The genomic architecture of the passerine MHC region: High repeat content and contrasting evolutionary histories of single copy and tandemly duplicated MHC genes

Westerdahl, Helena; Mellinger, Samantha; Sigeman, Hanna; Kutschera, Verena E.; Proux‐Wéra, Estelle; Lundberg, Max; Weissensteiner, Matthias H.; Churcher, Allison M.; Bunikis, Ignas; Hansson, Bengt; Wolf, Jochen B. W.; Strandh, Maria

doi:10.1111/1755-0998.13614

Cited by 24 publications

(32 citation statements)

References 86 publications

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“…Our analyses of allele segregation patterns indicated that MHC-I loci are tightly linked in the great reed warbler, with a recombination rate of 0.0030, corresponding to a genetic distance of 0.3 cM. A recent study confirmed this strong linkage by showing that MHC-I genes in the great reed warbler mainly are organized as tandemly duplicated genes within a small genomic region (Westerdahl et al, 2022).…”

Section: Discussionsupporting

confidence: 61%

MHCtools – an R package for MHC high‐throughput sequencing data: Genotyping, haplotype and supertype inference, and downstream genetic analyses in non‐model organisms

Roved

Hansson

Stervander

et al. 2022

Molecular Ecology Resources

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The major histocompatibility complex (MHC) plays a central role in the vertebrate adaptive immune system and has been of long‐term interest in evolutionary biology. While several protocols have been developed for MHC genotyping, there is a lack of transparent and standardized tools for downstream analysis of MHC data. Here, we present the r package mhctools and demonstrate the use of its functions to (i) assist accurate MHC genotyping from high‐throughput amplicon‐sequencing data, (ii) infer functional MHC supertypes using bootstrapped clustering analysis, (iii) identify segregating MHC haplotypes from family data, and (iv) analyse functional and genetic distances between MHC sequences. We employed mhctools to analyse MHC class I (MHC‐I) amplicon data of 559 great reed warblers (Acrocephalus arundinaceus). We identified 390 MHC‐I alleles which clustered into 14 functional supertypes. A phylogenetic analysis and analyses of positive selection suggested that the MHC‐I alleles belong to several distinct functional groups. We furthermore identified 107 segregating haplotypes among 116 families, and found substantial variation in diversity with 4–21 MHC‐I alleles and 3–13 MHC‐I supertypes per haplotype. Finally, we show that the great reed warbler haplotypes harboured combinations of MHC‐I supertypes with greater functional divergence than observed in simulated populations of possible haplotypes, a result that is in accordance with the divergent allele advantage hypothesis. Our study demonstrates the power of mhctools to support genotyping and analysis of MHC in non‐model species, which we hope will encourage broad implementation among researchers in MHC genetics and evolution.

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Section: Discussionsupporting

confidence: 61%

MHCtools – an R package for MHC high‐throughput sequencing data: Genotyping, haplotype and supertype inference, and downstream genetic analyses in non‐model organisms

Roved

Hansson

Stervander

et al. 2022

Molecular Ecology Resources

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“…Major Histocompatability Complex (MHC) diversity is altered in some avian species [ 17 ], which may affect susceptibility to disease [ 18 ]. We therefore compared MHC loci between black and mute swans.…”

Section: Resultsmentioning

confidence: 99%

The swan genome and transcriptome, it is not all black and white

et al. 2023

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Background The Australian black swan (Cygnus atratus) is an iconic species with contrasting plumage to that of the closely related northern hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune repertoire and increased susceptibility to infectious diseases, notably infectious diseases from which Australia has been largely shielded. Unlike mallard ducks and the mute swan (Cygnus olor), the black swan is extremely sensitive to highly pathogenic avian influenza. Understanding this susceptibility has been impaired by the absence of any available swan genome and transcriptome information. Results Here, we generate the first chromosome-length black and mute swan genomes annotated with transcriptome data, all using long-read based pipelines generated for vertebrate species. We use these genomes and transcriptomes to show that unlike other wild waterfowl, black swans lack an expanded immune gene repertoire, lack a key viral pattern-recognition receptor in endothelial cells and mount a poorly controlled inflammatory response to highly pathogenic avian influenza. We also implicate genetic differences in SLC45A2 gene in the iconic plumage of the black swan. Conclusion Together, these data suggest that the immune system of the black swan is such that should any avian viral infection become established in its native habitat, the black swan would be in a significant peril.

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“…MHC diversity is altered in some avian species 17 , which may affect susceptibility to disease 18 . We therefore compared MHC loci between black and mute swans.…”

Section: Black and Mute Swan Classical Mhc Class Loci Are Homologousmentioning

confidence: 99%

The swan genome and transcriptome: its not all black and white

Karawita

Cheng

Chew

et al. 2022

Preprint

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The Australian black swan (Cygnus atratus) is an iconic species with contrasting plumage to that of the closely related Northern Hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune repertoire and increased susceptibility to infectious disease, notably infectious diseases from which Australia has been largely shielded. Indeed, unlike Mallard ducks and the mute swan (Cygnus olor), the black swan is extremely sensitive to severe highly pathogenic avian influenza (HPAI). Understanding this susceptibility has been impaired by the absence of any available swan genome and transcriptome information. Here, we generate the first chromosome-length annotated black and mute swan genomes annotated with transcriptome data, all using long-read based pipelines generated for vertebrate species. We used these genomes and transcriptomes, to show that unlike other wild waterfowl, black swans lack an expanded immune gene repertoire, lack a key viral pattern-recognition receptor in endothelial cells and mount a poorly controlled inflammatory response to HPAI. We also implicate genetic differences in SLC45A2 in the iconic plumage of the Australian black swan. Together, these data suggest that the immune system of the black swan is such that should any avian viral infection become established in its native habitat the survival of the black swan would be in significant peril.

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The genomic architecture of the passerine MHC region: High repeat content and contrasting evolutionary histories of single copy and tandemly duplicated MHC genes

Cited by 24 publications

References 86 publications

MHCtools – an R package for MHC high‐throughput sequencing data: Genotyping, haplotype and supertype inference, and downstream genetic analyses in non‐model organisms

MHCtools – an R package for MHC high‐throughput sequencing data: Genotyping, haplotype and supertype inference, and downstream genetic analyses in non‐model organisms

The swan genome and transcriptome, it is not all black and white

The swan genome and transcriptome: its not all black and white

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