De Novo Genome Assembly and Annotation of an Andean Caddisfly, Atopsyche davidsoni Sykora, 1991, a Model for Genome Research of High-Elevation Adaptations

Abstract

We sequence, assemble, and annotate the genome of Atopsyche davidsoni Sykora, 1991, the first whole genome assembly for the caddisfly family Hydrobiosidae. This free-living and predatory caddisfly inhabits streams in the high-elevation Andes and is separated by more than 200 million years of evolutionary history from the most closely related caddisfly species with genome assemblies available. We demonstrate the promise of PacBio HiFi reads by assembling the most contiguous caddisfly genome assembly to date with a contig N50 of 14 Mbp, which is more than 6x more contiguous than the current most contiguous assembly for a caddisfly (Hydropsyche tenuis). We recover 98.8% of insect BUSCO genes indicating a high level of gene completeness. We also provide a genome annotation of 12,232 annotated proteins. This new genome assembly provides an important new resource for studying genomic adaptation of aquatic insects to harsh, high-altitude environments.

Characterization of primary structure of the major silk gene,h-fibroin, across caddisfly suborders (Trichoptera)

“…Recently, the Wellcome Sanger Institute published four high-quality caddisfly genomes ( Glyphotaelius pellucidus : GCA_936435175.1, GCA_936435185.1; Limnephilus lunatus : GCA_917563855.2, GCA_917563845.2; Limnephilus marmoratus : GCA_917880885.1, GCA_917880875.2; Limnephilus rhombicus : GCA_929108145.1, GCA_929113645.1) and one assembly was published from Ríos-Touma et al (2022). We identified the h-fibroin genes from these assemblies by using tBLASTn to identify conserved N- and C-termini with query sequences from the termini of Hesperophylax sp .…”

“…In this study, we used PacBio HiFi to sequence the full-length h-fibroin sequence of two caddisfly species, Leptonema lineaticorne OS Flint, 2008 (Annulipalpia, fixed retreat-maker) and Micrasema longulum R McLachlan, 1876 (Integripalpia, tube-case made of silk). In addition, we identified and annotated complete protein-coding h-fibroin gene sequences from five high-quality genomes (four recently published by the Darwin Tree of Life Project and one from Ríos-Touma et al (2022). This increases the number of high-quality, full-length h-fibroin sequences from two to nine.…”

Long-read HiFi sequencing correctly assembles repetitive heavy fibroin silk genes in new moth and caddisfly genomes

“…We show that PacBio HiFi sequencing allows accurate generation of repetitive protein-coding regions of the genome (silk fibroins), and this probably applies to other similarly repetitive regions of the genome. For Trichoptera, there are only four other HiFi genome assemblies available on Genbank, only one of which has been published [45].…”

Long-read HiFi Sequencing Correctly Assembles Repetitive heavy fibroin Silk Genes in New Moth and Caddisfly Genomes

“…We show that PacBio HiFi sequencing allows for accurate generation of repetitive protein-coding regions of the genome (silk fibroins ), and this likely applies to other similarly repetitive regions of the genome. For Trichoptera, there are only four other HiFi genome assemblies available on Genbank, only one of which has been published [38] and insects have generally been neglected (relative to their total species diversity) with respect to genome sequencing efforts [15-16], which is especially true for aquatic insects [14]. These data serve as the first step to study the evolution of adhesive silk in Amphiesmenoptera, which is an innovation that is beneficial for survival in aquatic and terrestrial environments.…”

“…We show that PacBio HiFi sequencing allows for accurate generation of repetitive protein-coding regions of the genome (silk fibroins), and this likely applies to other similarly repetitive regions of the genome. For Trichoptera, there are only four other HiFi genome assemblies available on Genbank, only one of which has been published [38] and insects have generally been neglected (relative to their total species diversity)…”