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

Akito Y KawaharaCaroline G StorerAmanda MarkeeJacqueline HeckenhauerAshlyn PowellDavid M PlotkinScott HotalingTimothy P ClelandRebecca B DikowTorsten DikowRyoichi B KuranishiRebeccah MesscherSteffen U PaulsRussell J StewartKoji TojoPaul B Frandsen
Published in: GigaByte (Hong Kong, China) (2022)
Insect silk is a versatile biomaterial. Lepidoptera and Trichoptera display some of the most diverse uses of silk, with varying strength, adhesive qualities, and elastic properties. Silk fibroin genes are long (>20 Kbp), with many repetitive motifs that make them challenging to sequence. Most research thus far has focused on conserved N- and C-terminal regions of fibroin genes because a full comparison of repetitive regions across taxa has not been possible. Using the PacBio Sequel II system and SMRT sequencing, we generated high fidelity (HiFi) long-read genomic and transcriptomic sequences for the Indianmeal moth ( Plodia interpunctella ) and genomic sequences for the caddisfly Eubasilissa regina . Both genomes were highly contiguous (N50  = 9.7 Mbp/32.4 Mbp, L50  = 13/11) and complete (BUSCO complete  = 99.3%/95.2%), with complete and contiguous recovery of silk heavy fibroin gene sequences. We show that HiFi long-read sequencing is helpful for understanding genes with long, repetitive regions.
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