巴西橡胶树转录组中SSR位点的信息分析

Bioinformatic analysis of SSR markers in transcriptome of rubber tree Hevea brasiliensis Muell. Arg.

摘要: 从NCBI网站下载橡胶树（Hevea brasiliensis）品种RRIM600的全转录组数据（登录号：JT914190-JT981478），利用SSR软件MicroSAtellite（MISA），并采用含有1~10个碱基重复尧碱基数在12 bp以上的鉴定标准对SSR基元进行鉴定分析。结果表明，从RRIM600的全转录组数据中，共发现91846个SSR，分布于42859条Unigene中，发生频率为63.71%。橡胶树转录组SSR的平均长度为9bp，平均分布频率是1/0.92 kb。其中含6个碱基重复基元类型最多，共有52615个，占所鉴定SSR总数的57.29%。同时对这些SSR的可用性进行了评价。

Abstract: Unigenes were downloaded from NCBI (http://www.ncbi.nlm.nih.gov/genbank/) to screen SSRs in completetranscriptome sequence of H. brasiliensis RRIM 600 (accession number：JT914190-JT981478). MicrosAtellite (MISA)software was used to identify and analyze the SSRs with 1-10 base repeat and bases above 12 bp. A total of 91 846 SSRswere found in H. brasiliensis RRIM 600, distributing in 42 859 unigenes, which accounted for 63.71% of the total numberof unigenes. The average length and distribution distance of the transcriptomic SSRs were about 9 bp and 1/0.92 kb,respectively. In the 91 846 SSRs, the hexamers were the main types with the SSR numbers of 52 615, accounting for 57.29% of all the SSRs. The potential of the transcriptomic SSRs for further usage was assessed.