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

GigaByte (Hong Kong, China) Pub Date : 2022-06-30 eCollection Date: 2022-01-01 DOI:10.46471/gigabyte.64

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

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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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长读数 HiFi 测序正确组装出新飞蛾和笛蝇基因组中的重复重纤维蛋白丝基因。

昆虫丝是一种用途广泛的生物材料。鳞翅目和毛翅目昆虫展示了蚕丝最多样化的用途，具有不同的强度、粘附性和弹性特性。蚕丝纤维素基因很长（>20 Kbp），有许多重复图案，这使它们的测序具有挑战性。迄今为止，大多数研究都集中在纤维蛋白基因的 N 端和 C 端保守区域，因为还不可能对不同类群的重复区域进行全面比较。利用 PacBio Sequel II 系统和 SMRT 测序技术，我们生成了印度小卷蛾（Plodia interpunctella）的高保真（HiFi）长序列基因组和转录组序列，以及笛蛉 Eubasilissa regina 的基因组序列。这两个基因组高度连续（N50 = 9.7 Mbp/32.4 Mbp，L50 = 13/11）和完整（BUSCO complete = 99.3%/95.2%），并完整连续地恢复了蚕丝重纤维蛋白基因序列。我们的研究表明，HiFi 长线程测序有助于了解具有长重复区域的基因。

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