家蚕全基因组微卫星分布规律及其生物信息学分析

Distribution Regularities and Bioinformatics Analysis of Microsatellite in the Whole Genomes of Silkworm, Bombyx mori

本研究利用MSDB v2.4软件以及生物信息学方法获取了家蚕全基因组的完整型SSRs序列,并对其分布规律进行比较分析。家蚕全基因组中SSRs总数量为141 311个,相对丰度为209.01 No/Mb,总长度为2.41 Mb,全基因组SSRs六种碱基重复类型的数量和密度分布模式为：单碱基〉四碱基〉三碱基〉二碱基〉五碱基〉六碱基,说明全基因以单碱基为主要碱基类型,六种碱基类型中五碱基SSRs G-C含量最高。对全基因组3＇非翻译区（3＇UTR）、5＇非翻译区（5＇UTR）、编码区（CDs）、内含子区（Introns）和基因间隔区（Intergenics）等不同区域SSRs分析表明,Introns区SSRs数量最高,为125 178个,最小的是5＇UTR,为278个,其数量大小顺序为Introns〉Intergenics〉3＇UTR〉CDs〉5＇UTR。5个不同区域的SSRs的碱基的总计数差异较大,编码区总计数最大的是三碱基,而其他4个区域最多的是单碱基。分别对5个区域SSRs中六种重复拷贝类别进行统计分析,碱基总计数（或频率）最多的分别是A;AC、AG、AT;AAT、CCG;AAAT、AAAC;AAATC、AAACT和TAAGTT、GAATTT、AATTAA,Introns和Intergenics区的重复类型总计数显著高于3＇UTR、CDs和5＇UTR。各重复类型拷贝数分布范围为4～100,主要集中在4～30之间。这为进一步系统分析家蚕SSRs分子标记筛选和遗传分析打下基础。

In this research, the perfect SSRs sequence were searched by using bioinformatics method and MSDB v2.4 in the complete genomes of silkworm （Bombyx mori L.） and their number, frequency, density and distribution of SSRs were comparative analyzed. The total SSRs number, relative abundance and the total length detected in the silkworm genomes were 141311 loci, 209.01 No/Mb and 2.41 Mb, respectively. The number, proportion, abundance and density distribution patterns of the six SSRs repeat types were abided by the following pattern： mono-〉tri-〉di-〉tetra-〉penta-〉Hexa-bases, indicating single base as the main base type of the whole gene, GC content of penta-bases SSRs was the highest in six base types. SSRs were analyzed in 3＇untranslated region （3＇UTR）, 5＇untranslated region （5＇UTR）, coding region （CDs）, intron region （Introns） and intergenic region （lnterg- enics） of the silkworm genome, the results showed that the number of SSRs in the Introns and 5＇UTR was the highest and the smallest, with the number of 125 178 and 278, respectively, followed by the pattern： Introns〉Intergenics〉3＇UTR〉CDs〉5＇UTR. The total number of SSRs in the five different regions was quite different, and the SSRs max number of CDs was tri-bases type, while the other four regions were mono-bases type. The statistical analysis of six repeat types in SSRs of five regions was carried out respectively, the highest total （or frequency） base type were A; AC, AG, AT; AAT, CCG; AAAT, AAAC; AAATC, AAACT and TAAGTT, GAATTT, AATTAA. The total number of repeat type in Introns and Intergenics were significantly higher than 3＇UTR, CDs and 5＇UTR. The number of repeat types was distributed in 4-100, mainly concentrated in the 4-30, Which provide a basis for further systematic analysis of silkworm SSRs molecular marker screening and genetic analysis.