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

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

doi:10.46471/gigabyte.64

Cited by 28 publications

(49 citation statements)

References 36 publications

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“…Spurious introns (those that did not affect reading frames and were not supported by transcript evidence) were manually removed. Annotated sequences are provided in the Gigascience GigaDB repository [26].…”

Section: Methodsmentioning

confidence: 99%

“…For EST evidence, we used the transcriptome of Ptilostomis semifasciata (111015_I297_FCD05HRACXX_ L1_INSbttTHRAAPEI-17, 1kite.org) for E. regina and Iso-seq data for P. interpunctella . Evidence used in Maker and the Maker config files can be found in the Gigascience GigaDB repository [26].…”

Section: Methodsmentioning

confidence: 99%

“…A total of 23.04% of the annotated repeats were interspersed repeats. Details on the repeat classes are given in the Gigascience GigaDB repository [26].…”

Section: Methodsmentioning

confidence: 99%

“…Evidence used in Maker and the Maker config files can be found in the Gigascience GigaDB repository [26].…”

Section: Genome Annotationmentioning

confidence: 99%

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Long-read HiFi Sequencing Correctly Assembles Repetitive heavy fibroin Silk Genes in New Moth and Caddisfly Genomes

Kawahara

Storer

Markee

et al. 2022

Preprint

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Insect silk is an incredibly versatile biomaterial. Lepidoptera and their sister lineage, Trichoptera, display some of the most diverse uses of silk with varying strength, adhesive qualities and elastic properties. It is well known that silk fibroin genes are long (> 20 kb) and have many repetitive motifs. These features make these genes 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. This study demonstrates that HiFi long-read sequencing can significantly help our understanding of genes with highly contiguous, repetitive regions.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Long-read HiFi Sequencing Correctly Assembles Repetitive heavy fibroin Silk Genes in New Moth and Caddisfly Genomes

Kawahara

Storer

Markee

et al. 2022

Preprint

Self Cite

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“…However, long-read assemblies have since yielded full-length sequences (Frandsen, et al 2019;Kawahara, et al 2022;Luo, et al 2018).…”

Section: Bodymentioning

confidence: 99%

Highly accurate long reads are crucial for realizing the potential of biodiversity genomics

Hotaling

Wilcox

Heckenhauer

et al. 2022

Preprint

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Generating the most contiguous, accurate genome assemblies given available sequencing technologies is a long-standing challenge in genome science. With the rise of long-read sequencing, assembly challenges have shifted from merely increasing contiguity to correctly assembling complex, repetitive regions of interest, ideally in a phased manner. At present, researchers largely choose between two types of long read data: longer, but less accurate sequences, often generated with Oxford Nanopore (ONT) technology, or highly accurate, but shorter, reads typically generated with Pacific Biosciences HiFi. To understand how both technologies influence genome assembly and to clarify how scale of data (i.e., mean length and sequencing depth) influence outcomes, we compared genome assemblies for a caddisfly, Hesperophylax magnus, generated with ONT and HiFi data. Despite shorter reads and less coverage, HiFi reads outperformed ONT reads in all assembly metrics tested and allowed for accurate assembly of the repetitive ~20-Kb H-fibroin gene. Next, we quantified the influence of data type on genome assemblies across 6,750 plant and animal genomes. We show that HiFi reads consistently outperform all other data types for both plants and animals and may represent a particularly valuable tool for assembling complex plant genomes. To realize the promise of biodiversity genomics, we call for greater uptake of highly accurate long-reads in future studies.

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Comparative Evolutionary Genomics in Insects

Feldmeyer,

Bornberg-Bauer,

Dohmen

et al. 2024

Methods in Molecular Biology

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

Cited by 28 publications

References 36 publications

Long-read HiFi Sequencing Correctly Assembles Repetitive heavy fibroin Silk Genes in New Moth and Caddisfly Genomes

Long-read HiFi Sequencing Correctly Assembles Repetitive heavy fibroin Silk Genes in New Moth and Caddisfly Genomes

Highly accurate long reads are crucial for realizing the potential of biodiversity genomics

Comparative Evolutionary Genomics in Insects

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