摘要
在不同物种中,微卫星(simple sequence repeats,SSR)序列的数目、类型及其分布情况有很大差异。本研究利用Perl语言开发用于探寻编码区SSR位点的程序,并用SSRHunter软件验证,来分析马铃薯基因组编码区中SSR位点的分布情况。结果显示:在马铃薯的56 218条编码区序列中,检索到2 920条共含有3 512个SSR位点的序列,其中2 519条序列只含有一个SSR位点(占86%);含三核苷酸、六核苷酸重复单元的SSR数目最多,分别为2 358和1 075个,两者占总数的98%,其他类型的重复单元出现次数较少;构成微卫星序列的不同重复单元有603个;六个核苷酸的重复单元重复次数一般最少为三个,三核苷酸GAA重复单元重复次数最高,为193次。在自然选择规律下,编码区中SSR序列长度趋向于密码子的整数倍。运用Pfam数据库对含有SSR的编码序列进行功能分类,其中最多的是RPW8抗性蛋白功能。可利用SSR序列的特异性,筛选马铃薯不同物种的相关编码序列。
The amount, type and distribution of simple sequence repeats （SSR） show great differences in different species. This research uses Perl language to develop the program using for exeploring SSR loci in encoding region and software SSR Hunter to verify, that is to analyse the SSR loci distribution in potato genome encoding area. The following result show： 2 920 of all the 56 218 potato coding sequences are found carrying 3 512 SSR loci in total and among of all of the sequences carrying SSR loci, 2 519 sequences carry just one loci （That represent 86% of all the sequences carrying SSR loci）; SSR loci contains Tri-nucleotide or Hexa-nucleotide repetitive units have the largest number, the amount of them is 2 358, 1 075 respectively, that means the sum of them represent 98% of all the SSR loci, while the rest type of repetitive unit have less occurrence; The quantity of the different repeats which make up SSR loci is 603; Hexa-nucleotide repetitive unit has at least three repetitions and Tri-nucleotide repetitive unit GAA has the largest number of repetition for 193 times. Under the law of natural selection, in encoding region, the SSR sequence length tends to be integral multiple of codon. Functional classification which piont to encoding region containning SSR loci was done using Pfam database, RPW8 resistant protein function was the most general one. The SSR loci speciality can be used to screen relative coding sequence of different potato spcies.
出处
《分子植物育种》
CAS
CSCD
北大核心
2015年第1期171-177,共7页
Molecular Plant Breeding
基金
国家863高技术研究发展计划项目(2012AA021801)资助
