DOI: 10.5061/dryad.wh70rxwvb
title: A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies

description: 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.
description: A total of 85 tissue samples were taken from individual animals
 across several cetacean species. The type of tissue were either from
 strandings or biopsies. Stranding samples in New Zealand were taken by the
 Department of Conservation New Zealand and sent to the New Zealand
 Cetacean Tissue Archive (NZCeTA) housed at the University of Auckland
 Waipapa Taumata Rau with approval from mana whenua (Māori indigenous
 groups). Biopsy samples from New Zealand cetaceans include two Hector’s
 dolphin (<em>Chephalorhyncus hectori</em>) (Hamner et al.,
 2017) and two bottlenose dolphins (<em>T. truncatus</em>)
 (Tezanos-Pinto et al., 2009). Further biopsies include two rough-toothed
 dolphins (<em>Steno bredanensis</em>) and two Blainville
 beaked whales (<em>Mesoplodon densirostris</em>) from
 French-Polynesia (Albertson et al., 2017; Oremus et al., 2012). Details on
 samples and associated permit numbers can be found in the published
 manuscript. DNA was extracted from tissue samples and
 genomic DNA underwent PCR for five Major Histocompatibility Complex loci.
 PCR products were pooled for each individual, indexed with Nextera indexes
 supplied by IDT, and sequenced on Illumina NanoSeq and MiSeq. Each
 individual amplicon-pool was sequenced multiple times on different
 sequencing runs. The reads provided here are the paired and merged reads
 from several sequencing runs combined for each individual in a fastq
 file.
description: # Merged paired end Illumina reads from five MHC loci for 85 cetaceans and
 their class I and assumed non-functional DRB alleles
 The dataset contains 85
 fastq files. Each file contains reads of amplicons from five MHC loci
 (DQA, DQB, DRA, DRB, and class I genes) combined across separate
 sequencing runs from a single cetacean. Details on individual cetacean
 sample abbreviations can be found in the manuscript. Reads are paired and
 merged with the Illumina adapter removed. It also contains one fastq file
 with all class I alleles found and one fastq file with non-functional DRB
 alleles found. Alleles are labeled with four letter species abbreviation
 followed by locus designation (DRB or N for class I) and are numbered in
 the order they were discovered.