梅nSSR、cpSSR开发及基于序列分析的核果类果树系统发育研究
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摘要
核微卫星(nuclear microsatellite,nSSR)和叶绿体微卫星(chloroplastmicrosatellite,cpSSR)都是非常有效的分子标记工具,广泛应用于植物遗传结构、系统发育、亲缘关系等研究,但目前梅的nSSR还很少,核果类果树的cpSSR也较少。因此,本文应用双抑制PCR法和精确预测法进行了核nSSR的开发,为核果类果树及其近缘种遗传结构、亲缘关系等方面的研究提供有效工具。
核果类果树间由于亲缘关系较近,相互间可通过自然或人工的方法进行杂交,从而导致其种质间的相互渗透,遗传背景复杂。前人已经采用传统的形态学、孢粉学、细胞学方法及RAPD、SSR、AFLP、SNP等分子标记方法进行了系统发育的研究,但仍存在一些争议。序列分析法是一种非常高效、准确的方法,广泛应用于多种植物的系统发育、遗传结构、基因渗透等方面的研究。因此为解决这些争议,本文采用核糖体ITS序列和叶绿体atpB-rbcL序列对核果类果树的系统发育进行了进一步研究。
1.梅作为观赏树种和果树在东亚栽培历史悠久,特别是在中国南方。但关于其遗传多样性和栽培种的起源等许多方面仍然不清楚。微卫星(SSR)是目前比较流行、有效的分子标记。然而很少有人进行梅nSSR的分离和描述。为开发更多的SSR应用于梅的遗传分析,我们改进了双抑制PCR开发方法.一共成功分离出11个梅nSSR(5个(GA)n、6个(AC)n),其中8个SSR在供检测的11个梅品种中表现出多态性。等位基因数量2-8个,观察到的杂合性从0.33到1.00不等,平均为0.71,表明分离的位点具有较高的多态性。这些信息位点在将来梅及其近缘种的遗传结构、起源、进化方面的研究中非常有用。
2.虽然目前已经研究出来许多SSR富集方法,以提高SSR分离的效率。但在克隆测序之前,插入片段中SSR的分布情况是完全不知道的,因此分离效率仍然很低,这大大限制了SSR的应用。我们构建了一个新的模型-精确预测(AFC)。这个模型可以在测序之前就去除那些无用的序列从而获得100%的效率,而且这个模型有较高的可行性和可转移性,适用于所有SSR富集的方法(只要添加到方法的后面)。为简化计算,将模型转化成一个数据库软件"Accurate Forecast Microsatellite 1.0”。利用改进的亲和捕捉法富集微卫星,再通过一个巢式PCR来检测阳性克隆。数据输入到软件中,由软件自动产生的推荐列表中前15个克隆被测序。结果所有的序列都是有用的,即包含SSR及其两侧相邻的、可以用来设计引物的足够长的序列。与亲和捕捉、双抑制PCR相比,AFC方法具有较高的SSR富集效率(65%)和高的测序效率(100%)、花费较少、便于操作。它是一种新的高效的SSR分离方法,特别对非模式生物来说。
3.为进一步了解植物cpSSR分布规律,进而开发核果类果树通用cpSSR引物,对拟南芥叶绿体DNA全序列的cpSSR进行了统计分析。结果表明拟南芥cpSSR以单碱基重复为主,占总数的78.6%,二碱基重复占总数的19%,三碱基重复占2.4%,三碱基以上重复为零.在单碱基重复中又以A和T重复为主,占98.5%。二碱基重复全部为AT重复。单碱基的重复中纯粹重复41个,占总数的62.1%。间断重复个数为23,占总数的34.8%。复合重复个数仅为2个。
4.采用2种方法来开发核果类果树通用的cpSSR.1)非编码区测序法:以甲州小梅的总DNA为模板,用一个巢式PCR来扩增和筛选16个叶绿体大单拷贝区基因间隔区和1个内含子。测序后共获得9个重复数人于8的梅cpSSR,设计相应的引物。2)生物信息学方法:从Genbank上下载桃、李、梅、杏和樱桃5大核果类果树相应叶绿体序列33个,共搜索到重复数人于8的单碱基重复(A)n或(T)n 38个,选择重复数大于10的cpSSR位点进行引物设计。可以设计引物的cpSSR共8个,另2个cpSSR位点因一侧序列太短或序列的特异性无法设计有效引物。取非编码区测序法开发的、有代表性的梅6对cpSSR引物在5种核果类果树24个基因型中进行了多态性验证。6对引物均具有多态性,扩增出18条多态性片段,组成14个单倍型,具有较高的分辨率,可以用来鉴别种甚至特异的基因型。单倍型的总杂合度(0.96)很高,说明核果类果树具有较丰富的单倍型类型。而杏和梅最低(0.32)。单倍型仅有2个,且分布不均衡,说明其起源单一,遗传背景狭窄。这些新开发的cpSSR引物为进一步研究核果类果树的起源、进化等问题提供一个新的有效工具。
5.为构建核果类果树的系统发育,选择桃、李、梅、杏、樱桃各4-5个主要种或变种,共24个基因型,测定了其叶绿体体非编码区。atpB-rbcL序列。以桂樱为外种群,PAUP计算数据集的得分,Modeltest筛选最佳模型和参数,Mega计算遗传距离、变异,最大简约法构建系统发育树。结果表明:1.atpB-rbcL在核果类果树各组间分子进化速率不同,差异分布不均衡;2.樱桃较其它核果类果树原始;李、梅、杏亲缘关系较近,梅、杏关系最近。核果类果树是一个单系群,由着一个共同的祖先沿着两个方向进化,一枝进化为樱桃,另一枝沿不同的途径产生桃、李、梅、杏等核果类果树。
6.为研究核果类果树的分子进化和系统发育,测定了桃、李、梅、杏、樱桃各2-4个主要种或变种,共16个基因型的ITS序列,并从Genbank下载了6个其它的核果类ITS序列,形成了较为全面的数据矩阵。扁核木为外种群,用Mega最大简约法构建系统发育树。以结果表明,樱桃较其它核果类果树原始。因扁核木与核果类果树差异较大,又采用二次置根法,以樱桃置根。用PAUP计算数据集的得分,Modeltest筛选最佳模型和参数,计算遗传距离、变异,用最大简约法构建了桃、李、梅、杏、樱桃的系统发育树.结果表明:1.核果类果树各树种ITS1和ITS2的分子进化速率不同,信息量也不同;2,核果类果树演化顺序为:共同的原始种分化成樱桃、李、杏,再由李进化产生桃,杏进化产生梅;3.辽杏较普通杏和西伯利亚杏原始,桃演化顺序是:巴旦杏-山桃-普通桃(新疆桃)。4.本文结果支持将核果类果树分成4个亚属。
Nuclear microsatellite (nSSR) and chloroplast microsatellite (cpSSR) are very useful molecular marker tools, widely used in the study of plant genetic structure, phylogeny and relationship. But there are few nSSRs and none cpSSRs of Prunus mume; this greatly limited the application of nSSR and cpSSR in P. mume. Dual-suppression-PCR and Accurate forecast methods were used to isolate nSSR in P. mume. These informational loci will be very useful in the study on the genetic structure, origin, evolution of P. mume and its closely related species
It is very close among the relationship stone fruit trees. They can be propagated both asexually and sexually, and easily hybridized naturally and artificially with other stone fruit trees. These features made the genetic background of stone fruit trees rather complex. Previous studies on taxonomy and genetic polymorphism for P. mume were carried out using morphology, cytology, sporule, isoenzyme markers, RAPD, AFLP, SNP and SSR. However, there are still some puzzles. Sequence analysis is a new accurate method with higher efficiency and has been used in the research of phylogeny, genetic structure, introgression in kinds of plant. To settle those puzzles nuclear ITS and chloroplast atpB-rbcL were used to construct the phylogeny of stone fruit trees.
1. Prunus mume Sieb. et Zucc, as an ornamental and fruit tree, has been cultivated for centuries in the East Asian, especially in the southern part of China. But much remain unknown about genetic variation and origin of various cultivars. Microsatellite (simple sequence repeat, SSR) is a very prevalent, effective molecular marker. However, there have been few attempts to isolate and characterize SSRs in Prunus mume. To develop more SSRs for the genetic analysis of P. mume, we modified the protocol, called dual-suppression -PCR. A total of eleven SSRs, five (GA)n and six (AC)n, were successful isolated. Eight SSRs were found to be polymorphic in a test sample of 11 P. mume cultivars. The observed number of alleles per locus ranged from 2 to 8 and observed heterozygosity ranged from 0.33 to 1.00 with an average of 0.71, suggesting a high degree of variation in isolated loci. These informational loci will be very useful in the study on the genetic structure, origin, evolution of P. mume and its closely related species.
2. At present, many microsatellite-enrichment methods were proposed to increase microsatellite (SSR) isolation efficiency, but it is a complete black-box about the SSR distribution in the insertion fragment in the clone before being sequenced, so the isolation efficiency is still low, which greatly limited the application of SSR. Here we constructed a new model, accurate forecast (AFC). The model can eliminate those useless sequences before being sequenced to gain 100% efficiency and has high feasibility, transferability and fits all the methods with SSRs enrichment (just add it to the end). To simplify the calculation procedure the model was transformed into database software 'Accurate Forecast Microsatellite 1.0'. After modified affinity capture to enrich microsatellite, positive clones were detected by a nested PCR and the data were inputted into the software. The first fifteen anterior clones in the recommendation list created automatically by software were sequenced and all of them sequences were usable for SSR isolation, containing SSR sequences and their corresponding flanking sequences, which were long enough to be used for primer design. Compared with Affinity Capture and Dual-Suppression-PCR, AFC pipeline has higher SSRs enrichment (65%), high sequence percentage (100%) and less cost per SSR locus. It is easy to be operated. It can be a new powerful SSR isolation approach, especially for non-model organisms.
3. To comprehend the distribution rule of plant chloroplast microsatellites (cpSSRs) and develop the universal cpSSR primers for stone fruit trees, the complete genome of Arabidopsis thaliana Chloroplast was downloaded and analysed. The mononucleotide cpSSRs were preponderant (78.6%), the dinucleotide cpSSRs, the trinucleotide cpSSRs and the others cpSSR accounted for 19%, 2.4 % and 0%, correspondly. The (T)n and (A)n cpSSRs were the most type in the mononucleotide cpSSRs (98.5%) while all the dinucleotide cpSSRs were (AT)n. 41 pure SSRs (62.1%), 23 interrupted SSRs (34.8%) and 2 multiple cpSSRs (3.1%) existed in the the mononucleotide cpSSRs.
4. Two methods were used to develop the universal cpSSR for stone fruit trees. 1) Non-coding region sequencing (NRS). Total Genomic DNA of Prunus mume 'Koshu Koume' was extracted. A nested PCR was performed to amplify and screened 16 chloroplast intergene sequences (IGSs) and 1 intron. 8 IGSs were successfully amplified in the secondary nested PCR. After sequencing 9 mononucleotide cpSSR loci, (A)n or (T)n with n≥8, were found. 2) Bio-informatics method. 33 chloroplast sequences of peach, plum, mume, apricot, cherry were downloaded form the Genbank. 38 mononucleotide cpSSRs, (A)n or (T)n with n≥8, were obtained by directly search, 8 of them with n≥10 were choosed to design universal primer. 6 pairs of cpSSR primer developed using NRS were tested in 24 Prunus genotypes and all of them were polymorphic. 18 fragments were yielded and formed 14 haplotypes. The high Heterozygosity (0.96) indicated there were rich haplotype types in stone fruit trees. But apricot and mume had lowest Heterozygosity (0.32) and only 2 haplotypes with disequilibrium distribution. This showed that apricot and mume had simplex origin and limited genetic background. These new developed cpSSRs provide a new alternative efficient tool to analyze the origin and evolution of stone fruit trees.
5. To reconstruct phylogeny of stone fruit trees, the atpB-rbcL noncoding spacer of chloroplast DNA from 24 genotypes of peach, plum, apricot, mume and cherry, 4-5 genotypes per specie, were sequenced and analyzed. With Zippeliana as outgroup, the data set was tested with 56 evolution models with PAUP and the score was used to screen the best model and parameter with Modeltest. Genetic distances, variances were calculated and the maximum parsimony tree was constructed with Mega. The result indicated: 1. Molecular evolution rates were different among stone fruit trees and the distribution of variance was unbalanced; 2. An initial split from the backbone of the Phylogenetic tree indicated that cherry was more original than other species. Mume had closest relationship with apricot and closer with plum. As a monophyletic group, stone fruit trees were come from an original plant with two clades, one evolved to cherry and the other to other stone fruit trees.
6. To analyze the molecular evolution and phylogeny of stone fruit trees, the internal transcribed spacers (ITS) of nuclear ribosomal DNA from 16 genotypes of peach, plum, apricot, mume, and cherry, 2-4 genotypes per species, were sequenced and analyzed with 6 ITS sequences downloaded from the GenBank. Prinsepia sinensis as outgroup, the maximum parsimony tree was constructed with Mega. An initial split from the backbone of the phylogenetic tree indicated that cherry was more original than other species. Because Prinsepia sinensis was greatly different with others, the second way of rooting with cherry was performed. The broad data set was tested with 56 evolution models with PAUP and the score was used to screen the best model and parameter with Modeltest. Mega was used to calculate genetic distance, variance and construct maximum parsimony phylogenetic tree. The result indicated: 1. Molecular evolution rate and information were different between ITS1 and ITS2, and also among stone fruit trees; 2. The evolution order of 5 stone fruit trees was analyzed. Cherry, plum and apricot were come from an original plant, and then plum evolved to peach and apricot to mume; 3. Prunus mandshurica is more original than P. sibirica and P. armeniaca. The evolution order of peach is from P. andersonii to P. davidiana and then to P. persica (P. ferganensis); 4. It is reasonable that stone fruit trees are divided into 4 subgenera.
核果类果树间由于亲缘关系较近,相互间可通过自然或人工的方法进行杂交,从而导致其种质间的相互渗透,遗传背景复杂。前人已经采用传统的形态学、孢粉学、细胞学方法及RAPD、SSR、AFLP、SNP等分子标记方法进行了系统发育的研究,但仍存在一些争议。序列分析法是一种非常高效、准确的方法,广泛应用于多种植物的系统发育、遗传结构、基因渗透等方面的研究。因此为解决这些争议,本文采用核糖体ITS序列和叶绿体atpB-rbcL序列对核果类果树的系统发育进行了进一步研究。
1.梅作为观赏树种和果树在东亚栽培历史悠久,特别是在中国南方。但关于其遗传多样性和栽培种的起源等许多方面仍然不清楚。微卫星(SSR)是目前比较流行、有效的分子标记。然而很少有人进行梅nSSR的分离和描述。为开发更多的SSR应用于梅的遗传分析,我们改进了双抑制PCR开发方法.一共成功分离出11个梅nSSR(5个(GA)n、6个(AC)n),其中8个SSR在供检测的11个梅品种中表现出多态性。等位基因数量2-8个,观察到的杂合性从0.33到1.00不等,平均为0.71,表明分离的位点具有较高的多态性。这些信息位点在将来梅及其近缘种的遗传结构、起源、进化方面的研究中非常有用。
2.虽然目前已经研究出来许多SSR富集方法,以提高SSR分离的效率。但在克隆测序之前,插入片段中SSR的分布情况是完全不知道的,因此分离效率仍然很低,这大大限制了SSR的应用。我们构建了一个新的模型-精确预测(AFC)。这个模型可以在测序之前就去除那些无用的序列从而获得100%的效率,而且这个模型有较高的可行性和可转移性,适用于所有SSR富集的方法(只要添加到方法的后面)。为简化计算,将模型转化成一个数据库软件"Accurate Forecast Microsatellite 1.0”。利用改进的亲和捕捉法富集微卫星,再通过一个巢式PCR来检测阳性克隆。数据输入到软件中,由软件自动产生的推荐列表中前15个克隆被测序。结果所有的序列都是有用的,即包含SSR及其两侧相邻的、可以用来设计引物的足够长的序列。与亲和捕捉、双抑制PCR相比,AFC方法具有较高的SSR富集效率(65%)和高的测序效率(100%)、花费较少、便于操作。它是一种新的高效的SSR分离方法,特别对非模式生物来说。
3.为进一步了解植物cpSSR分布规律,进而开发核果类果树通用cpSSR引物,对拟南芥叶绿体DNA全序列的cpSSR进行了统计分析。结果表明拟南芥cpSSR以单碱基重复为主,占总数的78.6%,二碱基重复占总数的19%,三碱基重复占2.4%,三碱基以上重复为零.在单碱基重复中又以A和T重复为主,占98.5%。二碱基重复全部为AT重复。单碱基的重复中纯粹重复41个,占总数的62.1%。间断重复个数为23,占总数的34.8%。复合重复个数仅为2个。
4.采用2种方法来开发核果类果树通用的cpSSR.1)非编码区测序法:以甲州小梅的总DNA为模板,用一个巢式PCR来扩增和筛选16个叶绿体大单拷贝区基因间隔区和1个内含子。测序后共获得9个重复数人于8的梅cpSSR,设计相应的引物。2)生物信息学方法:从Genbank上下载桃、李、梅、杏和樱桃5大核果类果树相应叶绿体序列33个,共搜索到重复数人于8的单碱基重复(A)n或(T)n 38个,选择重复数大于10的cpSSR位点进行引物设计。可以设计引物的cpSSR共8个,另2个cpSSR位点因一侧序列太短或序列的特异性无法设计有效引物。取非编码区测序法开发的、有代表性的梅6对cpSSR引物在5种核果类果树24个基因型中进行了多态性验证。6对引物均具有多态性,扩增出18条多态性片段,组成14个单倍型,具有较高的分辨率,可以用来鉴别种甚至特异的基因型。单倍型的总杂合度(0.96)很高,说明核果类果树具有较丰富的单倍型类型。而杏和梅最低(0.32)。单倍型仅有2个,且分布不均衡,说明其起源单一,遗传背景狭窄。这些新开发的cpSSR引物为进一步研究核果类果树的起源、进化等问题提供一个新的有效工具。
5.为构建核果类果树的系统发育,选择桃、李、梅、杏、樱桃各4-5个主要种或变种,共24个基因型,测定了其叶绿体体非编码区。atpB-rbcL序列。以桂樱为外种群,PAUP计算数据集的得分,Modeltest筛选最佳模型和参数,Mega计算遗传距离、变异,最大简约法构建系统发育树。结果表明:1.atpB-rbcL在核果类果树各组间分子进化速率不同,差异分布不均衡;2.樱桃较其它核果类果树原始;李、梅、杏亲缘关系较近,梅、杏关系最近。核果类果树是一个单系群,由着一个共同的祖先沿着两个方向进化,一枝进化为樱桃,另一枝沿不同的途径产生桃、李、梅、杏等核果类果树。
6.为研究核果类果树的分子进化和系统发育,测定了桃、李、梅、杏、樱桃各2-4个主要种或变种,共16个基因型的ITS序列,并从Genbank下载了6个其它的核果类ITS序列,形成了较为全面的数据矩阵。扁核木为外种群,用Mega最大简约法构建系统发育树。以结果表明,樱桃较其它核果类果树原始。因扁核木与核果类果树差异较大,又采用二次置根法,以樱桃置根。用PAUP计算数据集的得分,Modeltest筛选最佳模型和参数,计算遗传距离、变异,用最大简约法构建了桃、李、梅、杏、樱桃的系统发育树.结果表明:1.核果类果树各树种ITS1和ITS2的分子进化速率不同,信息量也不同;2,核果类果树演化顺序为:共同的原始种分化成樱桃、李、杏,再由李进化产生桃,杏进化产生梅;3.辽杏较普通杏和西伯利亚杏原始,桃演化顺序是:巴旦杏-山桃-普通桃(新疆桃)。4.本文结果支持将核果类果树分成4个亚属。
Nuclear microsatellite (nSSR) and chloroplast microsatellite (cpSSR) are very useful molecular marker tools, widely used in the study of plant genetic structure, phylogeny and relationship. But there are few nSSRs and none cpSSRs of Prunus mume; this greatly limited the application of nSSR and cpSSR in P. mume. Dual-suppression-PCR and Accurate forecast methods were used to isolate nSSR in P. mume. These informational loci will be very useful in the study on the genetic structure, origin, evolution of P. mume and its closely related species
It is very close among the relationship stone fruit trees. They can be propagated both asexually and sexually, and easily hybridized naturally and artificially with other stone fruit trees. These features made the genetic background of stone fruit trees rather complex. Previous studies on taxonomy and genetic polymorphism for P. mume were carried out using morphology, cytology, sporule, isoenzyme markers, RAPD, AFLP, SNP and SSR. However, there are still some puzzles. Sequence analysis is a new accurate method with higher efficiency and has been used in the research of phylogeny, genetic structure, introgression in kinds of plant. To settle those puzzles nuclear ITS and chloroplast atpB-rbcL were used to construct the phylogeny of stone fruit trees.
1. Prunus mume Sieb. et Zucc, as an ornamental and fruit tree, has been cultivated for centuries in the East Asian, especially in the southern part of China. But much remain unknown about genetic variation and origin of various cultivars. Microsatellite (simple sequence repeat, SSR) is a very prevalent, effective molecular marker. However, there have been few attempts to isolate and characterize SSRs in Prunus mume. To develop more SSRs for the genetic analysis of P. mume, we modified the protocol, called dual-suppression -PCR. A total of eleven SSRs, five (GA)n and six (AC)n, were successful isolated. Eight SSRs were found to be polymorphic in a test sample of 11 P. mume cultivars. The observed number of alleles per locus ranged from 2 to 8 and observed heterozygosity ranged from 0.33 to 1.00 with an average of 0.71, suggesting a high degree of variation in isolated loci. These informational loci will be very useful in the study on the genetic structure, origin, evolution of P. mume and its closely related species.
2. At present, many microsatellite-enrichment methods were proposed to increase microsatellite (SSR) isolation efficiency, but it is a complete black-box about the SSR distribution in the insertion fragment in the clone before being sequenced, so the isolation efficiency is still low, which greatly limited the application of SSR. Here we constructed a new model, accurate forecast (AFC). The model can eliminate those useless sequences before being sequenced to gain 100% efficiency and has high feasibility, transferability and fits all the methods with SSRs enrichment (just add it to the end). To simplify the calculation procedure the model was transformed into database software 'Accurate Forecast Microsatellite 1.0'. After modified affinity capture to enrich microsatellite, positive clones were detected by a nested PCR and the data were inputted into the software. The first fifteen anterior clones in the recommendation list created automatically by software were sequenced and all of them sequences were usable for SSR isolation, containing SSR sequences and their corresponding flanking sequences, which were long enough to be used for primer design. Compared with Affinity Capture and Dual-Suppression-PCR, AFC pipeline has higher SSRs enrichment (65%), high sequence percentage (100%) and less cost per SSR locus. It is easy to be operated. It can be a new powerful SSR isolation approach, especially for non-model organisms.
3. To comprehend the distribution rule of plant chloroplast microsatellites (cpSSRs) and develop the universal cpSSR primers for stone fruit trees, the complete genome of Arabidopsis thaliana Chloroplast was downloaded and analysed. The mononucleotide cpSSRs were preponderant (78.6%), the dinucleotide cpSSRs, the trinucleotide cpSSRs and the others cpSSR accounted for 19%, 2.4 % and 0%, correspondly. The (T)n and (A)n cpSSRs were the most type in the mononucleotide cpSSRs (98.5%) while all the dinucleotide cpSSRs were (AT)n. 41 pure SSRs (62.1%), 23 interrupted SSRs (34.8%) and 2 multiple cpSSRs (3.1%) existed in the the mononucleotide cpSSRs.
4. Two methods were used to develop the universal cpSSR for stone fruit trees. 1) Non-coding region sequencing (NRS). Total Genomic DNA of Prunus mume 'Koshu Koume' was extracted. A nested PCR was performed to amplify and screened 16 chloroplast intergene sequences (IGSs) and 1 intron. 8 IGSs were successfully amplified in the secondary nested PCR. After sequencing 9 mononucleotide cpSSR loci, (A)n or (T)n with n≥8, were found. 2) Bio-informatics method. 33 chloroplast sequences of peach, plum, mume, apricot, cherry were downloaded form the Genbank. 38 mononucleotide cpSSRs, (A)n or (T)n with n≥8, were obtained by directly search, 8 of them with n≥10 were choosed to design universal primer. 6 pairs of cpSSR primer developed using NRS were tested in 24 Prunus genotypes and all of them were polymorphic. 18 fragments were yielded and formed 14 haplotypes. The high Heterozygosity (0.96) indicated there were rich haplotype types in stone fruit trees. But apricot and mume had lowest Heterozygosity (0.32) and only 2 haplotypes with disequilibrium distribution. This showed that apricot and mume had simplex origin and limited genetic background. These new developed cpSSRs provide a new alternative efficient tool to analyze the origin and evolution of stone fruit trees.
5. To reconstruct phylogeny of stone fruit trees, the atpB-rbcL noncoding spacer of chloroplast DNA from 24 genotypes of peach, plum, apricot, mume and cherry, 4-5 genotypes per specie, were sequenced and analyzed. With Zippeliana as outgroup, the data set was tested with 56 evolution models with PAUP and the score was used to screen the best model and parameter with Modeltest. Genetic distances, variances were calculated and the maximum parsimony tree was constructed with Mega. The result indicated: 1. Molecular evolution rates were different among stone fruit trees and the distribution of variance was unbalanced; 2. An initial split from the backbone of the Phylogenetic tree indicated that cherry was more original than other species. Mume had closest relationship with apricot and closer with plum. As a monophyletic group, stone fruit trees were come from an original plant with two clades, one evolved to cherry and the other to other stone fruit trees.
6. To analyze the molecular evolution and phylogeny of stone fruit trees, the internal transcribed spacers (ITS) of nuclear ribosomal DNA from 16 genotypes of peach, plum, apricot, mume, and cherry, 2-4 genotypes per species, were sequenced and analyzed with 6 ITS sequences downloaded from the GenBank. Prinsepia sinensis as outgroup, the maximum parsimony tree was constructed with Mega. An initial split from the backbone of the phylogenetic tree indicated that cherry was more original than other species. Because Prinsepia sinensis was greatly different with others, the second way of rooting with cherry was performed. The broad data set was tested with 56 evolution models with PAUP and the score was used to screen the best model and parameter with Modeltest. Mega was used to calculate genetic distance, variance and construct maximum parsimony phylogenetic tree. The result indicated: 1. Molecular evolution rate and information were different between ITS1 and ITS2, and also among stone fruit trees; 2. The evolution order of 5 stone fruit trees was analyzed. Cherry, plum and apricot were come from an original plant, and then plum evolved to peach and apricot to mume; 3. Prunus mandshurica is more original than P. sibirica and P. armeniaca. The evolution order of peach is from P. andersonii to P. davidiana and then to P. persica (P. ferganensis); 4. It is reasonable that stone fruit trees are divided into 4 subgenera.
引文
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