A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies
This study was funded by a Royal Society Research Grants for Research Fellows (RGF\R1\181014) to E.C.G. E.C.G. is funded by a Royal Society University Research Fellowship (UF160081 & URF\R\221020). F.E. is supported by a University of St Andrews School of Biology Ph.D. scholarship and a Royal So...
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Online Access: | https://hdl.handle.net/10023/29556 https://doi.org/10.1111/1755-0998.13955 |
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ftstandrewserep:oai:research-repository.st-andrews.ac.uk:10023/29556 2024-05-12T08:04:59+00:00 A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies Heimeier, Dorothea Garland, Ellen Clare Eichenberger, Franca Garrigue, Claire Vella, Adriana Baker, C. Scott Carroll, Emma Louise The Royal Society University of St Andrews. Scottish Oceans Institute University of St Andrews. Centre for Biological Diversity University of St Andrews. Centre for Social Learning & Cognitive Evolution University of St Andrews. Sea Mammal Research Unit University of St Andrews. School of Biology 2024-03-26T17:30:02Z 19 4617823 application/pdf https://hdl.handle.net/10023/29556 https://doi.org/10.1111/1755-0998.13955 eng eng Molecular Ecology Resources 296384044 c635d73e-cde6-4953-b154-0ff89958783d 85189153212 Heimeier , D , Garland , E C , Eichenberger , F , Garrigue , C , Vella , A , Baker , C S & Carroll , E L 2024 , ' A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies ' , Molecular Ecology Resources , vol. Early View . https://doi.org/10.1111/1755-0998.13955 1755-098X ORCID: /0000-0002-8240-1267/work/156627482 https://hdl.handle.net/10023/29556 doi:10.1111/1755-0998.13955 RGF/R1/181014 RF\ERE\210306 URF/R/221020 Cetacean Humpback whale Major histocompatibility complex MHC evolution MHC organisation Southern right whale DAS Journal article 2024 ftstandrewserep https://doi.org/10.1111/1755-0998.13955 2024-04-17T14:02:43Z This study was funded by a Royal Society Research Grants for Research Fellows (RGF\R1\181014) to E.C.G. E.C.G. is funded by a Royal Society University Research Fellowship (UF160081 & URF\R\221020). F.E. is supported by a University of St Andrews School of Biology Ph.D. scholarship and a Royal Society Research Fellows Enhancement Award (RGF\EA\180213 to E.C.G). E.L.C. is funded by a Rutherford Discovery Fellowship from the Royal Society of New Zealand Te Apārangi. The major histocompatibility complex (MHC) is a highly polymorphic gene family that is crucial in immunity, and its diversity can be effectively used as a fitness marker for populations. Despite this, MHC remains poorly characterised in non-model species (e.g., cetaceans: whales, dolphins and porpoises) as high gene copy number variation, especially in the fast-evolving class I region, makes analyses of genomic sequences difficult. To date, only small sections of class I and IIa genes have been used to assess functional diversity in cetacean populations. Here, we undertook a systematic characterisation of the MHC class I and IIa regions in available cetacean genomes. We extracted full-length gene sequences to design pan-cetacean primers that amplified the complete exon2 from MHC class I and IIa genes in one combined sequencing panel. We validated this panel in 19 cetacean species and described 354 alleles for both classes. Furthermore, we identified likely assembly artefacts for many MHC class I assemblies based on the presence of class I genes in the amplicon data compared to missing genes from genomes. Finally, we investigated MHC diversity using the panel in 25 humpback and 30 southern right whales, including four paternity trios for humpback whales. This revealed copy-number variable class I haplotypes in humpback whales, which is likely a common phenomenon across cetaceans. These MHC alleles will form the basis for a cetacean branch of the Immuno-Polymorphism Database (IPD-MHC), a curated resource intended to aid in the systematic compilation ... Article in Journal/Newspaper Humpback Whale Southern Right Whale University of St Andrews: Digital Research Repository New Zealand Molecular Ecology Resources |
institution |
Open Polar |
collection |
University of St Andrews: Digital Research Repository |
op_collection_id |
ftstandrewserep |
language |
English |
topic |
Cetacean Humpback whale Major histocompatibility complex MHC evolution MHC organisation Southern right whale DAS |
spellingShingle |
Cetacean Humpback whale Major histocompatibility complex MHC evolution MHC organisation Southern right whale DAS Heimeier, Dorothea Garland, Ellen Clare Eichenberger, Franca Garrigue, Claire Vella, Adriana Baker, C. Scott Carroll, Emma Louise A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies |
topic_facet |
Cetacean Humpback whale Major histocompatibility complex MHC evolution MHC organisation Southern right whale DAS |
description |
This study was funded by a Royal Society Research Grants for Research Fellows (RGF\R1\181014) to E.C.G. E.C.G. is funded by a Royal Society University Research Fellowship (UF160081 & URF\R\221020). F.E. is supported by a University of St Andrews School of Biology Ph.D. scholarship and a Royal Society Research Fellows Enhancement Award (RGF\EA\180213 to E.C.G). E.L.C. is funded by a Rutherford Discovery Fellowship from the Royal Society of New Zealand Te Apārangi. The major histocompatibility complex (MHC) is a highly polymorphic gene family that is crucial in immunity, and its diversity can be effectively used as a fitness marker for populations. Despite this, MHC remains poorly characterised in non-model species (e.g., cetaceans: whales, dolphins and porpoises) as high gene copy number variation, especially in the fast-evolving class I region, makes analyses of genomic sequences difficult. To date, only small sections of class I and IIa genes have been used to assess functional diversity in cetacean populations. Here, we undertook a systematic characterisation of the MHC class I and IIa regions in available cetacean genomes. We extracted full-length gene sequences to design pan-cetacean primers that amplified the complete exon2 from MHC class I and IIa genes in one combined sequencing panel. We validated this panel in 19 cetacean species and described 354 alleles for both classes. Furthermore, we identified likely assembly artefacts for many MHC class I assemblies based on the presence of class I genes in the amplicon data compared to missing genes from genomes. Finally, we investigated MHC diversity using the panel in 25 humpback and 30 southern right whales, including four paternity trios for humpback whales. This revealed copy-number variable class I haplotypes in humpback whales, which is likely a common phenomenon across cetaceans. These MHC alleles will form the basis for a cetacean branch of the Immuno-Polymorphism Database (IPD-MHC), a curated resource intended to aid in the systematic compilation ... |
author2 |
The Royal Society University of St Andrews. Scottish Oceans Institute University of St Andrews. Centre for Biological Diversity University of St Andrews. Centre for Social Learning & Cognitive Evolution University of St Andrews. Sea Mammal Research Unit University of St Andrews. School of Biology |
format |
Article in Journal/Newspaper |
author |
Heimeier, Dorothea Garland, Ellen Clare Eichenberger, Franca Garrigue, Claire Vella, Adriana Baker, C. Scott Carroll, Emma Louise |
author_facet |
Heimeier, Dorothea Garland, Ellen Clare Eichenberger, Franca Garrigue, Claire Vella, Adriana Baker, C. Scott Carroll, Emma Louise |
author_sort |
Heimeier, Dorothea |
title |
A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies |
title_short |
A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies |
title_full |
A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies |
title_fullStr |
A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies |
title_full_unstemmed |
A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies |
title_sort |
pan-cetacean mhc amplicon sequencing panel developed and evaluated in combination with genome assemblies |
publishDate |
2024 |
url |
https://hdl.handle.net/10023/29556 https://doi.org/10.1111/1755-0998.13955 |
geographic |
New Zealand |
geographic_facet |
New Zealand |
genre |
Humpback Whale Southern Right Whale |
genre_facet |
Humpback Whale Southern Right Whale |
op_relation |
Molecular Ecology Resources 296384044 c635d73e-cde6-4953-b154-0ff89958783d 85189153212 Heimeier , D , Garland , E C , Eichenberger , F , Garrigue , C , Vella , A , Baker , C S & Carroll , E L 2024 , ' A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies ' , Molecular Ecology Resources , vol. Early View . https://doi.org/10.1111/1755-0998.13955 1755-098X ORCID: /0000-0002-8240-1267/work/156627482 https://hdl.handle.net/10023/29556 doi:10.1111/1755-0998.13955 RGF/R1/181014 RF\ERE\210306 URF/R/221020 |
op_doi |
https://doi.org/10.1111/1755-0998.13955 |
container_title |
Molecular Ecology Resources |
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1798847238030491648 |