Using bioinformatics to investigate functional diversity: a case study of MHC diversity in koalas.
Bioinformatics
Functional genomics
Koalas
MHC
TLR
Whole genome resequencing
Journal
Immunogenetics
ISSN: 1432-1211
Titre abrégé: Immunogenetics
Pays: United States
ID NLM: 0420404
Informations de publication
Date de publication:
05 Oct 2024
05 Oct 2024
Historique:
received:
17
06
2024
accepted:
15
09
2024
medline:
6
10
2024
pubmed:
6
10
2024
entrez:
5
10
2024
Statut:
aheadofprint
Résumé
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.
Identifiants
pubmed: 39367971
doi: 10.1007/s00251-024-01356-6
pii: 10.1007/s00251-024-01356-6
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Australian Research Council
ID : LP180100244
Organisme : Australian Research Council
ID : LP210100450
Organisme : Department of Climate Change, Energy, the Environment and Water
ID : GA2000526
Informations de copyright
© 2024. The Author(s).
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