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. 2024 Mar 27;27(4):109590.
doi: 10.1016/j.isci.2024.109590. eCollection 2024 Apr 19.

Organisation and evolution of the major histocompatibility complex class I genes in cetaceans

Grace Day  1   2 , Kate Robb  2 , Andrew Oxley  1 , Marina Telonis-Scott  3 , Beata Ujvari  1
Affiliations

Organisation and evolution of the major histocompatibility complex class I genes in cetaceans

Grace Day et al. iScience. .

Abstract

A quarter of marine mammals are at risk of extinction, with disease and poor habitat quality contributing to population decline. Investigation of the Major Histocompatibility Complex (MHC) provides insight into species' capacity to respond to immune and environmental challenges. The eighteen available cetacean chromosome level genomes were used to annotate MHC Class I loci, and to reconstruct the phylogenetic relationship of the described loci. The highest number of loci was observed in the striped dolphin (Stenella coeruleoalba), while the least was observed in the pygmy sperm whale (Kogia breviceps) and rough toothed dolphin (Steno bredanensis). Of the species studied, Mysticetes had the most pseudogenes. Evolutionarily, MHC Class I diverged before the speciation of cetaceans. Yet, locus one was genomically and phylogenetically similar in many species, persisting over evolutionary time. This characterisation of MHC Class I in cetaceans lays the groundwork for future population genetics and MHC expression studies.

Keywords: evolutionary biology; immune system evolution.

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Conflict of interest statement

The authors declare no competing interests.

Figures

None
Graphical abstract
Figure 1
Figure 1
Genomic organisation and characterisation of MHC Class I in cetaceans Balaenidae and Balaenopteridae MHC Class I loci. Loci were obtained via NCBI’s BLAST function and includes exons two, three and four. Loci marked with an asterisk are pseudogenes. See also Table S1 for gene lengths, premature stop codons and indels.
Figure 2
Figure 2
Genomic organisation and characterisation of MHC Class I in cetaceans Physeteridae, Kogiidae, Ziphiidae, Neophocaena and Phocoenidae MHC Class I loci. Loci were obtained via NCBI’s BLAST function and includes exons two, three and four. Loci marked with an asterisk are pseudogenes. See also Table S1 for gene lengths, premature stop codons and indels.
Figure 3
Figure 3
Genomic organisation and characterisation of MHC Class I in cetaceans Delphinidae MHC Class I loci. Loci were obtained via NCBI’s BLAST function and includes exons two, three and four. Loci marked with an asterisk are pseudogenes. See also Table S1 for gene lengths, premature stop codons and indels.
Figure 4
Figure 4
Evolution and phylogenetic reconstruction of MHC Class I in cetaceans Maximum likelihood phylogenetic tree generated using aLRT statistics with branch lengths shown. Scale bar indicates evolutionary distance. Nodes denote loci, with the loci name being derived from the first two letters of the species’ scientific name and the number indicating location in the genome (Tutr-1 indicates Tursiops truncatus, locus one). Loci with an asterisk are pseudogenes. Clades discussed in the text are labeled (A–H).
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