杉木转录因子unigene中微卫星的分布
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摘要
本研究以杉木转录组序列信息为基础,分析转录因子unigene中微卫星(transcription factor unigenederived microsatellites, TFUMs)的分布特征。结果表明,3 155个杉木转录因子(transcription factor, TFs) unigene中,存在527个TFUMs,25种基元。其中三、四核苷酸基元的类型最多,分别有10种和7种。由三、二核苷酸基元组成的TFUMs数目最多,分别为386和92个。AG/CT、AGC/CTG基元在TFUMs中分布最广,分别占二、三核苷酸重复TFUMs总数的53%和22%。根据基元的重复次数,杉木TFUMs主要可分为2个区间,重复5～8次的TFUMs分为第一区间,重复9～12次的分为第二区间。杉木TFUMs主要分布在第一区间,随着重复次数的增加,TFUMs数量呈现下降趋势。本研究首次运用卡方检验分析EST-SSRs在TFs及其余unigene中的分布差异,发现EST-SSRs特别是三核苷酸重复的EST-SSRs在TFs unigene中极显著富集。该研究为杉木TFUMs标记的开发与利用建立了基础。
The researc h was based on the sequence information of Chinese fir transcriptome. Distribution characteristics of transcription factor unigene-derived microsatellites(TFUMs) were analyzed. The results showed that 527 TFUMs and 25 types of motif were found in 3 155 transcription factor(TFs) unigene. Trinucleotide and tetranucleotide motif types were the most among TFUMs, with 10 and 7 types respectively. The number of TFUMs consisting of trinucleotide and dinucleotide motifs were the most, which were 386 and 92 respectively. AG/CT and AGC/CTG motifs were the most widely distributed in TFUMs, accounting for 53% and 22% of the total number of TFUMs for trinucleotide and dinucleotide repeats. According to the repetition times of motif, TFUMs of Chinese fir were mainly divided into two ranges. TFUMs in the first range had 5 to 8 motif repetitions, while that in the second range had 9 to 12 motif repetitions. TFUMs of Chinese fir were distributed mainly in the first range. The number of TFUMs declined with the increase of the motif repetition times. Chi-square test was used to analyze the distribution of EST-SSRs in TFs and other unigene fo r the first time. It was found that EST-SSRs, especially trinucleotide repeat EST-SSRs, were highly enriched in TFs unigene. This research might establish the foundation for the development and utilization of TFUMs in Chinese fir.
The researc h was based on the sequence information of Chinese fir transcriptome. Distribution characteristics of transcription factor unigene-derived microsatellites(TFUMs) were analyzed. The results showed that 527 TFUMs and 25 types of motif were found in 3 155 transcription factor(TFs) unigene. Trinucleotide and tetranucleotide motif types were the most among TFUMs, with 10 and 7 types respectively. The number of TFUMs consisting of trinucleotide and dinucleotide motifs were the most, which were 386 and 92 respectively. AG/CT and AGC/CTG motifs were the most widely distributed in TFUMs, accounting for 53% and 22% of the total number of TFUMs for trinucleotide and dinucleotide repeats. According to the repetition times of motif, TFUMs of Chinese fir were mainly divided into two ranges. TFUMs in the first range had 5 to 8 motif repetitions, while that in the second range had 9 to 12 motif repetitions. TFUMs of Chinese fir were distributed mainly in the first range. The number of TFUMs declined with the increase of the motif repetition times. Chi-square test was used to analyze the distribution of EST-SSRs in TFs and other unigene fo r the first time. It was found that EST-SSRs, especially trinucleotide repeat EST-SSRs, were highly enriched in TFs unigene. This research might establish the foundation for the development and utilization of TFUMs in Chinese fir.
引文
Chamb ers G.K.,and Macavoy E.S.,2000,Microsatellites:consensus and controversy,Comparative Biochemistry&Physiology Part B Biochemistry&Molecular Biology,126(4):455
Divyadharsini R.,Prabhu R.,Manivannan N.,and Vindhiyavarman P.,2017,Validation of SSR markers for foliar disease resistance in groundnut(Arachis hypogaea L.),Int.J.Curr.Microbiol.App.Sci.,6(4):1310-1317
Ellegren H.,2004,Microsatellites:Simple sequences with complex evolution,Nat.Rev.Genet.,5:435-445
Eujayl I.,Sorrells M E.,Baum M.,Wolters P.,and Powell W.,2002,Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat,Theoretical and Applied Genetics,104(2):399-407
Gao L.F.,Tang J.F.,Li H.W.,and Jia J.Z.,2003,Analysis of microsatellites in major crops assessed by computational and experimental approaches,Molecular Breeding,12:245-261
González M.,Salazar E.,Castillo J.,Morales P.,Mura-Jornet I.,Maldonado J.,Silva H.,and Carrasco B.,2016,Genetic structure based on EST-SSR:a putative tool for fruit color selection in Japanese plum(Prunus salicina L.)breeding programs,Molecular Breeding,36(6):68
Hu J.B.,Liu Y,Wang L.J.,and Li J.W.,2009,Characteristics of microsatellites in melon(Cucumis melo L.)EST sequences,Zhiwu Shengli Xuebao(Plant Physiology Communications),45(3):258-262(胡建斌,刘颖,王兰菊,李建吾,2009,甜瓜EST序列中微卫星的分布特征,植物生理学报,45(3):258-262)
Kashi Y.,and King D.G.,2006,Simple sequence repeats as advantageous mutators in evolution,Trends in Genetics,22(5):253-259
Katti M.V.,Ranjekar P.K.,and Gupta V.S.,2001,Differential distribution of simple sequence repeats in eukaryotic genome sequences,Mol.Biol.Evol.,18(7):1161-1167
Levinson G.,and Gutman G.A.,1987,Slipped-strand mispairing:A major mechanism for DNA sequence evolution,Mol.Biol.Evol.,4:203-221
Lu X.,Wang H.,Liu B.,and Xiang J.,2013,Three EST-SSRmarkers associated with QTL for the growth of the clam Meretrix meretrix revealed by selective genotyping,Marine Biotechnology,15(1):16-25
McCallum S.,Graham J.,Jorgensen L.,Rowland L.,Bassil N.,Hancock J.,Wheeler E.,Vining K.,Poland J.,Olmstead J.,Buck E.,Wiedow C.,Jackson E.,Brown A.,and Hackett C,2016,Construction of a SNP and SSR linkage map in autotetraploid blueberry using genotyping by sequencing,Molecular Breeding,36(4):41
Meyer L.,Causse R.,Pernin F.,Scalone R.,Bailly G.,Chauvel B.,Délye C.,and Le-Corre V.,2017,New g SSR and EST-SSRmarkers reveal high genetic diversity in the invasive plant Ambrosia artemisiifolia L.and can be transferred to other invasive Ambrosia species,PLo S One,12(5):e0176197
Morgante M.,Hanafey M.,and Powell W.,2002,Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes,Nat.Genet.,30:194-200
Mutai C.,Kamunya S.M.,and Muoki R.C.,2016,Development of EST-SSR primers for marker-assisted selection for drought tolerance in tea(Camellia sinensis(L.)O.Kuntze),Tea,37(1/2):129-138
Ohyama A.,Shirasawa K.,Matsunaga H.,Negoro S.,Miyatake K.,Yamaguchi H.,Nunome T.,Iwata H.,Fukuoka H.,and Hayashi T.,2017,Bayesian QTL mapping using genomewide SSR markers and segregating population derived from a cross of two commercial F1 hybrids of tomato,Theoretical and Applied Genetics,130(8):1601-1616
Spitz F.,and Furlong E.E.M.,2012,Transcription factors:from enhancer binding to developmental control,Nature reviews Genetics,13(9):613
Tóth G.,Gáspári Z.,and Jurka J.,2000,Microsatellites in different eukaryotic genomes:survey and analysis,Genome Research,10(7):967-981
Vergnaud G.,and Denoeud F.,2000,Minisatellites:Mutability and genome architecture,Genome Res.,10:899-907
Wen Y.F.,Han W.J.,Zhou H.,and Xu G.B.,2015,SSR mining and development of EST-SSR markers for Cunninghamia lanceolata based on transcriptome sequences,Linye Kexue(Scientia Silvae Sinicae),51(11):40-49(文亚峰,韩文军,周宏,徐刚标,2015,杉木转录组SSR挖掘及EST-SSR标记规模化开发,林业科学,51(11):40-49)
Xu Y.,Chen J.H.,Li Y.,2014,Development of EST-SSR and genomic-SSR in Chinese fir,Nanjing Linye Daxue Xuebao(Ziran Ban)(Journal of Nanjing Forestry University(Natural Science)),38(1):9-14(徐阳,陈金慧,李亚,洪舟,王颖,赵亚琦,王新民,施季森,2014,杉木EST-SSR与基因组SSR引物开发,南京林业大学学报(自然科学版),38(1):9-14)
Yamasaki K.,Kigawa T.,Seki M.,Shinozaki K.,and Yokoyama S.,2013,DNA-binding domains of plant-specific transcription factors:structure,function,and evolution,Trends in Plant Science,18(5):267-276
Divyadharsini R.,Prabhu R.,Manivannan N.,and Vindhiyavarman P.,2017,Validation of SSR markers for foliar disease resistance in groundnut(Arachis hypogaea L.),Int.J.Curr.Microbiol.App.Sci.,6(4):1310-1317
Ellegren H.,2004,Microsatellites:Simple sequences with complex evolution,Nat.Rev.Genet.,5:435-445
Eujayl I.,Sorrells M E.,Baum M.,Wolters P.,and Powell W.,2002,Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat,Theoretical and Applied Genetics,104(2):399-407
Gao L.F.,Tang J.F.,Li H.W.,and Jia J.Z.,2003,Analysis of microsatellites in major crops assessed by computational and experimental approaches,Molecular Breeding,12:245-261
González M.,Salazar E.,Castillo J.,Morales P.,Mura-Jornet I.,Maldonado J.,Silva H.,and Carrasco B.,2016,Genetic structure based on EST-SSR:a putative tool for fruit color selection in Japanese plum(Prunus salicina L.)breeding programs,Molecular Breeding,36(6):68
Hu J.B.,Liu Y,Wang L.J.,and Li J.W.,2009,Characteristics of microsatellites in melon(Cucumis melo L.)EST sequences,Zhiwu Shengli Xuebao(Plant Physiology Communications),45(3):258-262(胡建斌,刘颖,王兰菊,李建吾,2009,甜瓜EST序列中微卫星的分布特征,植物生理学报,45(3):258-262)
Kashi Y.,and King D.G.,2006,Simple sequence repeats as advantageous mutators in evolution,Trends in Genetics,22(5):253-259
Katti M.V.,Ranjekar P.K.,and Gupta V.S.,2001,Differential distribution of simple sequence repeats in eukaryotic genome sequences,Mol.Biol.Evol.,18(7):1161-1167
Levinson G.,and Gutman G.A.,1987,Slipped-strand mispairing:A major mechanism for DNA sequence evolution,Mol.Biol.Evol.,4:203-221
Lu X.,Wang H.,Liu B.,and Xiang J.,2013,Three EST-SSRmarkers associated with QTL for the growth of the clam Meretrix meretrix revealed by selective genotyping,Marine Biotechnology,15(1):16-25
McCallum S.,Graham J.,Jorgensen L.,Rowland L.,Bassil N.,Hancock J.,Wheeler E.,Vining K.,Poland J.,Olmstead J.,Buck E.,Wiedow C.,Jackson E.,Brown A.,and Hackett C,2016,Construction of a SNP and SSR linkage map in autotetraploid blueberry using genotyping by sequencing,Molecular Breeding,36(4):41
Meyer L.,Causse R.,Pernin F.,Scalone R.,Bailly G.,Chauvel B.,Délye C.,and Le-Corre V.,2017,New g SSR and EST-SSRmarkers reveal high genetic diversity in the invasive plant Ambrosia artemisiifolia L.and can be transferred to other invasive Ambrosia species,PLo S One,12(5):e0176197
Morgante M.,Hanafey M.,and Powell W.,2002,Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes,Nat.Genet.,30:194-200
Mutai C.,Kamunya S.M.,and Muoki R.C.,2016,Development of EST-SSR primers for marker-assisted selection for drought tolerance in tea(Camellia sinensis(L.)O.Kuntze),Tea,37(1/2):129-138
Ohyama A.,Shirasawa K.,Matsunaga H.,Negoro S.,Miyatake K.,Yamaguchi H.,Nunome T.,Iwata H.,Fukuoka H.,and Hayashi T.,2017,Bayesian QTL mapping using genomewide SSR markers and segregating population derived from a cross of two commercial F1 hybrids of tomato,Theoretical and Applied Genetics,130(8):1601-1616
Spitz F.,and Furlong E.E.M.,2012,Transcription factors:from enhancer binding to developmental control,Nature reviews Genetics,13(9):613
Tóth G.,Gáspári Z.,and Jurka J.,2000,Microsatellites in different eukaryotic genomes:survey and analysis,Genome Research,10(7):967-981
Vergnaud G.,and Denoeud F.,2000,Minisatellites:Mutability and genome architecture,Genome Res.,10:899-907
Wen Y.F.,Han W.J.,Zhou H.,and Xu G.B.,2015,SSR mining and development of EST-SSR markers for Cunninghamia lanceolata based on transcriptome sequences,Linye Kexue(Scientia Silvae Sinicae),51(11):40-49(文亚峰,韩文军,周宏,徐刚标,2015,杉木转录组SSR挖掘及EST-SSR标记规模化开发,林业科学,51(11):40-49)
Xu Y.,Chen J.H.,Li Y.,2014,Development of EST-SSR and genomic-SSR in Chinese fir,Nanjing Linye Daxue Xuebao(Ziran Ban)(Journal of Nanjing Forestry University(Natural Science)),38(1):9-14(徐阳,陈金慧,李亚,洪舟,王颖,赵亚琦,王新民,施季森,2014,杉木EST-SSR与基因组SSR引物开发,南京林业大学学报(自然科学版),38(1):9-14)
Yamasaki K.,Kigawa T.,Seki M.,Shinozaki K.,and Yokoyama S.,2013,DNA-binding domains of plant-specific transcription factors:structure,function,and evolution,Trends in Plant Science,18(5):267-276