野桑蚕基因组Survey分析及线粒体基因组注释

Genome Survey and Mitochondrial Genome Analysis of Wild Silkworm,Bombyx mandarina

为制定野桑蚕全基因组denovo测序策略及分析不同地理来源的野桑蚕(Bombyx mandarina)、家蚕(Bombyx mori)之间的亲缘关系,利用Illumina Hiseq 2500测序平台对单只雌性秦巴山区野桑蚕基因组进行Survey调研,分析基因组大小、杂合度、GC含量等基本信息,对基因组进行初步组装;从测序数据中提取并组装线粒体基因组,基于其分析家蚕、野桑蚕的系统进化关系。结果获得测序clean data 25.8 Gb,基因组预估大小为456.5 Mb,杂合率为1.94%;基因组预组装结果Scaffold N50为1792 bp,Scaffold数量为737055;Contig N50为587 bp,Contig数量为1477268。线粒体组装和注释表明,野桑蚕线粒体长度为15662 bp,包含基因37个,没有发生基因重排;系统进化分析表明,中国野桑蚕总体上可构成2个以地理来源区分的南北群体,其中北方野桑蚕群体与家蚕亲缘关系最为接近。本研究表明,野桑蚕基因组杂合率较高,后续需综合利用第二代、三代测序方法,辅以Hi-C技术,才能组装获得高质量的野桑蚕基因组图谱,同时本研究支持了家蚕驯化起源于中国北方的观点,表明陕南秦巴山区可能是家蚕的驯化起源地之一。

Aimed to lay references for the whole genome sequencing and provide basic data for the genetic relationships between Bombyx mandarina and Bombyx mori,the genome of Bombyx mandarina was investigated and the mitochondrial genome was analyzed.Using the Illumina Hiseq 2500 pair-end sequencing platform,a female Bombyx mandarina was sequenced,the genome size,heterozygosity and GC contend have been estimated based on the genomic survey analysis,and the genome of wild silkworm has been pre-assembled.Using the sequencing data,the mitochondrial genome sequences in the genome were extracted and assembled directly.As results,25.8 GB clean data was obtained,the estimated genome size of Bombyx mandarina was 456.5 Mb,the heterozygosity rate was 1.94%.After preliminary assembly,the scaffold N50 was 1792 bp,scaffold number was 737055,contig N50 was 587 bp,contig number was 1477268.As assemblyand annotation,the mitochondrial genome of wild silkworm was 15662 bp,a total of37 genes were arranged in the mitochondrial genome,which did not have a gene rearrangement.According the phylogenetic tree of mitochondrial genome,wild silkworm could be divided into north or south group according to the geographical source.Subgroup of Wild silkworm from the North China had the closest genetical relationship with the domestic silkworm.Since the genome of Qin-ba wild silkworm belonged to the complex genome,integrating the second,the third generation sequencing and Hi-C technology could be helpful to obtain high quality genomic of Bombyx mandarina.This study also supported the contention that domestic of silkworm descended from the Northern of China,and implied that the Qin-ba mountain area could be one of the original regions of domestic silkworm.