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为了开发甘蓝EST-SSR功能性标记,从NCBI公共数据库检索到63201条甘蓝ESTs,通过前处理和聚类去冗余后得到全长为14828.60kb的无冗余ESTs 23306条。在这些序列中搜索出3085个SSRs,分布于2616条ESTs中,出现频率是13.24%,与甘蓝开花过程中相关的EST-SSRs出现的频率为6.97%。这些EST-SSRs的平均长度为23.11bp,平均分布频率是1/4.81kb。在1～6核苷酸重复的基元中,二核苷酸重复和三核苷酸重复是主要类型,二者出现的频率基本相近,占总SSR的79.09%。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79%和34%,对这些含SSR的ESTs进行BLASTx同源性比较分析,发现2616条EST-SSRs中1981条在数据库中可以找到同源物,占EST-SSRs总数的75.73%,功能已知的蛋白质中拟南芥来源的EST-SSRs所占比例最大,为66.02%,同时针对与甘蓝开花相关的EST-SSRs进行功能分析。找到同源物的1981条EST通过GOA进行功能分类,有987条可划分为生物过程、分子功能和细胞成分3大功能类群,其中与生物代谢相关的EST-SSRs数量最多,为263条,994条未被功能注释。
In order to develop a functional marker of EST-SSR in Brassica oleracea, 63,201 ESTs of Brassica oleracea were retrieved from NCBI public database, and 23,306 non-redundant ESTs with total length of 14828.60kb were obtained by preprocessing and clustering. In these sequences, 3085 SSRs were found, which distributed in 2616 ESTs, the frequency was 13.24%, and the frequency of EST-SSRs associated with the flowering of cabbage was 6.97%. The average length of these EST-SSRs was 23.11 bp, with an average distribution frequency of 1 / 4.81 kb. In the 1 to 6 nucleotide repeat motif, dinucleotide repeat and trinucleotide repeat are the main types, the frequency of occurrence of the two are similar, accounting for 79.09% of the total SSR. AG / CT and AAG / CTT are the dominant repeat types in the second and third nucleotides, accounting for 79% and 34% of the second and third nucleotide repeats, respectively. BLASTx homology analysis of these SSR- It was found that among the 2,166 EST-SSRs, there were 1981 accessions in the database, accounting for 75.73% of the total EST-SSRs. The highest percentage of EST-SSRs with known function was 66.02% Functional analysis of EST-SSRs related to flowering of cabbage was also carried out. 1981 ESTs of homologues were classified by GOA. 987 ESTs could be divided into three functional groups of biological processes, molecular functions and cellular components. Among them, the ESTs with the highest number of EST-SSRs were 263 and 994 Article is not functionally annotated.