Leveraging an existing whole-genome resequencing population data set to characterize toll-like receptor gene diversity in a threatened bird

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dc.citation.issue7
dc.citation.volume22
dc.contributor.authorMagid M
dc.contributor.authorWold JR
dc.contributor.authorMoraga R
dc.contributor.authorCubrinovska I
dc.contributor.authorHouston DM
dc.contributor.authorGartrell BD
dc.contributor.authorSteeves TE
dc.contributor.editorHohenlohe PA
dc.coverage.spatialEngland
dc.date.accessioned2024-02-09T01:17:51Z
dc.date.accessioned2024-07-25T06:53:59Z
dc.date.available2022-06-14
dc.date.available2024-02-09T01:17:51Z
dc.date.available2024-07-25T06:53:59Z
dc.date.issued2022-10
dc.description.abstractSpecies recovery programs are increasingly using genomic data to measure neutral genetic diversity and calculate metrics like relatedness. While these measures can inform conservation management, determining the mechanisms underlying inbreeding depression requires information about functional genes associated with adaptive or maladaptive traits. Toll-like receptors (TLRs) are one family of functional genes, which play a crucial role in recognition of pathogens and activation of the immune system. Previously, these genes have been analysed using species-specific primers and PCR. Here, we leverage an existing short-read reference genome, whole-genome resequencing population data set, and bioinformatic tools to characterize TLR gene diversity in captive and wild tchūriwat'/tūturuatu/shore plover (Thinornis novaeseelandiae), a threatened bird endemic to Aotearoa New Zealand. Our results show that TLR gene diversity in tchūriwat'/tūturuatu is low, and forms two distinct captive and wild genetic clusters. The bioinformatic approach presented here has broad applicability to other threatened species with existing genomic resources in Aotearoa New Zealand and beyond.
dc.description.confidentialfalse
dc.edition.editionOctober 2022
dc.format.pagination2810-2825
dc.identifier.author-urlhttps://www.ncbi.nlm.nih.gov/pubmed/35635119
dc.identifier.citationMagid M, Wold JR, Moraga R, Cubrinovska I, Houston DM, Gartrell BD, Steeves TE. (2022). Leveraging an existing whole-genome resequencing population data set to characterize toll-like receptor gene diversity in a threatened bird.. Mol Ecol Resour. 22. 7. (pp. 2810-2825).
dc.identifier.doi10.1111/1755-0998.13656
dc.identifier.eissn1755-0998
dc.identifier.elements-typejournal-article
dc.identifier.issn1755-098X
dc.identifier.urihttps://mro.massey.ac.nz/handle/10179/71118
dc.languageeng
dc.publisherJohn Wiley and Sons, Ltd
dc.publisher.urihttps://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13656
dc.relation.isPartOfMol Ecol Resour
dc.rights(c) The author/sen
dc.rights.licenseCC BY-NC 4.0en
dc.rights.urihttps://creativecommons.org/licenses/by-nc/4.0/en
dc.subjectconservation genomics
dc.subjectimmune genes
dc.subjectshore plover
dc.subjecttoll-like receptors
dc.subjectwhole-genome sequences
dc.subjectAnimals
dc.subjectBirds
dc.subjectEndangered Species
dc.subjectGenome
dc.subjectSequence Analysis, DNA
dc.subjectToll-Like Receptors
dc.titleLeveraging an existing whole-genome resequencing population data set to characterize toll-like receptor gene diversity in a threatened bird
dc.typeJournal article
pubs.elements-id453723
pubs.organisational-groupOther
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