Highly contiguous, phased genome assemblies generated from PacBio HiFi sequencing shed light on the genomics basis of silk in caddisflies (Insecta: Trichoptera)

Caddisflies (Insecta: Trichoptera) construct a variety of underwater architectures using adhesive
silk that adheres to a variety of wet substrates. These structures provide protection and
camouflage and even facilitate respiration in poor oxygen environments. Caddisflies’ use of silk
is thought to have played a central role in their diversification underwater. The study of
caddisfly silk presents an excellent framework for linking genotype to phenotype and
unravelling the interplay between genetics and the environment. In this study, we generate
data from each stage of the central dogma of molecular biology—genomes, transcriptomes,
and proteomes—and connect them to shed light on the genetic basis of silk production across
caddisfly suborders. Silk genes are repetitive and modular. We compare various long read
sequencing techniques (Oxford Nanopore, PacBio CLR, & PacBio HiFi) and find that high fidelity
long reads (PacBio HiFi) are necessary in order to resolve the highly heterozygous and repetitive
silk genes. Enabled with high-quality, phased silk gene haplotypes, we examine how silk gene
structure and the resultant proteins interact with the environment to produce the array of
extended phenotypes exhibited by caddisflies.