Abstract
BackgroundCaddisflies (Insecta: Trichoptera) are a highly adapted freshwater group of insects split from a common ancestor with Lepidoptera. They are the most diverse (>16,000 species) of the strictly aquatic insect orders and are widely employed as bio-indicators in water quality assessment and monitoring. Among the numerous adaptations to aquatic habitats, caddisfly larvae use silk and materials from the environment (e.g., stones, sticks, leaf matter) to build composite structures such as fixed retreats and portable cases. Understanding how caddisflies have adapted to aquatic habitats will help explain the evolution and subsequent diversification of the group.FindingsWe sequenced a retreat-builder caddisfly Stenopsyche tienmushanensis Hwang and assembled a high-quality genome from both Illumina and Pacific Biosciences (PacBio) sequencing. In total, 601.2 M Illumina reads (90.2 Gb) and 16.9 M PacBio subreads (89.0 Gb) were generated. The 451.5 Mb assembled genome has a contig N50 of 1.29 M, has a longest contig of 4.76 Mb, and covers 97.65% of the 1,658 insect single-copy genes as assessed by Benchmarking Universal Single-Copy Orthologs. The genome comprises 36.76% repetitive elements. A total of 14,672 predicted protein-coding genes were identified. The genome revealed gene expansions in specific groups of the cytochrome P450 family and olfactory binding proteins, suggesting potential genomic features associated with pollutant tolerance and mate finding. In addition, the complete gene complex of the highly repetitive H-fibroin, the major protein component of caddisfly larval silk, was assembled.ConclusionsWe report the draft genome of Stenopsyche tienmushanensis, the highest-quality caddisfly genome so far. The genome information will be an important resource for the study of caddisflies and may shed light on the evolution of aquatic insects.
Highlights
Caddisflies (Insecta: Trichoptera) are a highly adapted freshwater group of insects split from a common ancestor with Lepidoptera
The estimated heterozygosity of S. tienmushanensis is within the normal range for non-model insects with a published genome, the pooling of DNA from two wild-caught caddisfly adults represents a potential source for inflated heterozygosity
The assembly of the complete H-fibroin region in our study provides a significant expansion over existing genetic resources on caddisfly H-fibroin genes, which will be important for studying caddisworm silk structure and adaptation to aquatic environments
Summary
Comprising >16,000 species and distributed worldwide except for Antarctica, caddisflies (Insecta: Trichoptera) are the most diverse of the strictly aquatic insect orders [1]. The estimated heterozygosity of S. tienmushanensis is within the normal range for non-model insects with a published genome, the pooling of DNA from two wild-caught caddisfly adults represents a potential source for inflated heterozygosity To address this potential issue, we used LAST (v852, RRID:SCR 006119) [31] and Redundans (v 0.14a) [32] to identify redundant contigs in the intermediate assembly. We marked a contig as a contaminant if it had all three of the following characteristics: (1) had a best hit to a reference sequence from non-Arthropoda, (2) had no mapping of full-length transcripts, and (3) contained no homologous insect genes from the Benchmarking Universal Single-Copy Orthologs (BUSCO v3.0, RRID:SCR 015008) [34] Four contigs met these characteristics, and were subsequently removed from the assembly (TAGC plots for the final assembly shown in Supplementary Fig. S6, Table S3). Transcriptome and gene expression analysis from larval silk glands will help elucidate additional structural details of H-fibroin
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