A pan‐cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies
Type | Article | ||||||||||||||||
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Acceptance Date | 2024-03-23 IN PRESS | ||||||||||||||||
Language | English | ||||||||||||||||
Author(s) | Heimeier Dorothea1, Garland Ellen C.2, Eichenberger Franca2, Garrigue Claire3, 4, Vella Adriana5, Baker C. Scott6, Carroll Emma L.1 | ||||||||||||||||
Affiliation(s) | 1 : School of Biological Sciences University of Auckland—Waipapa Taumata Rau Auckland, New Zealand 2 : Sea Mammal Research Unit, School of Biology University of St. Andrews Fife, UK 3 : UMR ENTROPIE, (IRD, Université de La Réunion, Université de la Nouvelle‐Calédonie, IFREMER, CNRS, Laboratoire d'Excellence—CORAIL) Nouméa ,New Caledonia 4 : Opération Cétacés ,Nouméa, New Caledonia 5 : Conservation Biology Research Group, Department of Biology University of Malta Msida, Malta 6 : Marine Mammal Institute, Hatfield Marine Science Center Oregon State University Corvallis Oregon, USA |
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Source | Molecular Ecology Resources (1755-098X) (Wiley) In Press | ||||||||||||||||
DOI | 10.1111/1755-0998.13955 | ||||||||||||||||
Keyword(s) | cetacean, humpback whale, major histocompatibility complex, MHC evolution, MHC organisation, southern right whale | ||||||||||||||||
Abstract | The 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 exon 2 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. |
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