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dc.contributor.authorHeimeier, Dorothea
dc.contributor.authorGarland, Ellen Clare
dc.contributor.authorEichenberger, Franca
dc.contributor.authorGarrigue, Claire
dc.contributor.authorVella, Adriana
dc.contributor.authorBaker, C. Scott
dc.contributor.authorCarroll, Emma Louise
dc.date.accessioned2024-03-26T17:30:02Z
dc.date.available2024-03-26T17:30:02Z
dc.date.issued2024-03-23
dc.identifier296384044
dc.identifierc635d73e-cde6-4953-b154-0ff89958783d
dc.identifier85189153212
dc.identifier.citationHeimeier , D , Garland , E C , Eichenberger , F , Garrigue , C , Vella , A , Baker , C S & Carroll , E L 2024 , ' A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies ' , Molecular Ecology Resources , vol. Early View . https://doi.org/10.1111/1755-0998.13955en
dc.identifier.issn1755-098X
dc.identifier.otherORCID: /0000-0002-8240-1267/work/156627482
dc.identifier.urihttps://hdl.handle.net/10023/29556
dc.descriptionThis study was funded by a Royal Society Research Grants for Research Fellows (RGF\R1\181014) to E.C.G. E.C.G. is funded by a Royal Society University Research Fellowship (UF160081 & URF\R\221020). F.E. is supported by a University of St Andrews School of Biology Ph.D. scholarship and a Royal Society Research Fellows Enhancement Award (RGF\EA\180213 to E.C.G). E.L.C. is funded by a Rutherford Discovery Fellowship from the Royal Society of New Zealand Te Apārangi.en
dc.description.abstractThe major histocompatibility complex (MHC) is a highly polymorphic gene family that is crucial in immunity, and its diversity can be effectively used as a fitness marker for populations. Despite this, MHC remains poorly characterised in non-model species (e.g., cetaceans: whales, dolphins and porpoises) as high gene copy number variation, especially in the fast-evolving class I region, makes analyses of genomic sequences difficult. To date, only small sections of class I and IIa genes have been used to assess functional diversity in cetacean populations. Here, we undertook a systematic characterisation of the MHC class I and IIa regions in available cetacean genomes. We extracted full-length gene sequences to design pan-cetacean primers that amplified the complete exon2 from MHC class I and IIa genes in one combined sequencing panel. We validated this panel in 19 cetacean species and described 354 alleles for both classes. Furthermore, we identified likely assembly artefacts for many MHC class I assemblies based on the presence of class I genes in the amplicon data compared to missing genes from genomes. Finally, we investigated MHC diversity using the panel in 25 humpback and 30 southern right whales, including four paternity trios for humpback whales. This revealed copy-number variable class I haplotypes in humpback whales, which is likely a common phenomenon across cetaceans. These MHC alleles will form the basis for a cetacean branch of the Immuno-Polymorphism Database (IPD-MHC), a curated resource intended to aid in the systematic compilation of MHC alleles across several species, to support conservation initiatives.
dc.format.extent19
dc.format.extent4617823
dc.language.isoeng
dc.relation.ispartofMolecular Ecology Resourcesen
dc.subjectCetaceanen
dc.subjectHumpback whaleen
dc.subjectMajor histocompatibility complexen
dc.subjectMHC evolutionen
dc.subjectMHC organisationen
dc.subjectSouthern right whaleen
dc.subjectDASen
dc.titleA pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assembliesen
dc.typeJournal articleen
dc.contributor.sponsorThe Royal Societyen
dc.contributor.sponsorThe Royal Societyen
dc.contributor.sponsorThe Royal Societyen
dc.contributor.institutionUniversity of St Andrews. Scottish Oceans Instituteen
dc.contributor.institutionUniversity of St Andrews. Centre for Biological Diversityen
dc.contributor.institutionUniversity of St Andrews. Centre for Social Learning & Cognitive Evolutionen
dc.contributor.institutionUniversity of St Andrews. Sea Mammal Research Uniten
dc.contributor.institutionUniversity of St Andrews. School of Biologyen
dc.identifier.doi10.1111/1755-0998.13955
dc.description.statusPeer revieweden
dc.identifier.grantnumberRGF/R1/181014en
dc.identifier.grantnumberRF\ERE\210306en
dc.identifier.grantnumberURF/R/221020en


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