张 悦,李 丹,陈子牛,王丽燕.核盘菌基因组微卫星序列分析[J].广东农业科学,2015,42(1):128-132 |
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核盘菌基因组微卫星序列分析 |
SSRs analysis of genome in Sclerotinia sclerotiorum |
投稿时间:2014-07-02 |
DOI: |
中文关键词: 微卫星序列 核盘菌 基因组 分子标记 |
英文关键词: SSR Sclerotinia sclerotiorum genome molecular marker |
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中文摘要: |
利用已经公布的核盘菌基因组测序结果,对已有的核盘菌基因组中 SSR 的类型、大小及分
布等数据进行统计分析。 在核盘菌基因组内发现 1 693 个 SSR 序列,其中出现频率最高的
为 6 碱基和 4 碱基的 SSR 序列,分别达到 577 次和 449 次,1 碱基、3 碱基和 5 碱基的 SSR
则分别出现 97、180、57 次。 其中有 340 个 SSR 序列出现在 308个基因内。 大多数基因
(284 个基因)都只含有 1 个 SSR,占含 SSR 基因总数的 92.21%曰17 个基因中含有 2 个
SSR,6个基因中含有 3 个 SSR,含 4 个 SSR 的基因只有 1 个。 在基因序列内,出现最多的
是 3 碱基与 6 碱基的 SSR,这表明较之基因间区,在选择压力下基因内 SSR 多趋向于密码
子的整数倍,这与其他物种的分析结果一致。 为了解含有较多 SSR 序列与核盘菌基因功能
的关系,将含 2 个以上 SSR 的基因预测蛋白序列根据 NCBI 网站 CDD 软件进行比对发现,
24 个基因只有 6 个具有保守的蛋白结构域,且这些结构域多与转录、DNA 修复有关。 |
英文摘要: |
This study analyzed the SSRs in the genome of Sclerotinia sclerotiorum according to the genome sequence
data from public database. Totally we found 1 693 SSRs, most of them were 6 and 4 bases SSRs which appeared 577 and
449 times, respectively. 1 base, 3 bases and 5 bases SSRs appeared 97, 180 and 57 times, respectively. There were 340
SSRs from 308 putative gene sequences, 284 of them contained only 1 SSR, accounting for 92.21% of the total; 17 of genes
contained 2 SSRs, 6 genes contained 3 SSRs and only 1 gene contained 4 SSRs. Compared with SSRs from whole genome,
the SSRs with most frequency were 3 and 6 bases SSRs, which meant that under the selection pressure, the SSRs in gene
sequences were tend to be integer multiples of gene code number 3, this was consistent with the research on other species.
To analyze the functions of the genes contained more than 2 SSRs of S. sclerotiorum, we blast all these 24 genes by CCD
software from NCBI. Among them, only 6 genes contained conserved proteins domains and most of these domains were
related to transcription and DNA reparation. |
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