A draft genome assembly for the eastern fox squirrel, Sciurus niger

Simple item page
dc.contributor.authorKang, Linen
dc.contributor.authorMichalak, Pawelen
dc.contributor.authorHallerman, Eric M.en
dc.contributor.authorMoncrief, Nancy D.en
dc.date.accessioned2022-02-06T17:03:38Zen
dc.date.available2022-02-06T17:03:38Zen
dc.date.issued2021-12-01en
dc.date.updated2022-02-06T17:03:36Zen
dc.description.abstractThe eastern fox squirrel, Sciurus niger, exhibits marked geographic variation in size and coat color, is a model organism for studies of behavior and ecology, and a potential model for investigating physiological solutions to human porphyrias. We assembled a genome using Illumina HiSeq, PacBio SMRT, and Oxford Nanopore MinION sequencing platforms. Together, the sequencing data resulted in a draft genome of 2.99 Gb, containing 32,830 scaffolds with an average size of 90.9 Kb and N50 of 183.8 Kb. Genome completeness was estimated to be 93.78%. A total of 24,443 protein-encoding genes were predicted from the assembly and 23,079 (94.42%) were annotated. Repeat elements comprised an estimated 38.49% of the genome, with the majority being LINEs (13.92%), SINEs (6.04%), and LTR elements. The topology of the species tree reconstructed using maximum-likelihood phylogenetic analysis was congruent with those of previous studies. This genome assembly can prove useful for comparative studies of genome structure and function in this rapidly diversifying lineage of mammals, for studies of population genomics and adaptation, and for biomedical research. Predicted amino acid sequence alignments for genes affecting heme biosynthesis, color vision, and hibernation showed point mutations and indels that may affect protein function and ecological adaptation.en
dc.description.versionPublished versionen
dc.format.extent5 page(s)en
dc.format.mimetypeapplication/pdfen
dc.identifierARTN jkab315 (Article number)en
dc.identifier.doihttps://doi.org/10.1093/g3journal/jkab315en
dc.identifier.eissn2160-1836en
dc.identifier.issn2160-1836en
dc.identifier.issue12en
dc.identifier.orcidHallerman, Eric [0000-0002-5839-858X]en
dc.identifier.other6373894 (PII)en
dc.identifier.pmid34550334en
dc.identifier.urihttp://hdl.handle.net/10919/108159en
dc.identifier.volume11en
dc.language.isoenen
dc.publisherOxford University Pressen
dc.relation.urihttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000735920300010&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=930d57c9ac61a043676db62af60056c1en
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectLife Sciences & Biomedicineen
dc.subjectGenetics & Heredityen
dc.subjectwhole-genome sequencingen
dc.subjectde novo assemblyen
dc.subjecttree squirrelsen
dc.subjectcandidate genesen
dc.subjectheme biosynthesisen
dc.subjectcolor visionen
dc.subjecthibernationen
dc.subjecteastern fox squirrelen
dc.subjectSciurus nigeren
dc.subjectSciuridaeen
dc.subjectPORPHYRIAen
dc.subject0604 Geneticsen
dc.subject.meshAnimalsen
dc.subject.meshHumansen
dc.subject.meshSciuridaeen
dc.subject.meshSequence Analysis, DNAen
dc.subject.meshPhylogenyen
dc.subject.meshGenomeen
dc.subject.meshNigeren
dc.titleA draft genome assembly for the eastern fox squirrel, Sciurus nigeren
dc.title.serialG3-Genes Genomes Geneticsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.otherArticleen
dc.type.otherJournalen
dcterms.dateAccepted2021-08-27en
pubs.organisational-group/Virginia Techen
pubs.organisational-group/Virginia Tech/Natural Resources & Environmenten
pubs.organisational-group/Virginia Tech/Natural Resources & Environment/Fish and Wildlife Conservationen
pubs.organisational-group/Virginia Tech/University Research Institutesen
pubs.organisational-group/Virginia Tech/University Research Institutes/Fralin Life Sciencesen
pubs.organisational-group/Virginia Tech/All T&R Facultyen
pubs.organisational-group/Virginia Tech/Natural Resources & Environment/CNRE T&R Facultyen
pubs.organisational-group/Virginia Tech/University Research Institutes/Fralin Life Sciences/Durelle Scotten

Files

Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
jkab315.pdf
Size:
291.81 KB
Format:
Adobe Portable Document Format
Description:
Published version
Download

Collections

All Faculty Deposits
Scholarly Works, Fish and Wildlife Conservation