The First Chromosome-level Genome Assembly ofCheumatopsyche charitesMalicky and Chantaramongkol, 1997 (Trichoptera: Hydropsychidae) Reveals How It Responds to Pollution

Abstract

Trichoptera is a highly adapted group of freshwater insects. They are generally more sensitive to dissolved oxygen and water quality than most freshwater organisms, and this sensitivity allows them to be used as reliable biological indicators of water quality. At present, there exists no chromosome-level genome of a hydropsychid species. Cheumatopsyche charites Malicky & Chantaramongkol, 1997 can successfully survive and thrive in polluted streams where other caddisflies are infrequent, suggesting that they are tolerant to latent contamination. Here we report a high-quality chromosome-level genome assembly of C. charites generated combining PacBio long reads and Hi-C reads. We obtained a genome assembly of 223.23 Mb, containing 68 scaffolds with an N50 length of 13.97 Mb, and 155 contigs (99.67%) anchored into 16 pseudochromosomes. We identified 36.12 Mb (16.18%) of the genome as being composed of repetitive elements, identified 369 noncoding RNAs, and predicted 8,772 protein-coding genes (96.80% BUSCO completeness). Gene family evolution analyses identified 7,148 gene families, of which 41 experienced rapid evolution. The expanded gene families were shown to be involved in detoxification metabolism, digestive absorption, and resistance to viruses or bacteria. This high-quality genome provides a valuable genomic basis for the study of trichopteran evolution.

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

“… 65/n.a. C:96.1%[S:95.3%,D:0.8%],F:2.3%,M:1.6% Cheumatopsyche charites 44 Annulipalpia (retreat) GCA_024721215.1 223,232,897 2,851,765/13,966,006 207/68 C:96.4%[S:95.9%,D:0.5%],F:1.9%,M:1.7% Arctopsyche grandis 37 Annulipalpia (retreat) GCA_029955255.1 485,663,687 6,470,670/n.a. 676/n.a.…”

“…In this study, we report eight new full-length h-fibroin sequences for caddisflies across a diverse set of silk usage. Two of these were generated from new genomic resources, whereas five were mined from previously published genomes, 41 , 42 , 43 , 44 highlighting the relevance of genome sequencing projects for the wider scientific community. The new full-length h-fibroins represent a substantial increase in the number of genomic resources available for the study of caddisfly silk and allowed us to compare the major silk gene for eleven species across the primary clades of Trichoptera, in which species exhibit different silk usage.…”

“…An additional high-quality genome of a retreat-making caddisfly was published by Ge et al. 44 We identified the h-fibroin genes in these assemblies by using tBLASTn to search the assemblies with the conserved n- and c-termini with query sequences from previously published species Hesperophylax sp., 17 Limnephilus decipiens AB214509 27 and Rhyacophila obliterata AB354689.1 and AB354588.1 23 in Geneious Prime 2022.1.1 ( https://www.geneious.com ) with default settings. After verifying that both BLAST hits (hit with n- and hit with c-terminus) were isolated to the same contig in the genome assembly, we extracted the sequences and 1,000 bp of flanking regions from the assembly using the sequence view “extract” in Geneious and annotated this region using Augustus v.3.3.3.…”

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, Limnephilus lunatus: GCA_917563855.2, Limnephilus marmoratus : GCA_917880885.1, Limnephilus rhombicus: GCA_929108145.1). An additional high-quality genome was published by [48]. We identified the h-fibroin genes in these assemblies by using tBLASTn to search the assemblies with the conserved n- and c-termini with query sequences from previously published species Hesperophylax sp .…”

Chromosome-scale genome assemblies of Himalopsyche anomala and Eubasilissa splendida (Insecta: Trichoptera)

“…Additionally, a female individual underwent DNA sequencing using the Illumina platform to identify sex chromosome. DNA and RNA were extracted from samples using the Qiagen DNeasy Blood & Tissue Kit (Qiagen) and TRIzol Reagent Kit (Invitrogen) 15 .…”