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

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.

Highly accurate genome assembly of an improved high-yielding silkworm strain, Nichi01

“…However, it has not been validated and does not uncover the other three misassembled points. Moreover, although another de novo genome assembly of a different silkworm strain has been constructed previously using a combination of PacBio long-read sequencing and Hi-C, it contained many structural differences against the p50T assemblies, indicating that it contained many misscaffoldings ( Tang et al . 2021 ).…”

High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptidea spp.)

“…However, why do we not observe an elevated rate of chromosome rearrangements in butterflies and moths in general? Bombyx mori , for example, has a similar repeat density as Leptidea (Tang et al, 2021 ) and shares the potential for inverted meiosis (Banno et al, 1995 ). Still B. mori , and the majority of lepidopteran taxa with chromosome structure information, have retained the ancestral lepidopteran karyotype (Ahola et al, 2014 ; Pringle et al, 2007 ).…”

High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptideaspp.)

“…However, why do we not observe an elevated rate of chromosome rearrangements in butterflies and moths in general? Bombyx mori , for example, has a similar repeat density as Leptidea (Tang et al, 2021) and shares the potential for inverted meiosis (Banno et al, 1995). Still B. mori , and the majority of lepidopteran taxa with chromosome structure information, have retained the ancestral lepidopteran karyotype (Ahola et al, 2014; Pringle et al, 2007).…”