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

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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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Most cited references 40

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Minimap2: pairwise alignment for nucleotide sequences

Heng Li (2018)

Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 Mb in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms.

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BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

Mosè Manni, Matthew Berkeley, Mathieu Seppey … (2021)

Methods for evaluating the quality of genomic and metagenomic data are essential to aid genome assembly procedures and to correctly interpret the results of subsequent analyses. BUSCO estimates the completeness and redundancy of processed genomic data based on universal single-copy orthologs. Here, we present new functionalities and major improvements of the BUSCO software, as well as the renewal and expansion of the underlying data sets in sync with the OrthoDB v10 release. Among the major novelties, BUSCO now enables phylogenetic placement of the input sequence to automatically select the most appropriate BUSCO data set for the assessment, allowing the analysis of metagenome-assembled genomes of unknown origin. A newly introduced genome workflow increases the efficiency and runtimes especially on large eukaryotic genomes. BUSCO is the only tool capable of assessing both eukaryotic and prokaryotic species, and can be applied to various data types, from genome assemblies and metagenomic bins, to transcriptomes and gene sets.

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Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

Haoyu Cheng, Gregory Concepcion, Xiaowen Feng … (2021)

Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome. However, existing algorithms either collapse heterozygous alleles into one consensus copy or fail to cleanly separate the haplotypes to produce high-quality phased assemblies. Here we describe hifiasm, a de novo assembler that takes advantage of long high-fidelity sequence reads to faithfully represent the haplotype information in a phased assembly graph. Unlike other graph-based assemblers that only aim to maintain the contiguity of one haplotype, hifiasm strives to preserve the contiguity of all haplotypes. This feature enables the development of a graph trio binning algorithm that greatly advances over standard trio binning. On three human and five nonhuman datasets, including California redwood with a ~30-Gb hexaploid genome, we show that hifiasm frequently delivers better assemblies than existing tools and consistently outperforms others on haplotype-resolved assembly.

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Author and article information

Contributors

Akito Y. Kawahara:

ORCID: https://orcid.org/0000-0002-3724-4610

Role: ConceptualizationRole: Project administrationRole: SupervisionRole: Writing - original draftRole: Writing - review editing

Caroline G. Storer:

ORCID: https://orcid.org/0000-0002-0349-0653

Role: ConceptualizationRole: Formal analysisRole: Writing - original draftRole: Writing - review editing

Amanda Markee: Role: Formal analysisRole: InvestigationRole: Writing - original draftRole: Writing - review editing

Jacqueline Heckenhauer:

ORCID: https://orcid.org/0000-0001-8771-9154

Role: Data curationRole: Formal analysisRole: InvestigationRole: Writing - original draftRole: Writing - review editing

Ashlyn Powell: Role: Formal analysisRole: InvestigationRole: Writing - original draft

David Plotkin:

ORCID: https://orcid.org/0000-0002-2339-655X

Role: Data curationRole: Writing - original draftRole: Writing - review editing

Scott Hotaling:

ORCID: https://orcid.org/0000-0002-5965-0986

Role: VisualizationRole: Writing - original draftRole: Writing - review editing

Timothy P. Cleland:

ORCID: https://orcid.org/0000-0001-9198-2828

Role: Funding acquisitionRole: Writing - original draftRole: Writing - review editing

Rebecca B. Dikow: Role: Funding acquisitionRole: Writing - original draftRole: Writing - review editing

Torsten Dikow:

ORCID: https://orcid.org/0000-0003-4816-2909

Role: Funding acquisitionRole: Writing - original draftRole: Writing - review editing

Ryoichi B. Kuranishi:

ORCID: https://orcid.org/0000-0002-6353-0450

Role: ResourcesRole: Writing - original draftRole: Writing - review editing

Rebeccah Messcher: Role: InvestigationRole: Writing - original draftRole: Writing - review editing

Steffen U. Pauls:

ORCID: https://orcid.org/0000-0002-6451-3425

Role: ResourcesRole: Writing - original draftRole: Writing - review editing

Russell J. Stewart:

ORCID: https://orcid.org/0000-0002-8389-8877

Role: Funding acquisitionRole: Writing - original draftRole: Writing - review editing

Koji Tojo:

ORCID: https://orcid.org/0000-0002-9362-604X

Role: ResourcesRole: Writing - original draftRole: Writing - review editing

Paul B. Frandsen:

ORCID: https://orcid.org/0000-0002-4801-7579

Role: ConceptualizationRole: Formal analysisRole: ResourcesRole: Writing - original draftRole: Writing - review editing

Journal

Journal ID (nlm-ta): GigaByte

Journal ID (iso-abbrev): GigaByte

Journal ID (publisher-id): Gigabyte

Title: GigaByte

Publisher: GigaScience Press (Sha Tin, New Territories, Hong Kong SAR )

ISSN (Electronic): 2709-4715

Publication date (Electronic): 30 June 2022

Publication date Collection: 2022

Volume: 2022

Electronic Location Identifier: gigabyte64

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

Author notes

[ ^* ] Corresponding authors. E-mail: kawahara@ 123456flmnh.ufl.edu ; paul_frandsen@ 123456byu.edu

[ † ]

Contributed equally.

Author information

Akito Y. Kawahara https://orcid.org/0000-0002-3724-4610

Caroline G. Storer https://orcid.org/0000-0002-0349-0653

Jacqueline Heckenhauer https://orcid.org/0000-0001-8771-9154

David Plotkin https://orcid.org/0000-0002-2339-655X

Scott Hotaling https://orcid.org/0000-0002-5965-0986

Timothy P. Cleland https://orcid.org/0000-0001-9198-2828

Torsten Dikow https://orcid.org/0000-0003-4816-2909

Ryoichi B. Kuranishi https://orcid.org/0000-0002-6353-0450

Steffen U. Pauls https://orcid.org/0000-0002-6451-3425

Russell J. Stewart https://orcid.org/0000-0002-8389-8877

Koji Tojo https://orcid.org/0000-0002-9362-604X

Paul B. Frandsen https://orcid.org/0000-0002-4801-7579

Article

Publisher-manuscript ID: DRR-202204-02 Publisher ID: 64

DOI: 10.46471/gigabyte.64

PMC ID: 9693786

SO-VID: 34cd5ca3-d034-44f8-94d1-15aef65b18ba

License:

This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

History

Date received : 07 April 2022

Date accepted : 24 June 2022

Funding

Funded by: Smithsonian National Museum of Natural History Global Genome Initiative;

Award ID: GGI-Peer-2018-182

Award Recipient :

ORCID: https://orcid.org/0000-0001-9198-2828

T. P. Cleland

Funded by: Smithsonian National Museum of Natural History Global Genome Initiative;

Award ID: GGI-Peer-2018-182

Award Recipient :

ORCID: https://orcid.org/

R. B. Dikow

Funded by: Smithsonian National Museum of Natural History Global Genome Initiative;

Award ID: GGI-Peer-2018-182

Award Recipient :

ORCID: https://orcid.org/0000-0003-4816-2909

T. Dikow

Funded by: Smithsonian National Museum of Natural History Global Genome Initiative;

Award ID: GGI-Peer-2018-182

Award Recipient :

ORCID: https://orcid.org/0000-0002-3724-4610

A. Y. Kawahara

Funded by: Smithsonian Museum Conservation Institute Federal;

Funded by: Trust;

Award Recipient :

ORCID: https://orcid.org/0000-0001-9198-2828

T. P. Cleland

Funded by: Trust;

Award Recipient :

ORCID: https://orcid.org/0000-0002-4801-7579

P. B. Frandsen

Funded by: University of Florida Research Opportunity Seed Fund;

Award ID: AWD06265

Award Recipient :

ORCID: https://orcid.org/0000-0002-3724-4610

A. Y. Kawahara

Funded by: University of Florida Research Opportunity Seed Fund;

Award ID: AWD06265

Award Recipient :

ORCID: https://orcid.org/0000-0002-0349-0653

C. G. Storer

Funded by: Hessen State Ministry of Higher Education, Research and the Arts (HMWK);

Award Recipient :

ORCID: https://orcid.org/0000-0001-8771-9154

J. Heckenhauer

Funded by: Hessen State Ministry of Higher Education, Research and the Arts (HMWK);

Award Recipient :

ORCID: https://orcid.org/0000-0002-6451-3425

S. U. Pauls

Funded by: National Science Foundation award;

Award ID: #OPP-1906015

Award Recipient :

ORCID: https://orcid.org/0000-0002-5965-0986

S. Hotaling

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.

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

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Abstract

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G3: Genes|Genomes|Genetics

Most cited references 40

Minimap2: pairwise alignment for nucleotide sequences

BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

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