Chromosomal-level reference genome assembly of the North American wolverine (Gulo gulo luscus): a resource for conservation genomics
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We report a chromosomal-level genome assembly of a male North American wolverine (Gulo gulo luscus) from the Kugluktuk region of Nunavut, Canada. The genome was assembled directly from long-reads, comprising: 758 contigs with a contig N50 of 36.6 Mb; contig L50 of 20; base count of 2.39 Gb; and a near complete representation (99.98%) of the BUSCO 5.2.2 set of 9,226 genes. A presumptive chromosomal-level assembly was generated by scaffolding against two chromosomal-level Mustelidae reference genomes, the ermine and the Eurasian river otter, to derive a final scaffold N50 of 144.0 Mb and a scaffold L50 of 7. We annotated a comprehensive set of genes that have been associated with models of aggressive behavior, a trait which the wolverine is purported to have in the popular literature. To support an integrated, genomics-based wildlife management strategy at a time of environmental disruption from climate change, we annotated the principal genes of the innate immune system to provide a resource to study the wolverine’s susceptibility to new infectious and parasitic diseases. As a resource, we annotated genes involved in the modality of infection by the coronaviruses, an important class of viral pathogens of growing concern as shown by the recent spillover infections by severe acute respiratory syndrome coronavirus-2 to naïve wildlife. Tabulation of heterozygous single nucleotide variants in our specimen revealed a heterozygosity level of 0.065%, indicating a relatively diverse genetic pool that would serve as a baseline for the genomics-based conservation of the wolverine, a rare cold-adapted carnivore now under threat.
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Undercounting of genes by BUSCO was exemplified by the wolverine genome assembly and by the human reference genome GRCh38.p14, where 369 BUSCO genes were called as fragmented or missing despite being annotated as complete and experimentally verified.
“Undercounting of genes by BUSCO was exemplified by our recent genome assembly for the wolverine60 and by the current build of the gold standard human reference genome, GRCh38.p14, where 369 BUSCO genes were called as fragmented or missing (Fig. 2), despite those genes being annotated by the NCBI Genome Data Viewer as complete and experimentally verified.”
From Chromosomal-level reference genome assembly of muskox (Ovibos moschatus) from Banks Island in the Canadian Arctic, a resource for conservation genomics (2024) · cites this paper as [60]
BUSCO can under-count genes in species whose orthologs deviate significantly from the consensus, resulting in an under-estimation of the quality of an assembly being evaluated.
“Due to this compromise, it is possible that subsets of BUSCO profiles could have difficulties detecting their cognate genes in species whose orthologs deviate significantly from the consensus. Accordingly, BUSCO could under-count those genes, resulting in an under-estimation of the quality of an assembly being evaluated.”
From Chromosomal-level reference genome assembly of muskox (Ovibos moschatus) from Banks Island in the Canadian Arctic, a resource for conservation genomics (2024) · cites this paper as [60]
The 15-20% pseudorandom sequencing errors typically associated with CLRs can be effectively mitigated by the Flye assembler and ensuing polishing regimens to yield a high-quality assembly essentially free of residual sequencing errors.
“As shown here and in our previous study of the North American wolverine genome60, the 15–20% pseudorandom sequencing errors typically associated with CLRs51 can be effectively mitigated by the Flye assembler and the ensuing polishing regimens to yield a high-quality assembly that is essentially free of residual sequencing errors.”
From Chromosomal-level reference genome assembly of muskox (Ovibos moschatus) from Banks Island in the Canadian Arctic, a resource for conservation genomics (2024) · cites this paper as [60]
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Cited by
Sorted by citations
Lok, S., Lau, T. N. H., Trost, B., Tong, A. H. Y., Paton, T., Wintle, R. F., Engstrom, M. D., Gunn, A., & Scherer, S. W. (2024) · Scientific Reports · doi:10.1038/s41598-024-67270-9 · Cited by 4 · see citing works
“As shown here and in our previous study of the North American wolverine genome 60 , the 15–20% pseudor-andom sequencing errors typically associated with CLRs 51 can be effectively mitigated by the Flye assembler and the ensuing polishing regimens to yield a high-quality assembly that is essentially…”
BackgroundSelf-citation
- Authors
- Lok, S., Lau, T. N. H., Trost, B., Tong, A. H. Y., Wintle, R. F., Engstrom, M. D., Stacy, E., Waits, L. P., Scrafford, M., & Scherer, S. W.
- Affiliations
- Hospital for Sick Children (CA)
- University of Toronto (CA)
- Royal Ontario Museum (CA)
- Wildlife Conservation Society (US)
- University of Idaho (US)
- Wildlife Conservation Society Canada (CA)
- Corresponding author
- Lok, Si
- Scherer, Stephen W
- ORCID
- Venue
- G3 Genes|Genomes|Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2022-06-08
- Volume
- 12
- Issue
- 8
- ISSN
- 2160-1836 (ISSN-L)
- PMC
- PMC9339297
- OpenAlex
- W4282920263
- Cited by
- 6
- References
- 120
- Citations by year
- 2026: 2 · 2024: 2 · 2023: 2
- FWCI
- 0.33
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- G3 Genes Genomes Genetics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- Lau Family Endowment for Genome Science Development through the CGEn CanSeq150 Project
- Genome Canada’s Disruptive Innovation in Genomics Program (9425)
- The Centre for Applied Genomics (TCAG) using infrastructure funded by the Canada Foundation for Innovation and was operationally supported by Genome Canada through Ontario Genomics
- Canada Foundation for Innovation
- Government of Ontario, and The Hospital for Sick Children (SickKids) Foundation
- W Garfield Weston Foundation
- College of Natural Resources at the University of Idaho
- Northbridge Chair in Paediatric Research, The Hospital for Sick Children and University of Toronto
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- chromosome-level genome assembly, conservation genomics, heterozygosity, genetic diversity, Mustelidae, long-read sequencing
- MeSH terms
- COVID-19, Animals, Chromosomes, Humans, Male, North America, Genomics, Mustelidae
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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