The genomic architecture of the passerine MHC region: High repeat content and contrasting evolutionary histories of single copy and tandemly duplicated MHC genes.
Passeriformes
gene order
major histocompatibility complex (MHC)
repeats
single copy genes
tandemly duplicated genes
Journal
Molecular ecology resources
ISSN: 1755-0998
Titre abrégé: Mol Ecol Resour
Pays: England
ID NLM: 101465604
Informations de publication
Date de publication:
Aug 2022
Aug 2022
Historique:
revised:
09
03
2022
received:
11
11
2021
accepted:
23
03
2022
pubmed:
30
3
2022
medline:
7
7
2022
entrez:
29
3
2022
Statut:
ppublish
Résumé
The major histocompatibility complex (MHC) is of central importance to the immune system, and an optimal MHC diversity is believed to maximize pathogen elimination. Birds show substantial variation in MHC diversity, ranging from few genes in most bird orders to very many genes in passerines. Our understanding of the evolutionary trajectories of the MHC in passerines is hampered by lack of data on genomic organization. Therefore, we assembled and annotated the MHC genomic region of the great reed warbler (Acrocephalus arundinaceus), using long-read sequencing and optical mapping. The MHC region is large (>5.5 Mb), characterized by structural changes compared to hitherto investigated bird orders and shows higher repeat content than the genome average. These features were supported by analyses in three additional passerines. MHC genes in passerines are found in two different chromosomal arrangements, either as single copy MHC genes located among non-MHC genes, or as tandemly duplicated tightly linked MHC genes. Some single copy MHC genes are old and putative orthologues among species. In contrast tandemly duplicated MHC genes are monophyletic within species and have evolved by simultaneous gene duplication of several MHC genes. Structural differences in the MHC genomic region among bird orders seem substantial compared to mammals and have possibly been fuelled by clade-specific immune system adaptations. Our study provides methodological guidance in characterizing complex genomic regions, constitutes a resource for MHC research in birds, and calls for a revision of the general belief that avian MHC has a conserved gene order and small size compared to mammals.
Identifiants
pubmed: 35348299
doi: 10.1111/1755-0998.13614
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
2379-2395Subventions
Organisme : Vetenskapsrådet
ID : 621-2013-4510
Organisme : Vetenskapsrådet
ID : 621-2016-689
Organisme : H2020 European Research Council
ID : 336536
Organisme : H2020 European Research Council
ID : 679799
Organisme : Knut and Alice Wallenberg Foundation
Organisme : National Bioinformatics Infrastructure Sweden
Organisme : SciLifeLab
Organisme : NGI/Uppsala Genome Center
Organisme : UPPMAX
Organisme : Science for Life Laboratory, Sweden
Informations de copyright
© 2022 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.
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