetics analysis (MEGA) software version 4.0 [J]. Molecular Biology and Evolution,2007,24(8):1596-1599.
227. Tang YM, Ma YZ, Li LC, et al. Identification and characterization of reverse transcriptase domain of transcriptionally active retrotransposons in wheat genomes [J]. Journal of Integrative Plant Biology,2005,47(5):604-612.
228. Tapia G, Verdugo I, Yanez M, et al. Involvement of ethylene in stress-induced expression of the TLCl.1 retrotransposon from Lycopersicon chilense Dun. [J]. Plant Physiology,2005,138(4): 2075-2086.
229. Thompson JD, Higgins DG, Gibson TJ. Clustal W:improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice [J]. Nucleic Acids Research,1994,22(22):4673-4680.
230. Tikhonov AP, SanMiguel PJ, Nakajima Y, et al. Colinearity and its exceptions in orthologous adh regions of maize and sorghum [J]. Proceedings of the National Academy of Sciences of the United States of America,1999,96(13):7409-7414.
231. Vershinin AV, Ellis THN. Heterogeneity of the internal structure of PDR1, a family of Tyl-copia-like retrotransposons in pea [J]. Molecular and General Genetics,1999,262(45): 703-713.
232. Vicient CM, Schulman AH. Copia-like retrotransposons in the rice genome:few and assorted [J]. Genome letters,2002,1(1):35-47.
233. Vicient CM, Suoniemi A, Anamthawat-Jonsson K, et al. Retrotransposon BARE-1 and its role in genome evolution in the genus Hordeum [J]. Plant Cell,1999,11(9):1769-1784.
234. Volkov RA, Borisjuk NV, Panchuk Ⅱ, et al. Elimination and rearrangement of parental rDNA in the allotetraploid Nicotiana tabacum [J]. Molecular Biology and Evolution,1999,16(3):311-320.
235. Voytas DF, Cummings MP, Konieczny A, et al. Copia-Iike retrotransposon are ubiquitous among plants [J]. Proceedings of the National Academy of Sciences of the United States of America,1992, 89(15):7124-7128.
236. Waugh R, McLean K, Flavell S, et al. Genetic distribution of Bare-1-Iike retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP) [J]. Molecular and General Genetics,1997,253(6):687-694.
237. Wendel JF. Genome evolution in polyploids [J]. Plant Molecular Biology,2000,42:225-249.
238. Wendel JF, Schnabel A, Seelanan T. Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium) [J]. Proceedings of the National Academy of Sciences of the United States of America,1995,92(1):280-284.
239. White SE, Habera LF, Wessler SR. Retrotransposons in the flanking regions of normal plant genes: a role for copia-Iike elements in the evolution of gene structure and expression [J]. Proceedings of the National Academy of Sciences of the United States of America,1994,91(25):11792-11796.
240. Williamson VM. Transposable elements in yeast [J]. International Review of Cytology,1983,83: 1-25.
241. Wright DA, Ke N, Smalle J, et al. Multiple non-LTR retrotransposons in the genome of Arabidopsis thaliana [J]. Genetics,1996,142(2):569-578.
242. Wu R, Guo WL, Wang XR, et al. Unintended consequence of plant transformation:biolistic transformation caused transpositional activation of an endogenous retrotransposon Tosl7 in rice ssp. japonica cv. Matsumae [J]. Plant Cell Reports,2009,28(7):1043-1051.
243. Yanez M, Verdugo I, Rodriguez M, et al. High heterogeneous families of Tyl-copia retrotransposons in the Lycopersicon chilense genome [J]. Gene,1998,222(2):223-228.
244. Yang Z. Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A [J]. Journal of Molecular Evolution,2000,51 (5):423-432.
245. Yao JL, Dong YH, Morris BAM. Parthenocarpic apple fruit production conferred by transposon insertion mutations in a MADS-box transcription factor [J]. Proceedings of the National Academy of Sciences of the United States of America,2001,98(3):1306-1311.
246. Yu GX, Wise RP. An anchored AFLP-and retrotransposon-based map of diploid,Avena [J]. Genome, 2000,43(5):736-749.
247. Zhang D, Sang T. Physical mapping of ribosomal RNA genes in peonies (Paeonia; Paeoniaceae) by fluorescent in situ hybridization:implications for phylogeny and concerted evolution [J]. American Journal of Botany,1999,86(5):735-740.
248. Zhao XP, Si Y, Hanson R, et al. Dispersed repetitive DNA has spread to new genomes since polyploid formation in cotton [J]. Genome Research,1998,8(5):479-492.
249. Zhong CX, Marshall JB, Topp C, et al. Centromeric retroelements and satellites interact with maize kinetochore protein CENH3 [J]. Plant Cell,2002,14(11):2825-2836.
250. Zhuang Y, Chen JF. Changes of gene expression in early generations of the synthetic allotetraploid Cucumis x hytivus Chen et Kirkbride [J]. Genetic Resources and Crop Evolution,2009,56(8): 1071-1076.
251. Zhuang FY, Chen JF, Staub JE, et al. Assessment of genetic relationships among Cucumis spp. by SSR and RAPD marker analysis [J]. Plant Breeding,2004,123(2):167-172.
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