Chromosome‐level genome assembly of an important pine defoliator, Dendrolimus punctatus (Lepidoptera; Lasiocampidae)

Abstract

Dendrolimus spp. are important destructive pests of conifer forests, and Dendrolimus punctatus Walker (Lepidoptera; Lasiocampidae) is the most widely distributed Dendrolimus species. During periodic outbreaks, this species is said to make "fire without smoke" because large areas of pine forest can be quickly and heavily damaged. Yet, little is known about the molecular mechanisms that underlie the unique ecological characteristics of this forest insect. Here, we combined Pacific Biosciences (PacBio) RSII single-molecule long reads and high-throughput chromosome conformation capture (Hi-C) genomics-linked reads to produce a high-quality, chromosomelevel reference genome for D. punctatus. The final assembly was 614 Mb with contig and scaffold N50 values of 1.39 and 22.15 Mb, respectively, and 96.96% of the contigs anchored onto 30 chromosomes. Based on the prediction, this genome contained 17,593 protein-coding genes and 56.16% repetitive sequences. Phylogenetic analyses indicated that D. punctatus diverged from the common ancestor of Hyphantria cunea, Spodoptera litura and Thaumetopoea pityocampa ~ 108.91 million years ago. Many gene families that were expanded in the D. punctatus genome were significantly enriched for the xenobiotic biodegradation system, especially the cytochrome P450 gene family. This high-quality, chromosome-level reference genome will be a valuable resource for understanding mechanisms of D. punctatus outbreak and host resistance adaption. Because this is the first Lasiocampidae insect genome to be sequenced, it also will serve as a reference for further comparative genomics.

Chromosome‐level genome assembly of the aphid parasitoid Aphidius gifuensis using Oxford Nanopore sequencing and Hi‐C technology

“…Using café , we estimated the gene family expansion and contraction in A. gifuensis genome, compared with 13 hymenopteran species (Table S1) in the phylogenetic analyses. Significant expansions and contractions of gene families are usually related to the adaptive evolution of the species (Wu, Zhang, et al, 2019; Zhang et al, 2020). In the genome of A. gifuensis , a total of 405 and 663 orthologous groups were significantly expanded and contracted, respectively (Viterbi p < .05), compared to the most recent common ancestor (MRCA) of A. gifuensis and Fopius arisanus (Figure 3a).…”

Coding and Non-coding RNAs: Molecular Basis of Forest-Insect Outbreaks

“…Use the Bowtie tools software (Langmead and Salzberg, 2012), clean reads were used as queries against the Silva, GtRNAdb, Rfam, and Repbase databases for sequence alignments, and to filter out rRNA, transfer RNA, small nuclear RNA, small nucleolar RNA, other ncRNAs as well as any repeats. The remaining reads were used to detect miRNAs through comparisons with D. punctatus genome (Zhang et al, 2020) and known miRNAs from the miRBase (v21) 3 , and novel miRNA were predicted by miRDeep3 (Friedländer et al, 2012).…”

The transposable element-rich genome of the cereal pestSitophilus oryzae

“…Aedes aegypti and Ae. albopictus 40-50% [46,47], L. migratoria 60-65% [40,41], Dendrolimus punctatus 56% [48]). Here we present the genome of S. oryzae , with a strong focus on the repeatome, its largest genomic compartment, spanning over 72% of the assembly.…”

“…Aedes aegypti and Ae. albopictus 40-50% (Goubert et al 2015; Nene et al 2007), L. migratoria 60-65% (Wang et al 2014; Petersen et al 2019), Dendrolimus punctatus 56% (Zhang et al 2020), Vandiemenella viatica species 66-75% (Palacios-Gimenez et al 2020)).…”