蒙药冷蒿转录组SSR信息分析

Data Mining of Simple Sequence Repeats in Transcriptome Sequences of Mongolia Medicinal Plant Artemisia frigida Willd

利用MISA（Micro SAtelite）软件对测序得到的蒙药冷蒿转录组序列143 700条跨叠群（contigs）进行简单重复序列（SSR）位点的挖掘,发现3 614条序列含有3 753个SSR位点,发生频率为2.51%,共有122种重复基元,平均每18.46 kb出现1个SSR位点。冷蒿转录组序列的SSR主要集中在三核苷酸重复（56.12%）,其次是二核苷酸重复（31.60%）。AC/TG、AT/TA、CA/GT、AAT/TTA和AAC/TTG是二核苷酸、三核苷酸中的优势重复基元。冷蒿转录组SSR以5~12次重复为主,基序长度主要集中于12~36 bp。冷蒿转录组共注释43 415个contigs,其中578个SSRs位于编码区,主要以三核苷酸重复为主（397,68.69%）。从分子水平和生物信息学角度介绍了蒙药冷蒿转录组SSR信息的开发利用,其出现频率高、重复类型丰富,将为冷蒿的分子标记辅助育种、遗传多样性分析、遗传图谱构建和功能基因挖掘提供了候选序列。

MISA（Micro SAtelite） software was used to screen SSRs in 143 700 contigs of Artemisia frigida Willd.transcriptome sequences. 3 753 SSR sites were identified among 3 614 contigs which accounted for 2.51% of 143 700 contigs. There were 122 kinds of SSR motifs existing in A. frigida Willd. transcriptome. On average,SSRs occurred every 18.46 kb in length. In the SSRs,the tri-nucleotide repeat motif was the most abundant（ 56.12%）,followed by the di-nucleotide（ 31.60%）. AC/TG,AT/TA,CA/GT,AAT/TTA and AAC/TTG were the main types of motif in di-nucleotide,tri-nucleotide repeats. The repeat number of SSRs which from A. frigida Willd. transcriptome SSRs were mainly from 5 to 12 and their motif length mostly ranged from 12 ~ 32 bp. A total of 43 415 contigs were annotated,and only 578 SSRs were occurred in protein-coding regions,the tri-nucleotide repeats were the most abundant in coding regions（ 397,68. 69%）. This paper introduced the development and utilization of A. frigida Willd. transcriptome from the molecular level and biological information angle. With high occurrence frequency and multiple repeated A. frigida Willd. transcriptome types,A. frigida Willd. transcriptome had provided candidate sequenses for breeding assisted by A. frigida Willd. molecular marker,analyzing genetic diversity,constructing genetic map and mining functional gene.