Sequence Analysis of MHC Class II Genes in Cetaceans

Yang, Wei-Cheng; Chou, Lien‐Siang; Hu, Jer‐Ming

doi:10.5772/35761

Cited by 2 publications

(1 citation statement)

References 77 publications

(136 reference statements)

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“…In cetaceans, MHC diversity of small segments of class II exon 2 (less than 200 bp of mostly DQB and DRB1) has been characterised with Sanger sequencing (e.g., Arbanasić et al., 2014; Heimeier et al., 2018; Villanueva‐Noriega et al., 2013; Yang et al., 2012) while only a handful of studies have investigated class I diversity (e.g., Flores‐Ramírez et al., 2000; Gillett et al., 2014; Xu et al., 2007). Amplicon sequencing is a well‐used tool to genotype MHC diversity in individuals for model species.…”

Section: Introductionmentioning

confidence: 99%

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

Heimeier,

Garland,

Eichenberger

et al. 2024

Molecular Ecology Resources

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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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Section: Introductionmentioning

confidence: 99%

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

Heimeier,

Garland,

Eichenberger

et al. 2024

Molecular Ecology Resources

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Characterization of Class I– and Class II–Like Major Histocompatibility Complex Loci in Pedigrees of North Atlantic Right Whales

Gillett

Murray

White

2013

JHERED

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North Atlantic right whales have one of the lowest levels of genetic variation at minisatellite loci, microsatellite loci, and mitochondrial control region haplotypes among mammals. Here, adaptive variation at the peptide binding region of class I and class II DRB-like genes of the major histocompatibility complex was assessed. Amplification of a duplicated region in 222 individuals revealed at least 11 class II alleles. Six alleles were assigned to the locus Eugl-DRB1 and 5 alleles were assigned to the locus Eugl-DRB2 by assessing segregation patterns of alleles from 81 parent/offspring pedigrees. Pedigree analysis indicated that these alleles segregated into 12 distinct haplotypes. Genotyping a smaller subset of unrelated individuals (n = 5 and 10, respectively) using different primer sets revealed at least 2 class II pseudogenes (with ≥ 4 alleles) and at least 3 class I loci (with ≥ 6 alleles). Class II sequences were significantly different from neutrality at peptide binding sites suggesting loci may be under the influence of balancing selection. Trans-species sharing of alleles was apparent for class I and class II sequences. Characterization of class II loci represents the first step in determining the relationship between major histocompatibility complex variability and factors affecting health and reproduction in this species.

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Sequence Analysis of MHC Class II Genes in Cetaceans

Cited by 2 publications

References 77 publications

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

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

Characterization of Class I– and Class II–Like Major Histocompatibility Complex Loci in Pedigrees of North Atlantic Right Whales

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