1st Place: Long-read sequencing is revolutionizing silk research: Comparing repetitive heavy fibroin silk genes in new moth and caddisfly genomes

Monday, November 14, 2022

11:30 AM – 11:42 AM PT

Location: Vancouver Convention Centre, Meeting Room 221/222

Presenting Author(s)

Amanda Markee

Graduate Student
Florida Museum of Natural History
Gainesville, Florida

Co-Author(s)

Amanda Markee

Graduate Student
Florida Museum of Natural History
Gainesville, Florida
Paul B. Frandsen

Assistant Professor
Brigham Young University
Provo, Utah
JH

Jacqueline Heckenhauer

LOEWE Centre for Translational Biodiversity Genomics
Frankfurt am Main, Hessen, Germany
DP

David Plotkin

Project Manager, Kawahara Lab
University of Florida
Gainesville, Florida
Akito Y. Kawahara

Associate Curator
University of Florida
Gainesville, Florida

Insect silk is an important and versatile biomaterial that is used by over 800,000 species on Earth. Lepidoptera and their sister lineage, Trichoptera, are the dominant groups of silk-producers, and display some of the most diverse phenotypes with varying strength, chemical, and mechanical properties. Silk fibroin genes are long ( > 20 kb) and have many repetitive motifs, which have historically created challenges in sequencing. Most silk research has focused on the conserved N- and C-terminal regions of fibroin genes because this was the extent that could be captured by short-read sequencing platforms. Using the PacBio Sequel II system, we generated high fidelity (HiFi) long-read genomic and transcriptomic sequences for the Indian meal 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 full recovery of the challenging heavy fibroin repetitive domain. This study demonstrates that HiFi long-read sequencing can help provide a deeper understanding of silk research by capturing highly contiguous, repetitive gene regions.