High-Quality de novo Chromosome-Level Genome Assembly of a Single Bombyx mori With BmNPV Resistance by a Combination of PacBio Long-Read Sequencing, Illumina Short-Read Sequencing, and Hi-C Sequencing.

Min Tang,Keping Chen,Rehab H Taha,Suqun He,Xun Gong,Peng Lü

doi:10.3389/fgene.2021.718266

Abstract

The reference genomes of Bombyx mori (B. mori), Silkworm Knowledge-based database (SilkDB) and SilkBase, have served as the gold standard for nearly two decades. Their use has fundamentally shaped model organisms and accelerated relevant studies on lepidoptera. However, the current reference genomes of B. mori do not accurately represent the full set of genes for any single strain. As new genome-wide sequencing technologies have emerged and the cost of high-throughput sequencing technology has fallen, it is now possible for standard laboratories to perform full-genome assembly for specific strains. Here we present a high-quality de novo chromosome-level genome assembly of a single B. mori with nuclear polyhedrosis virus (BmNPV) resistance through the integration of PacBio long-read sequencing, Illumina short-read sequencing, and Hi-C sequencing. In addition, regular bioinformatics analyses, such as gene family, phylogenetic, and divergence analyses, were performed. The sample was from our unique B. mori species (NB), which has strong inborn resistance to BmNPV. Our genome assembly showed good collinearity with SilkDB and SilkBase and particular regions. To the best of our knowledge, this is the first genome assembly with BmNPV resistance, which should be a more accurate insect model for resistance studies.

Highlights

Bombyx mori (B. mori) or domestic silkworm is a well-known bioreactor that produces natural silk in sericulture and is frequently used as a lepidopteran model to study insect immunology and disease resistance (Maekawa et al, 1988; Arunkumar et al, 2006)
Since approximately 5,000 years ago, B. mori has been one of the most important agricultural economic insects for silk production in Asia (Xiang et al, 2018). As it is completely domesticated in sericulture, its survival and reproduction totally depend on human beings (Jiang and Xia, 2014)
Because of their intermediate genome size, short life cycle, affordability, and ability to be used for drug screening, B. mori is a perfect model organism for scientific discovery, especially for lepidopterans, and is useful for economic research (Kaito et al, 2002; International Silkworm Genome, 2008; Tabunoki et al, 2016; Meng et al, 2017)

Summary

Introduction

Bombyx mori (B. mori) or domestic silkworm is a well-known bioreactor that produces natural silk in sericulture and is frequently used as a lepidopteran model to study insect immunology and disease resistance (Maekawa et al, 1988; Arunkumar et al, 2006). At almost the same time, an independent Chinese group performed a similar whole-genome sequencing (BAC-end) with 5.9× coverage, and the B. mori strain used was Dazao (Xia et al, 2004). Both studies declared that the estimated genome coverage was more than 90%. The p50T strain was sequenced again by making use of the combination of PacBio and Illumina sequencing technologies, and this genome assembly with increased accuracy was released as SilkBase v2.1 (Kawamoto et al, 2019). They are recognized as the basis for a number of B. mori studies and databases (Cao et al, 2017; Li et al, 2019; Zhu et al, 2019; Fujimoto et al, 2020)

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