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

Akito Y. Kawahara; Caroline G. Storer; Amanda Markee; Jacqueline Heckenhauer; Ashlyn Powell; David Plotkin; Scott Hotaling; Timothy P. Cleland; Rebecca B. Dikow; Torsten Dikow; Ryoichi B. Kuranishi; Rebeccah Messcher; Steffen U. Pauls; Russell J. Stewart; Koji Tojo; Paul B. Frandsen

doi:10.46471/gigabyte.64

GigaByte (Jun 2022)

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

Akito Y. Kawahara ,
Caroline G. Storer ,
Amanda Markee ,
Jacqueline Heckenhauer ,
Ashlyn Powell ,
David Plotkin ,
Scott Hotaling ,
Timothy P. Cleland ,
Rebecca B. Dikow ,
Torsten Dikow ,
Ryoichi B. Kuranishi ,
Rebeccah Messcher ,
Steffen U. Pauls ,
Russell J. Stewart ,
Koji Tojo ,
Paul B. Frandsen

Affiliations

Akito Y. Kawahara: ORCiD; McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
Caroline G. Storer: ORCiD; McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA, Pacific Biosciences, 1305 O’Brien Dr., Menlo Park, CA 94025, USA
Amanda Markee: McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA, School of Natural Resources and the Environment, University of Florida, Gainesville, FL 32611, USA
Jacqueline Heckenhauer: ORCiD; LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt 60325, Germany, Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt 60325, Germany
Ashlyn Powell: Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA
David Plotkin: ORCiD; McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
Scott Hotaling: ORCiD; School of Biological Sciences, Washington State University, Pullman, WA, USA
Timothy P. Cleland: ORCiD; Museum Conservation Institute, Smithsonian Institution, Suitland, MD 20746, USA
Rebecca B. Dikow: Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20002, USA
Torsten Dikow: ORCiD; Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
Ryoichi B. Kuranishi: ORCiD; Graduate School of Science, Chiba University, Chiba 263-8522, Japan, Kanagawa Institute of Technology, Kanagawa 243-0292, Japan
Rebeccah Messcher: McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
Steffen U. Pauls: ORCiD; LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt 60325, Germany, Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt 60325, Germany, Institute for Insect Biotechnology, Justus-Liebig-University, Gießen 35390, Germany
Russell J. Stewart: ORCiD; Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
Koji Tojo: ORCiD; Department of Biology, Shinshu University, Matsumoto, Nagano 390-8621, Japan
Paul B. Frandsen: ORCiD; Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA, Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20002, USA

DOI: https://doi.org/10.46471/gigabyte.64

Abstract

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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.

Published in GigaByte

ISSN: 2709-4715 (Online)
Publisher: GigaScience Press
Country of publisher: Hong Kong
LCC subjects: Science: Mathematics: Instruments and machines: Electronic computers. Computer science
Website: https://gigabytejournal.com/

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