基于转录组的曼氏无针乌贼SSR与SNP位点信息分析

Analysis on SSR and SNP Information in Transcriptome Sequences of Sepiella japonica

利用IlluminaHiseq平台对曼氏无针乌贼进行了转录组测序,采用生物信息学方法分析了转录组序列中的SSR、SNP位点信息并设计了SSR引物。利用MISA工具筛选了转录组测序获得的127 575条Unigene序列,共得到分布于50 626条序列中的SSR位点108 685个,SSR发生率39.68%,出现频率为85.19%。平均每949 bp含有1个SSR位点。在50 626条含有SSR位点的Unigene序列中,有25 548条Unigene包含SSR位点数目在2个及以上。其中单碱基重复是EST微卫星序列的主要形式(42.84%),其次是二碱基重复(28.73%),三碱基重复(14.93%)和四碱基重复(12.79%)。在所有微卫星序列所包含的重复单元中,优势重复基元类型为A/T(占总SSRs的42.23%),其次为AT/AT (13.33%),AC/GT (9.32%),AAAG/CTTT (10.00%)。运用Primer premier 5软件共设计了46 520对SSR引物。在12 323条Unigene中发掘出SNP位点64 732个,每条Unigene平均含5.25个SNP位点。其中转换(Transition) 45 975个(71.02%),颠换(Transversion) 18 757个(28.98%)。本研究通过第二代高通量测序技术,结合生物信息学方法对曼氏无针乌贼进行了SSR位点与SNP位点的开发,为其遗传多样性分析、分子辅助育种和增殖放流效果评估等提供了有力研究工具。

Transcriptome sequencing was performed on Sepiella japonica using the Illumina Hiseq platform. SSR and SNP locus information in transcriptome sequences was analyzed using bioinformatics methods, and SSR primers were designed. By using MISA, 127 575 Unigene sequences obtained from transcriptome sequencing were screened. A total of 108 685 SSRs were found in 50 626 sequences. The incidence of SSR was 39.68% and the frequency of occurrence was 85.19%. On average, every 949 bp contains 1 SSR site. 25 548 Unigene contain two or more SSR sites. Mono-nucleotide SSR is the main type of microsatellites (42.84%), foll owed by di-nucleotide (28.73%), tri-nucleotide (14.93%) and quad-nucleotide (12.79%). A/T (42.23%), AT/AT (13.33%), AC/GT (9.32%), AAAG/CCCT (10.00%) were the main types of SSRs. A total of 46 520 SSR primers were designed using Primer premier 5 software. In 12 323 Unigene, 64 432 SNP sites were discovered, and each Unigene contained an average of 5.25 SNP sites. And the Transition sites were 45 975 (71.02%), the Transversion were 18 757 (28.98%). In this study, SSRs and SNPs were developed using the high-throughput sequencing technology combined with bioinformatics methods for the analysis of genetic diversity, molecular-assisted breeding, and proliferation and release of S. japonica.