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

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

Akito Y Kawahara  1 , Caroline G Storer  1   2 , Amanda Markee  1   3 , Jacqueline Heckenhauer  4   5 , Ashlyn Powell  6 , David Plotkin  1 , Scott Hotaling  7 , Timothy P Cleland  8 , Rebecca B Dikow  9 , Torsten Dikow  10 , Ryoichi B Kuranishi  11   12 , Rebeccah Messcher  1 , Steffen U Pauls  4   5   13 , Russell J Stewart  14 , Koji Tojo  15 , Paul B Frandsen  6   9
Affiliations

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

Akito Y Kawahara et al. GigaByte. .

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.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1.
Figure 1.
Length of assembled heavy fibroin (HFib) gene for Plodia interpunctella using two approaches. Top shows HiFi assembly, bottom shows Illumina assembly. In the HiFi genome, we recovered the entire length of the sequence, but in the Illumina assembly we could not assemble the genome through the repetitive region.
Figure 2.
Figure 2.
Schematic of the identity and ordering of repeat motifs in Plodia interpunctella. On the right panel are the repetitive units with the N-terminus at the beginning and the C-terminus at the end. The numbers in parentheses refer to the number of times that particular motif is repeated across the gene. The color corresponds with the ordering of the repeats shown on the left. The gene is split into two panels, starting in the left panel and continuing in the right panel. “X” indicates a variable site.
Figure 3.
Figure 3.
Schematic of the identity and ordering of repeat motifs in Eubasilissa regina. On the right panel are the repetitive units with the N-terminus at the beginning and the C-terminus at the end. The numbers in parentheses refer to the number of times that particular motif is repeated across the gene. The color corresponds with the ordering of the repeats shown on the left. The gene is split into two panels, starting in the left panel and continuing in the right panel.
Figure 4.
Figure 4.
BlobPlot for Eubasilissa regina.
Figure 5.
Figure 5.
BlobPlot for Plodia interpunctella.
See this image and copyright information in PMC

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