@article{fdi:010089687,
  title = {{A} pan-cetacean {MHC} amplicon sequencing panel developed and evaluated in combination with genome assemblies},
  author = {{H}eimeier, {D}. and {G}arland, {E}. {C}. and {E}ichenberger, {F}. and {G}arrigue, {C}laire and {V}ella, {A}. and {B}aker, {C}. {S}. and {C}arroll, {E}. {L}.},
  editor = {},
  language = {{ENG}},
  abstract = {{T}he 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. {D}espite 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. {T}o date, only small sections of class {I} and {II}a genes have been used to assess functional diversity in cetacean populations. {H}ere, we undertook a systematic characterisation of the {MHC} class {I} and {II}a regions in available cetacean genomes. {W}e extracted full-length gene sequences to design pan-cetacean primers that amplified the complete exon 2 from {MHC} class {I} and {II}a genes in one combined sequencing panel. {W}e validated this panel in 19 cetacean species and described 354 alleles for both classes. {F}urthermore, 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. {F}inally, we investigated {MHC} diversity using the panel in 25 humpback and 30 southern right whales, including four paternity trios for humpback whales. {T}his revealed copy-number variable class {I} haplotypes in humpback whales, which is likely a common phenomenon across cetaceans. {T}hese {MHC} alleles will form the basis for a cetacean branch of the {I}mmuno-{P}olymorphism {D}atabase ({IPD}-{MHC}), a curated resource intended to aid in the systematic compilation of {MHC} alleles across several species, to support conservation initiatives.},
  keywords = {cetacean ; humpback whale ; major histocompatibility complex ; {MHC} ; evolution ; {MHC} organisation ; southern right whale ; {MONDE} ; {NOUVELLE} {ZELANDE}},
  booktitle = {},
  journal = {{M}olecular {E}cology {R}esources},
  volume = {[{E}arly access]},
  numero = {},
  pages = {[19 p.]},
  ISSN = {1755-098{X}},
  year = {2024},
  DOI = {10.1111/1755-0998.13955},
  URL = {https://www.documentation.ird.fr/hor/fdi:010089687},
}