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

Roved, Jacob ; Hansson, Bengt LU orcid ; Stervander, Martin ; Hasselquist, Dennis LU and Westerdahl, Helena LU (2022) In Molecular Ecology Resources
Abstract

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... (More)

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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organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
cluster analysis, divergent allele advantage, functional divergence, major histocompatibility complex, MHC haplotypes, MHC supertypes
in
Molecular Ecology Resources
publisher
Wiley-Blackwell
external identifiers
  • pmid:35587892
  • scopus:85132330228
ISSN
1755-098X
DOI
10.1111/1755-0998.13645
language
English
LU publication?
yes
additional info
Funding Information: We wish to thank A. Drews and T. Johansson for library constructions and high‐throughput sequencing. Furthermore, we are grateful to S. Bensch, B. Nielsen, M. Åkesson, and staff at Kvismare Bird Observatory for considerable help with the great reed warbler fieldwork. Funding and support were provided by the Swedish Research Council (2016‐04391, 2020‐03976 to DH; 621‐2014‐5222, 2016‐00689 to BH; 2015‐05149, 2020‐04285 to HW), the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Starting grant 679799 to HW; Advanced grant 742646 to DH), a Linnaeus research excellence grant (349‐2007‐8690) from the Swedish Research Council and Lund University to the Centre for Animal Movement Research (CAnMove), Lunds Djurskyddsfond, Kungl. Fysiografiska Sällskapet i Lund (JR), and Kvismare Bird Observatory (report number 193). Publisher Copyright: © 2022 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.
id
bf8c5074-b842-47e2-9c2c-3db289d9962a
date added to LUP
2022-09-15 12:05:19
date last changed
2024-04-14 15:38:24
@article{bf8c5074-b842-47e2-9c2c-3db289d9962a,
  abstract     = {{<p>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.</p>}},
  author       = {{Roved, Jacob and Hansson, Bengt and Stervander, Martin and Hasselquist, Dennis and Westerdahl, Helena}},
  issn         = {{1755-098X}},
  keywords     = {{cluster analysis; divergent allele advantage; functional divergence; major histocompatibility complex; MHC haplotypes; MHC supertypes}},
  language     = {{eng}},
  publisher    = {{Wiley-Blackwell}},
  series       = {{Molecular Ecology Resources}},
  title        = {{MHCtools – an R package for MHC high-throughput sequencing data : Genotyping, haplotype and supertype inference, and downstream genetic analyses in non-model organisms}},
  url          = {{http://dx.doi.org/10.1111/1755-0998.13645}},
  doi          = {{10.1111/1755-0998.13645}},
  year         = {{2022}},
}