香菇基因组中EST-SSR的构成和分布

Compose and Distribution of EST-SSR in Genomes of Lentinula edodes

摘要:

从真菌基因组计划网站(FGP)和NCBI网站数据库下载了符合条件的总长度为8.1×10⁶bp的11150条香菇的EST(包括10条cDNA)序列，通过SSRhunter 1.3软件结合手工查找，从中发现2.83％即316条EST含有一共469个SSR，平均每17.3kb出现一个EST-SSR。在所有EST-SSR中，三碱基和六碱基SSR出现最多，分别占EST-SSR总数的38.00%和20.00%。出现较多的基序为(A)_n、(T)_n、(GA)_n、(AG)_n、(TGA)_n、(GAT)_n和(TCTTT)_n，占所有EST-SSR的35.39%。

Abstract:

In this study, 11,150 qualified ESTs(including 10 cDNAs), about 8.1×10⁶ bp in length, were downloaded from ESTs databases of Lentinula edodes in Fungal Genomics Project(FGP) and NCBI. By searching with SSRhunter 1.3 and handwork, 469 SSRs were identified in 316 ESTs, approximately 2.83% of total ESTs. The average distance between SSRs was about 17.3kb. Trinucleotide and hexanucleotide ESR-SSRs were found to be the two most aboundent repeats, accounting for 38.00% and 20.00% of the total ESR-SSRs respectively. The most familiar motifs are(A)_n,(T)_n,(GA)_n,(AG)_n,(TGA)_n,(GAT)_n and(TCTTT)_n, which comprised about 35.94% of all EST-SSRs.