Genome Survey and Mitochondrial Genome Analysis of Wild Silkworm, <i>Bombyx mandarina</i>

Abstract

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 is investigated and the mitochondrial genome is analyzed. Using the Illumina NovaSeq 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 obtained, the estimated genome size of Bombyx mandarina is 456.5 Mb, the heterozygosity rate is 1.94%. After preliminary assembly, the scaffold N50 is 1 792 bp, scaffold number is 737055, contig N50 is 587 bp, contig number is 1477268. As assembly and annotation, the mitochondrial genome of wild silkworm is 15 662 bp, a total of 37 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 has the closest genetical relationship with the domestic silkworm. Since the genome of Qin-ba wild silkworm belong 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 supports 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.