三角鲂肝脏EST序列微卫星信息分析

利用RNA-Seq技术对三角鲂的肝脏进行了转录组测序,获得了大量EST序列后,利用MISA软件进行微卫星信息分析。结果表明,通过转录组测序获得三角鲂EST序列62780条,长度31.9 Mb,发现8853个SSR,出现频率为14.1%。在三角鲂EST-SSR中,重复单元以1-2碱基重复为最多,并以长度小于16 bp的短重复序列为主,间隔SSR和复合SSR的EST序列RPKM均值低于单纯型SSR的EST序列RPKM均值,且在单纯型SSR中SSR长度越长,其RPKM均值则越低。因此,对富含SSR位点的EST序列的挖掘将为开发SSR特异性标记,并应用于三角鲂生物多样性和选育提供了参考。...

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Bibliographic Details
Published in江西农业学报 Vol. 28; no. 6; pp. 87 - 91
Main Author 刘凯 谢楠 冯晓宇 刘新轶 潘彬斌 姚桂桂
Format Journal Article
LanguageChinese
Published 杭州市农业科学研究院,浙江杭州,310024 2016
Subjects
三角鲂
序列分析
微卫星
表达序列标签
Microsatellite
微卫星
表达序列标签
Megalobrama terminalis
序列分析
Sequence analysis
三角鲂
Expressed sequence tags
Online AccessGet full text
ISSN1001-8581
DOI10.19386/j.cnki.jxnyxb.2016.06.18

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Summary:利用RNA-Seq技术对三角鲂的肝脏进行了转录组测序,获得了大量EST序列后,利用MISA软件进行微卫星信息分析。结果表明,通过转录组测序获得三角鲂EST序列62780条,长度31.9 Mb,发现8853个SSR,出现频率为14.1%。在三角鲂EST-SSR中,重复单元以1-2碱基重复为最多,并以长度小于16 bp的短重复序列为主,间隔SSR和复合SSR的EST序列RPKM均值低于单纯型SSR的EST序列RPKM均值,且在单纯型SSR中SSR长度越长,其RPKM均值则越低。因此,对富含SSR位点的EST序列的挖掘将为开发SSR特异性标记,并应用于三角鲂生物多样性和选育提供了参考。
Bibliography:36-1124/S
Megalobrama terminalis; Expressed sequence tags; Microsatellite; Sequence analysis
A lot of expressed sequence tags（ EST） obtained from transcriptome sequencing of livers in Megalobrama terminalis based on high-throughput RNA sequencing technology,and perform analysis of simple sequence repeats（ SSR） information in EST. The results showed that,62780 EST with 31.9 Mb length were obtained,and 8853 EST-SSR mined out by MISA,the frequency of which was 14.1%. In the EST- SSR of Megalobrama terminalis,nucleotide and binucleotide repeats were the main types,in a short length of less than 16 bp mainly,mean RPKM of EST contain interrupted and compound SSR were lower than mean RPKM of EST contain pure SSR,and in the pure EST- SSR,the longer SSR in length,the lower mean of RPKM. These EST sequences containing SSR would facilitate the further development of specific SSR markers,as well as providing reference for applying the biodiversity of Megalobrama terminalis and breeding.
LIU Kai, XIE Nan, FENG Xiao-yu, LIU X
ISSN:1001-8581
DOI:10.19386/j.cnki.jxnyxb.2016.06.18