银杏EST序列中微卫星的分布特征

Characteristics of EST-SSR Distribution in Ginkgo ESTs

本文利用从NCBI下载的21590条银杏EST序列,分析了银杏（表达序列标签微卫星）EST-SSR在银杏EST序列的分布和比较了在不同长度EST序列中的SSR特性。在剔除冗余和低质量序列后,得到总长为5708.385kb的无冗余EST序列7961条,发现了405个EST序列（5.09%）含有475个SSR,长度400~1000bp的EST序列含SSR位点数为445个,占SSR总数的93.68%。二核苷酸和三核苷酸基元类型是银杏EST-SSR的主要类型,分别占SSR总数的73.89%和24.00%,最常见的SSR基元是：（AT）n、（AG）n、（AC）n、（AAG）n和（AAT）n。通过对银杏EST序列中SSR位点信息的发掘分析,为有针对性地设计EST-SSR引物,开发银杏EST-SSR分子标记奠定基础。

In this study, we analyzed the distribution of EST-SSR in ginkgo EST database and compared the characters of EST-SSRs derived from the ginkgo expressed sequence tags （ESTs） in different length based on the 21 590 ginkgo ESTs online downloaded in the NCBI database. 7 961 non-redundant EST sequences that totaled 5 708.385 kb length were acquired posterior to removing some redundant and poor quality, EST sequences. It was found out that 475 SSRs distributed in 405 EST sequences which accounted for 5.09% of the 7 961 non-redundant ESTs, and 445 SSRs in the range of 400 bp to 1 000 bp length were identified which accounted for 93.68% of the total number of acquired SSRs. Dinucleotide and trinucleotide would be the major repeat types, which accounted for 73.89% and 24.00% of the total number of acquired SSRs, resepectively, and the motifs of （AT）n, （AG）~, （AC）n, （AAG）n and （AAT）n might be the most frequent motifs. This research might lay the foundation for designing the targeted EST-SSR primers and developing EST-SSR molecular markers by mining the information of EST-SSR loci in ginkgo EST sequence data.