油菜EST资源的SSR信息分析

Analysis of SSR information in EST resource of oilseed rape

从NCBI公共数据库获得63 334条油菜EST,通过前处理得到全长为12 165.38kb的无冗余EST17 987条。在这些序列中搜索出2 803个SSR,分布于2 443条EST中,出现频率是15.58%。这些EST-SSR的平均长度为18.84bp,平均分布频率是1/4.34kb。二核苷酸重复和三核苷酸重复是主要的类型,二者出现的频率基本相近,占总SSR的89.05%。AG/CT和AAG/CTT是二、三核苷酸中的优势重复类型,分别占二、三核苷酸重复的84.04%和35.71%,同时对这些SSR的可用性进行了评价。

63 334 ESTs of oilseed rape in the database of NCBI were downloaded and analysed, resulting in 17 987 non - redundant ESTs with total length about 12 165.38kb. Totally 2 803 SSRs distributed in 2 443 ESTs were detected, accounting for 15.58% of the non - redundant ESTs. The average length and distribution distance of the EST - SSRs were about 18.84 bp and 4.34 kb respectively. Dinucleotide and trinucleofide repeats with similar frequency are the main types, accounting for 89.05% of all the SSRs. AG/CT and AAG/CTT are the most frequent motifs, accounting for 84.04% and 35.71% in dinucleotide and trinucleotide repeats, respectively. The potential of the EST - SSRs for designing primers specific to flanking sequences was assessed.