青稞转录组SSR位点及其基因功能分析  

Characterization and Gene Function Analysis of SSR Sequences in Hulless Barley Transcriptome

作　　者：徐金青[1,2] 夏腾飞[1,2] 王蕾[1,3] 王寒冬[1] 张怀刚[1,3] 刘登才[4] 昌西[5] 沈裕虎[1,3] 

机构地区：[1]中国科学院高原适应与进化重点实验室中国科学院西北高原生物研究所,青海西宁810001 [2]中国科学院大学,北京100039 [3]青海省作物分子育种重点实验室,青海西宁810001 [4]四川农业大学小麦研究所,四川温江611830 [5]西藏农牧学院,西藏林芝860000

出　　处：《麦类作物学报》2017年第2期175-184,共10页Journal of Triticeae Crops

基　　金：青海省应用基础研究计划项目(2015-ZJ-702);中国科学院"西部之光"联合学者项目;西藏自治区西部提升计划"作物学学科建设"项目(XBTSZWXK-01)

摘　　要：为了探讨青稞转录中SSR位点信息及其所在基因的生物学功能,使用MISA软件分析青稞转录组中SSR的分布频率和重复基元的基本类型,通过BLASTX对含有SSR的Unigene与nr、COG、Swiss-Prot和KEGG等公共数据库进行比对和功能注释。结果表明,在青稞转录组拼接得到的58 065个Unigene中发现9 576条序列中含有11 930个SSR位点,SSR发生频率为16.49%,平均每6.63kb出现1个SSR位点,共有119种重复基元(motif)。青稞转录组SSR出现频率最高的是三核苷酸重复基元(64.19%),其次是二核苷酸重复基元(24.05%)。AG/CT和AGG/CCT、CCG/CGG、AGC/CTG分别是二核苷酸重复和三核苷酸重复中的优势重复基元。在转录组中SSR重复次数以5~12次为主,基序长度主要集中在12~25bp,平均长度为21.15bp。9 576个含SSR的Unigene与nr、COG、Swiss-Prot和KEGG等公共数据库进行BLASTX比对,分别得到7 987、5 559、5 588和2 077个注释。通过基因功能注释发现青稞转录组中含SSR的序列主要与生物的基础代谢相关。In order to characterize the SSRs in hulless barley （Hordeum vulgare L. var. nudum HK. f. ） transcriptome and annotate the SSR sequences based on bioinformatics analysis, the distribution frequency and basic repeat motifs of SSRs in hulless barley transcriptiome were screened by MISA software. The gene annotation of SSR sequences were obtained by BLASTX against nr, COG, Swiss- Prot and KEGG databases. A total of 11 930 SSRs with 119 kinds of repeat motifs were found in 58065 Unigenes,distributed in 9 576 Unigenes,which accounted for 16. 49% of all Unigenes,and the density of distribution was 6. 63 kb per SSR. Among the SSRs in hulless barley transcriptome, the most abundant repeat motif was the tri-nucleotide （64. 19%） , followed by the di-nucleotide （24. 05%）. AG/CT and AGG/CCT,CCG/CGG and AGC/CTG were the superior type in di-,and tri-nucleotide repeat motif（s）. Most of the repeat number of SSRs was from 5 to 12,and the length of the motif ranged from 12 to 25 bp,with an average of 21. 15 bp. 9 576 SSR sequences were annotated with BLASTX against protein databases （nr, COG, Swiss-Prot and KEGG） , of which, 7 987,5 559,5 588 and 2 077 were annotated,respectively. The annotation of the SSR sequences in hulless barley sugges-ted that they were mainly related to the basic biological metabolism.

关 键 词：青稞 转录组 SSR 功能注释 

分 类 号：S512.3[农业科学—作物学] S330