桂花(Osmanthus fragrans)转录组SSR特征分析
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摘要
为解析桂花转录组数据中SSR的特点及潜在利用价值,本研究基于‘早银桂’和‘橙红丹桂’转录组数据信息,利用MISA软件从桂花的117 595个Unigenes中进行SSR位点的查找、分析,共检测到16 015个SSR位点,平均密度是1/5.2 kb。桂花SSR基序97.73%的重复次数在5～10次之间,重复次数最多的是6次(28.12%);SSR长度分布在12～36 bp之间,其中12～16 bp的最多,占66.8%,其总体变化趋势是随着重复次数增加重复次数急速下降。基于已知的SSR位点,利用primer3设计引物并从中挑选出196对引物,其中92对引物(占46.94%)已被注释到参与信号的转录翻译、苯丙氨酸代谢、植物激素信号转导等功能。综上所述‘,早银桂’和‘橙红丹桂’转录组SSR位点出现频率高,类型较丰富、多态性潜能较高,为今后桂花分子育种提供了理论依据。
In order to illustrate the characteristics and potential utilizable value of SSR in the transcriptome of Osmanthus fragrans, software MISA was used to detect and analyze SSR locus from 117 595 Unigenes of the transcriptome data of two varieties of' Zaoyin gui' and 'Chenghongdangui'. As a result, 16 015 SSR loci were detected in total and its average distribution density was 1/5.2 kb. The highest SSR motif repeat number fall among 5～10,which reached 97.73%. Meanwhile, the repeat number 6 was the most type(28.12%). The length of SSR was distributed between 12～36 bp, and 12～16 bp was the largest, accounting for 66.8%. Furthermore, the overall trend was that the number of repetitions decreased rapidly with the increase of repetitions. Based on known SSR loci,primer3 was used to design primers and 196 pairs of primers were selected from them. 92 pairs of primers(46.94%) were annotated to participate in signal transcription and translation, phenylalanine metabolism, plant hormone signal transduction and other functions. In summary, the SSR of 'Zaoyin Gui' and 'Chenghong Dangui' had high frequency, abundant types and high polymorphism potential, which could provide a theoretical basis for the molecular breeding of O. fragrans in the future.
In order to illustrate the characteristics and potential utilizable value of SSR in the transcriptome of Osmanthus fragrans, software MISA was used to detect and analyze SSR locus from 117 595 Unigenes of the transcriptome data of two varieties of' Zaoyin gui' and 'Chenghongdangui'. As a result, 16 015 SSR loci were detected in total and its average distribution density was 1/5.2 kb. The highest SSR motif repeat number fall among 5～10,which reached 97.73%. Meanwhile, the repeat number 6 was the most type(28.12%). The length of SSR was distributed between 12～36 bp, and 12～16 bp was the largest, accounting for 66.8%. Furthermore, the overall trend was that the number of repetitions decreased rapidly with the increase of repetitions. Based on known SSR loci,primer3 was used to design primers and 196 pairs of primers were selected from them. 92 pairs of primers(46.94%) were annotated to participate in signal transcription and translation, phenylalanine metabolism, plant hormone signal transduction and other functions. In summary, the SSR of 'Zaoyin Gui' and 'Chenghong Dangui' had high frequency, abundant types and high polymorphism potential, which could provide a theoretical basis for the molecular breeding of O. fragrans in the future.
引文
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Chen L.,Li L.N.,Yang G.D.,and Dai Y.P.,2016,Microsatellites characteristics of transcriptomic sequences from Osmanthus serrulatus,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),14(4):959-965(陈林,李龙娜,杨国栋,戴亚平,2016,特有植物短丝木犀(Osmanthus serrulatus)转录组微卫星特征分析,分子植物育种,14(4):959-965)
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Hou X.G.,Wang J.,Guo D.L.,Liu G.X.,Ma H.L.,and Wang X.Y.,2011,Analysis of SSR motifs in tree peony(Paeonia suffruticosa Andrews.)EST sequences,Hunan Nongye Daxue Xuebao(Journal of Hunan Agricultural University),37(2):172-176(侯小改,王娟,郭大龙,刘改秀,马慧丽,王小燕,2011,牡丹EST资源中SSR的信息分析,湖南农业大学学报,37(2):172-176)
Huang H.Y.,Du H.Y.,Wuyun T.N.,and Liu P.F.,2013,Development of SSR molecular markers based on transcriptome sequencing of Eucommia ulmoides,Linye Kexue(Scientia Sil-vae Sinicae),49(5):176-181(黄海燕,杜红岩,乌云塔娜,刘攀峰,2013,基于杜仲转录组序列的SSR分子标记的开发,林业科学,49(5):176-181)
Jiang C.,Yuan Y.,Liu G.M.,Huang L.Q.,Wang X.M.,Yu J.,and Chen M.,2012,EST-SSR identification of Lonicera japonica Thunb.,Yaoxue Xuebao(Acta Pharmaceutica Sinica),47(6):803-810(蒋超,袁媛,刘贵明,黄璐琦,王绪敏,于军,陈敏,2012,基于EST-SSR的金银花分子鉴别方法研究,药学学报,47(6):803-810)
Jin J.Q.,Cui H.R.,Chen W.Y.,Lu M.Z.,Yao Y.L.,Xin Y.,and Gong X.C.,2016,Data mining for SSRs in ESTs and development of EST-SSR marker in tea plant(Camellia sinensis),Chaye Kexue(Journal of Tea Science),26(1):17-23(金基强,崔海瑞,陈文岳,卢美贞,姚艳玲,忻雅,龚晓春,2006,茶树EST-SSR的信息分析与标记建立,茶叶科学,26(1):17-23)
Kelleher C.T.,Hodkinson T.R.,and Kelly D.L.,2004,Species status,hybridisation and geographic distribution of Irish populations of Quercus petraea(Matt.)Liebl.and Q.robur L.,Watsonia,25(1):83-97
Liu Y.L.,Li W.,and Dong S.B.,2017,Characterization of SSRs and development of EST-SSR markers in transcriptome of Xanthoceras sorbifolium,Xibei Nonglin Keji Daxue Xuebao(Journal of Northwest A&F University),45(3):89-95(刘玉林,李伟,董树斌,2017,文冠果转录组SSR特征分析及EST-SSR标记开发,西北农林科技大学学报,45(3):89-95)
Temnykh S.,Declerck G.,Luashova A.,Lipovich L.,Cartinhour S.,and McCouch S.R.,2001,Computational and experimental analysis of microsatellites in rice(Oryza sativa L.):frequency,length variation,transposon associations,and genetic marker potential,Genome Research,59(19):1441-1452
Xu M.,and Li H.G.,2008,Development and characterization of microsatellite markers from expressed sequence tags for liriodendron,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),6(3):615-618(胥猛,李火根,2008,鹅掌楸EST-SSR引物开发及通用性分析,分子植物育种,6(3):615-618)
Yang X.L.,Shi T.T.,Wen A.L.,and Wang L.G.,2015,Variance analysis of aromatic components from different varieties of Osmanthus fragrans,Dongbei Linye Daxue Xuebao(Journal of Northeast Forestry University),43(1):83-87(杨秀莲,施婷婷,文爱林,王良桂,2015,不同桂花品种香气成分的差异分析,东北林业大学学报,43(1):83-87)
Zhang Y.Y.,and Fang Y.M.,2014,Analysis of SSR information in EST resource of four quercus species,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),33(1):133-140(张元燕,方炎明,2014,四种栎树EST-SSR信息分析,基因组学与应用生物学,33(1):133-140)
Chen L.,Li L.N.,Yang G.D.,and Dai Y.P.,2016,Microsatellites characteristics of transcriptomic sequences from Osmanthus serrulatus,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),14(4):959-965(陈林,李龙娜,杨国栋,戴亚平,2016,特有植物短丝木犀(Osmanthus serrulatus)转录组微卫星特征分析,分子植物育种,14(4):959-965)
Hao R.M.,Zang D.K.,and Xiang Q.B.,2005,Investigation on natural resources of Osmanthus fragrans lour.at Zhouluocun in Hunan,Yuanyi Xuebao(Acta Horticulturae Sinica),32(5):926-929(郝日明,臧德奎,向其柏,2005,湖南省浏阳市周洛村桂花峡野生桂花资源调查,园艺学报,32(5):926-929)
Hou X.G.,Wang J.,Guo D.L.,Liu G.X.,Ma H.L.,and Wang X.Y.,2011,Analysis of SSR motifs in tree peony(Paeonia suffruticosa Andrews.)EST sequences,Hunan Nongye Daxue Xuebao(Journal of Hunan Agricultural University),37(2):172-176(侯小改,王娟,郭大龙,刘改秀,马慧丽,王小燕,2011,牡丹EST资源中SSR的信息分析,湖南农业大学学报,37(2):172-176)
Huang H.Y.,Du H.Y.,Wuyun T.N.,and Liu P.F.,2013,Development of SSR molecular markers based on transcriptome sequencing of Eucommia ulmoides,Linye Kexue(Scientia Sil-vae Sinicae),49(5):176-181(黄海燕,杜红岩,乌云塔娜,刘攀峰,2013,基于杜仲转录组序列的SSR分子标记的开发,林业科学,49(5):176-181)
Jiang C.,Yuan Y.,Liu G.M.,Huang L.Q.,Wang X.M.,Yu J.,and Chen M.,2012,EST-SSR identification of Lonicera japonica Thunb.,Yaoxue Xuebao(Acta Pharmaceutica Sinica),47(6):803-810(蒋超,袁媛,刘贵明,黄璐琦,王绪敏,于军,陈敏,2012,基于EST-SSR的金银花分子鉴别方法研究,药学学报,47(6):803-810)
Jin J.Q.,Cui H.R.,Chen W.Y.,Lu M.Z.,Yao Y.L.,Xin Y.,and Gong X.C.,2016,Data mining for SSRs in ESTs and development of EST-SSR marker in tea plant(Camellia sinensis),Chaye Kexue(Journal of Tea Science),26(1):17-23(金基强,崔海瑞,陈文岳,卢美贞,姚艳玲,忻雅,龚晓春,2006,茶树EST-SSR的信息分析与标记建立,茶叶科学,26(1):17-23)
Kelleher C.T.,Hodkinson T.R.,and Kelly D.L.,2004,Species status,hybridisation and geographic distribution of Irish populations of Quercus petraea(Matt.)Liebl.and Q.robur L.,Watsonia,25(1):83-97
Liu Y.L.,Li W.,and Dong S.B.,2017,Characterization of SSRs and development of EST-SSR markers in transcriptome of Xanthoceras sorbifolium,Xibei Nonglin Keji Daxue Xuebao(Journal of Northwest A&F University),45(3):89-95(刘玉林,李伟,董树斌,2017,文冠果转录组SSR特征分析及EST-SSR标记开发,西北农林科技大学学报,45(3):89-95)
Temnykh S.,Declerck G.,Luashova A.,Lipovich L.,Cartinhour S.,and McCouch S.R.,2001,Computational and experimental analysis of microsatellites in rice(Oryza sativa L.):frequency,length variation,transposon associations,and genetic marker potential,Genome Research,59(19):1441-1452
Xu M.,and Li H.G.,2008,Development and characterization of microsatellite markers from expressed sequence tags for liriodendron,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),6(3):615-618(胥猛,李火根,2008,鹅掌楸EST-SSR引物开发及通用性分析,分子植物育种,6(3):615-618)
Yang X.L.,Shi T.T.,Wen A.L.,and Wang L.G.,2015,Variance analysis of aromatic components from different varieties of Osmanthus fragrans,Dongbei Linye Daxue Xuebao(Journal of Northeast Forestry University),43(1):83-87(杨秀莲,施婷婷,文爱林,王良桂,2015,不同桂花品种香气成分的差异分析,东北林业大学学报,43(1):83-87)
Zhang Y.Y.,and Fang Y.M.,2014,Analysis of SSR information in EST resource of four quercus species,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),33(1):133-140(张元燕,方炎明,2014,四种栎树EST-SSR信息分析,基因组学与应用生物学,33(1):133-140)
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