Using bioinformatics to investigate functional diversity: a case study of MHC diversity in koalas

Luke W Silver; Elspeth A McLennan; Julian Beaman; Karen Burke da Silva; Peter Timms; Carolyn J Hogg; Katherine Belov

doi:10.1007/s00251-024-01356-6

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Using bioinformatics to investigate functional diversity: a case study of MHC diversity in koalas

Journal article

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Using bioinformatics to investigate functional diversity: a case study of MHC diversity in koalas

Luke W Silver, Elspeth A McLennan, Julian Beaman, Karen Burke da Silva, Peter Timms, Carolyn J Hogg and Katherine Belov

Immunogenetics, Vol.76, pp.381-395

2024

DOI: https://doi.org/10.1007/s00251-024-01356-6

PMCID: PMC11496358

PMID: 39367971

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Abstract

Whole genome resequencing

MHC

TLR

Koalas

Bioinformatics

Functional genomics

Conservation genomics can greatly improve conservation outcomes of threatened populations, including those impacted by disease. Understanding diversity within immune gene families, including the major histocompatibility complex (MHC) and toll-like receptors (TLR), is important due to the role they play in disease resilience and susceptibility. With recent advancements in sequencing technologies and bioinformatic tools, the cost of generating high-quality sequence data has significantly decreased and made it possible to investigate diversity across entire gene families in large numbers of individuals compared to investigating only a few genes or a few populations previously. Here, we use the koala as a case study for investigating functional diversity across populations. We utilised previous target enrichment data and 438 whole genomes to firstly, determine the level of sequencing depth required to investigate MHC diversity and, secondly, determine the current level of diversity in MHC genes in koala populations. We determined for low complexity, conserved genes such as TLR genes 10 × sequencing depth is sufficient to reliably genotype more than 90% of variants, whereas for complex genes such as the MHC greater than 20 × and preferably 30 × sequencing depth is required. We used whole genome data to identify 270 biallelic SNPs across 24 MHC genes as well as copy number variation (CNV) within class I and class II genes and conduct supertype analysis. Overall, we have provided a bioinformatic workflow for investigating variation in a complex immune gene family from whole genome sequencing data and determined current levels of diversity within koala MHC genes.

Details

Title: Using bioinformatics to investigate functional diversity: a case study of MHC diversity in koalas
Authors: Luke W Silver - The University of Sydney
Elspeth A McLennan - The University of Sydney
Julian Beaman - Flinders University
Karen Burke da Silva - Flinders University
Peter Timms (Author) - University of the Sunshine Coast, Queensland, Centre for Bioinnovation
Carolyn J Hogg (Corresponding Author) - The University of Sydney
Katherine Belov - The University of Sydney
Publication details: Immunogenetics, Vol.76, pp.381-395
Publisher: Springer
Date published: 2024
DOI: 10.1007/s00251-024-01356-6
ISSN: 1432-1211
PMID: 39367971; PMC11496358
Copyright note: This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
Grants: Will genetic rescue save the Tasmanian devil?, LP180100244, Australian Research Council (Australia, Canberra) - ARC
Designing successful genetic-rescue approaches for threatened species, LP210100450, Australian Research Council (Australia, Canberra) - ARC
Grant note: The Koala Genome Survey was funded by the NSW Government and the Australian Government’s Bushfire Recovery for Wildlife and their Habitats program (GA2000526).
Organisation Unit: Centre for Bioinnovation
Language: English
Record Identifier: 991066184302621
Output Type: Journal article

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Collaboration types: Domestic collaboration
Web Of Science research areas: Genetics & Heredity; Immunology

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