A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies

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 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.