Cargando…
Reconstructing Macroevolutionary Patterns in Avian MHC Architecture With Genomic Data
The Major Histocompatibility Complex (MHC) is a hyper-polymorphic genomic region, which forms a part of the vertebrate adaptive immune system and is crucial for intra- and extra-cellular pathogen recognition (MHC-I and MHC-IIA/B, respectively). Although recent advancements in high-throughput sequenc...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2022
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8893315/ https://www.ncbi.nlm.nih.gov/pubmed/35251132 http://dx.doi.org/10.3389/fgene.2022.823686 |
_version_ | 1784662366029348864 |
---|---|
author | He, Ke Liang, Chun-hong Zhu, Ying Dunn, Peter Zhao, Ayong Minias, Piotr |
author_facet | He, Ke Liang, Chun-hong Zhu, Ying Dunn, Peter Zhao, Ayong Minias, Piotr |
author_sort | He, Ke |
collection | PubMed |
description | The Major Histocompatibility Complex (MHC) is a hyper-polymorphic genomic region, which forms a part of the vertebrate adaptive immune system and is crucial for intra- and extra-cellular pathogen recognition (MHC-I and MHC-IIA/B, respectively). Although recent advancements in high-throughput sequencing methods sparked research on the MHC in non-model species, the evolutionary history of MHC gene structure is still poorly understood in birds. Here, to explore macroevolutionary patterns in the avian MHC architecture, we retrieved contigs with antigen-presenting MHC and MHC-related genes from available genomes based on third-generation sequencing. We identified: 1) an ancestral avian MHC architecture with compact size and tight linkage between MHC-I, MHC-IIA/IIB and MHC-related genes; 2) three major patterns of MHC-IIA/IIB unit organization in different avian lineages; and 3) lineage-specific gene translocation events (e.g., separation of the antigen-processing TAP genes from the MHC-I region in passerines), and 4) the presence of a single MHC-IIA gene copy in most taxa, showing evidence of strong purifying selection (low dN/dS ratio and low number of positively selected sites). Our study reveals long-term macroevolutionary patterns in the avian MHC architecture and provides the first evidence of important transitions in the genomic arrangement of the MHC region over the last 100 million years of bird evolution. |
format | Online Article Text |
id | pubmed-8893315 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-88933152022-03-04 Reconstructing Macroevolutionary Patterns in Avian MHC Architecture With Genomic Data He, Ke Liang, Chun-hong Zhu, Ying Dunn, Peter Zhao, Ayong Minias, Piotr Front Genet Genetics The Major Histocompatibility Complex (MHC) is a hyper-polymorphic genomic region, which forms a part of the vertebrate adaptive immune system and is crucial for intra- and extra-cellular pathogen recognition (MHC-I and MHC-IIA/B, respectively). Although recent advancements in high-throughput sequencing methods sparked research on the MHC in non-model species, the evolutionary history of MHC gene structure is still poorly understood in birds. Here, to explore macroevolutionary patterns in the avian MHC architecture, we retrieved contigs with antigen-presenting MHC and MHC-related genes from available genomes based on third-generation sequencing. We identified: 1) an ancestral avian MHC architecture with compact size and tight linkage between MHC-I, MHC-IIA/IIB and MHC-related genes; 2) three major patterns of MHC-IIA/IIB unit organization in different avian lineages; and 3) lineage-specific gene translocation events (e.g., separation of the antigen-processing TAP genes from the MHC-I region in passerines), and 4) the presence of a single MHC-IIA gene copy in most taxa, showing evidence of strong purifying selection (low dN/dS ratio and low number of positively selected sites). Our study reveals long-term macroevolutionary patterns in the avian MHC architecture and provides the first evidence of important transitions in the genomic arrangement of the MHC region over the last 100 million years of bird evolution. Frontiers Media S.A. 2022-02-17 /pmc/articles/PMC8893315/ /pubmed/35251132 http://dx.doi.org/10.3389/fgene.2022.823686 Text en Copyright © 2022 He, Liang, Zhu, Dunn, Zhao and Minias. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Genetics He, Ke Liang, Chun-hong Zhu, Ying Dunn, Peter Zhao, Ayong Minias, Piotr Reconstructing Macroevolutionary Patterns in Avian MHC Architecture With Genomic Data |
title | Reconstructing Macroevolutionary Patterns in Avian MHC Architecture With Genomic Data |
title_full | Reconstructing Macroevolutionary Patterns in Avian MHC Architecture With Genomic Data |
title_fullStr | Reconstructing Macroevolutionary Patterns in Avian MHC Architecture With Genomic Data |
title_full_unstemmed | Reconstructing Macroevolutionary Patterns in Avian MHC Architecture With Genomic Data |
title_short | Reconstructing Macroevolutionary Patterns in Avian MHC Architecture With Genomic Data |
title_sort | reconstructing macroevolutionary patterns in avian mhc architecture with genomic data |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8893315/ https://www.ncbi.nlm.nih.gov/pubmed/35251132 http://dx.doi.org/10.3389/fgene.2022.823686 |
work_keys_str_mv | AT heke reconstructingmacroevolutionarypatternsinavianmhcarchitecturewithgenomicdata AT liangchunhong reconstructingmacroevolutionarypatternsinavianmhcarchitecturewithgenomicdata AT zhuying reconstructingmacroevolutionarypatternsinavianmhcarchitecturewithgenomicdata AT dunnpeter reconstructingmacroevolutionarypatternsinavianmhcarchitecturewithgenomicdata AT zhaoayong reconstructingmacroevolutionarypatternsinavianmhcarchitecturewithgenomicdata AT miniaspiotr reconstructingmacroevolutionarypatternsinavianmhcarchitecturewithgenomicdata |