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

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

GigaByte. 2022 Jun 30:2022:gigabyte64. doi: 10.46471/gigabyte.64. eCollection 2022.

Authors

Akito Y Kawahara¹, Caroline G Storer^{1

2}, Amanda Markee^{1

3}, Jacqueline Heckenhauer^{4

5}, Ashlyn Powell⁶, David Plotkin¹, Scott Hotaling⁷, Timothy P Cleland⁸, Rebecca B Dikow⁹, Torsten Dikow¹⁰, Ryoichi B Kuranishi^{11

12}, Rebeccah Messcher¹, Steffen U Pauls^{4

5

13}, Russell J Stewart¹⁴, Koji Tojo¹⁵, Paul B Frandsen^{6

9}

Affiliations

¹ McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.
² Pacific Biosciences, 1305 O'Brien Dr., Menlo Park, CA 94025, USA.
³ School of Natural Resources and the Environment, University of Florida, Gainesville, FL 32611, USA.
⁴ LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt 60325, Germany.
⁵ Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt 60325, Germany.
⁶ Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA.
⁷ School of Biological Sciences, Washington State University, Pullman, WA, USA.
⁸ Museum Conservation Institute, Smithsonian Institution, Suitland, MD 20746, USA.
⁹ Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20002, USA.
¹⁰ Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.
¹¹ Graduate School of Science, Chiba University, Chiba 263-8522, Japan.
¹² Kanagawa Institute of Technology, Kanagawa 243-0292, Japan.
¹³ Institute for Insect Biotechnology, Justus-Liebig-University, Gießen 35390, Germany.
¹⁴ Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA.
¹⁵ Department of Biology, Shinshu University, Matsumoto, Nagano 390-8621, Japan.

Abstract

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.

Grants and funding

This study was funded by the Smithsonian National Museum of Natural History Global Genome Initiative (GGI-Peer-2018-182) to TPC, RD, TD, AYK; the Smithsonian Museum Conservation Institute Federal; and Trust funds to TPC and PBF. A grant from the University of Florida Research Opportunity Seed Fund internal award (number AWD06265) was awarded to principal investigators AYK and CGS. The LOEWE Centre for Translational Biodiversity Genomics (TBG) is funded by the Hessen State Ministry of Higher Education, Research and the Arts (HMWK), which financially supported JH and SUP. SH was supported by National Science Foundation award #OPP-1906015.