The complete mitochondrial genome of the silkworm, Bombyx mori strain BaiyuN

Abstract

Here, we report the complete mitochondrial genome of a Bombyx mori strain BaiyuN, which is identified to be highly resistant to Bombyx mori nucleopolyhedrovirus (BmNPV). Its complete mitochondrial genome is 15,655 bp in length (GenBank accession no. MG797555), consisting of 13 protein-coding genes, 22 tRNA genes, 2 rRNA, and 1 control region (494 bp). The complete mitogenome of the B. mori strain BaiyuN could provide a basic data for further phylogenetics and antivirus research.

Keywords:

• Bombyx mori nucleopolyhedrovirus
• mitogenome
• next-generation sequencing

The silkworm, Bombyx mori, holometabolous insect, is a key model of the Lepidoptera (Xia et al. 2009). BaiyuN is one strain, which was collected from Zhenjiang city, Jiangsu Province in China (N 32.20’, E 119.44’). Samples have been conserved in the national centre for silkworm genetic resources preservation, Chinese academy of agricultural sciences (SGRP, CAAS, www.cnsilkworm.com) and identified to be highly resistant to Bombyx mori nucleopolyhedrovirus (BmNPV) (Li et al. 2016). For better understanding of the mechanism of its antivirus, we analyzed the mitochondrial genome of B. mori BaiyuN. Total genomic DNA was extracted from the 3rd day of pupa and sequenced using the Illumina Miseq platform (Illumina lnc., San Diego, CA). A5-miseq v20150522 (Coil et al. 2015) and SPAdesv3.9.0 (Bankevich et al. 2012) software were used to assemble the obtained high quality paired-end reads. Finally, we got the complete mitochondrial genome of B. mori BaiyuN was 15,655 bp in length (GenBank accession no. MG797555), and included 13 protein-coding genes (PCGs), two rRNA genes (rrnL and rrnS), 22 tRNA genes, and a D-loop region (494 bp). The gene order and orientation of B. mori stain BaiyuN were similar to that of B. mori strains published (Zhang et al. 2016).

The nucleotide composition of B. mori strain BaiyuN was significantly biased (A, G, C, and T was 43.07%, 7.31%, 11.33%, and 38.29%, respectively) with A + T contents of 81.36%. The AT-skew and GC-skew of this genome were 0.059 and −0.216, respectively. Fourteen genes were transcribed on the J-strand included four PCGs (ND1, ND4, ND4L, ND5), two rRNAs, and eight tRNAs (tRNA^Gln, tRNA^Cys, tRNA^Tyr, tRNA^Phe, tRNA^His, tRNA^Pro, tRNA^Leu, tRNA^Val), whereas the others were oriented on the N-strand. Most of the protein-coding genes use ATN (N represents A, T, C, G) as the initiation codon whereas the cox1 gene initiated with CGA, meanwhile, all the protein-coding genes ended with TAA.

To validate the phylogenetic position of B. mori BaiyuN, we used MEGA6 software (Tamura et al. 2013) to construct a maximum-likelihood tree (with 500 bootstrap replicates and Kimura 2-parameter model) containing complete mitogenomes of nine species (B. mori, B. mandarina, Antheraea, respectively, and Drosophila melanogaster as a outgroup control) derived from GenBank. The mitogenome sequence of B. mori BaiyuN is similar to the sequence published by Lee et al (GenBank accession no. AF149768). So, five strains (Aojuku, Backokjam, C108, BaiyuN, Xiafang) of B. mori were first clustered together in the ML phylogenetic tree (Figure 1). The mitochondrial DNA of B. mori used in different geographic varieties and different tissues suggesting that the mitochondrial DNA of B. mori are may very conservative.

Figure 1. A maximum-likelihood tree illustrating the phylogenetic position of B. mori BaiyuN among other Bombyx species. The Maximum-likelihood analysis was conducted using the complete mitogenomes, and numbers at each node are bootstrap probabilities by 500 replications shown only when they are 50% or larger. GenBank accession numbers of mitogenomic sequences for each taxon are shown.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by a grant from the China Agriculture Research System (Sericulture industry, CARS-18); The Natural Science Foundation of the Jiangsu Higher Education Institutions of China [17KJB230001]; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture [KL201701]; Key Research & Development program of Zhenjiang [NY2017017].