Genome Survey and Mitochondrial Genome Analysis of Wild Silkworm, Bombyx mandarina
1 Shaanxi Key Laboratory of Sericulture, Ankang University, Ankang, Shaanxi 725000, China
2 College of Modern Agriculture and Biotechnology, Ankang University, Ankang, Shaanxi 725000, China
Molecular Entomology, 2020, Vol. 11, No. 2 doi: 10.5376/me.2020.11.0002
Received: 02 Jun., 2020 Accepted: 13 Jul., 2020 Published: 17 Jul., 2020
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This article was first published in Genomics and Applied Biology in Chinese, and here was authorized to translate and publish the paper in English under the terms of Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:
Meng G., Wang R.X., and Chu Q. 2020, Genome survey and mitochondrial genome analysis of wild silkworm, Bombyx mandarina, Molecular Entomology, 11(2): 1-9 (doi:10.5376/me.2020.11.0002)
In this study, the genome of Bombyx mandarina is investigated and the mitochondrial genome is analyzed, which lays a reference for the whole genome sequencing and to provide basic data for the genetic relationships between Bombyx mandarina and Bombyx mori. Using the Illumina HiSeq2000 pair-end sequencing platform, a female Bombyx mandarina was sequenced. K-mer analysis was adopted to estimate genome size, heterozygosity and GC contend. SOAPdenove tools was applied to genome pre-assembled. The mitochondrial genome was assembled by NOVOPlasty, annotated and visualized by GeSeq online tool, MEGA-X used to build phylogenetic tree. Obtained 25.8 GB clean data, the estimated genome size of Bombyx mandarina is 456.5 Mb, the heterozygosity rate is 1.94%. After preliminary assembly, the scaffold N50 is 1792 bp, scaffold number is 737055, contig N50 is 587 bp, contig number is 1477268. As assembly and annotation, the mitochondrial genome of Qin-Ba wild silkworm is 15662 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. Wild silkworm came from the North China as Shaanxi, Shandong and Liaoning province 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.
Bombyx mandarina; Size of Genome