Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula
Autor(a) principal: | |
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Data de Publicação: | 2018 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/10198/18645 |
Resumo: | The availability of powerful high-throughput genomic tools, combined with genome scans, has helped identifying genes and genetic changes responsible for environmental adaptation in many organisms, including the honeybee. Here, we resequenced 87 whole genomes of the honeybee native to Iberia and used conceptually different selection methods (Samβada, LFMM, PCAdapt, iHs) together with in sillico protein modelling to search for selection footprints along environmental gradients. We found 670 outlier SNPs, most of which associated with precipitation, longitude and latitude. Over 88.7% SNPs laid outside exons and there was a significant enrichment in regions adjacent to exons and UTRs. Enrichment was also detected in exonic regions. Furthermore, in silico protein modelling suggests that several non-synonymous SNPs are likely direct targets of selection, as they lead to amino acid replacements in functionally important sites of proteins. We identified genomic signatures of local adaptation in 140 genes, many of which are putatively implicated in fitness-related functions such as reproduction, immunity, olfaction, lipid biosynthesis and circadian clock. Our genome scan suggests that local adaptation in the Iberian honeybee involves variations in regions that might alter patterns of gene expression and in protein-coding genes, which are promising candidates to underpin adaptive change in the honeybee. |
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Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian PeninsulaAdaptationGenomicsLocal adaptationThe availability of powerful high-throughput genomic tools, combined with genome scans, has helped identifying genes and genetic changes responsible for environmental adaptation in many organisms, including the honeybee. Here, we resequenced 87 whole genomes of the honeybee native to Iberia and used conceptually different selection methods (Samβada, LFMM, PCAdapt, iHs) together with in sillico protein modelling to search for selection footprints along environmental gradients. We found 670 outlier SNPs, most of which associated with precipitation, longitude and latitude. Over 88.7% SNPs laid outside exons and there was a significant enrichment in regions adjacent to exons and UTRs. Enrichment was also detected in exonic regions. Furthermore, in silico protein modelling suggests that several non-synonymous SNPs are likely direct targets of selection, as they lead to amino acid replacements in functionally important sites of proteins. We identified genomic signatures of local adaptation in 140 genes, many of which are putatively implicated in fitness-related functions such as reproduction, immunity, olfaction, lipid biosynthesis and circadian clock. Our genome scan suggests that local adaptation in the Iberian honeybee involves variations in regions that might alter patterns of gene expression and in protein-coding genes, which are promising candidates to underpin adaptive change in the honeybee.Biblioteca Digital do IPBHenriques, DoraWallberg, AndreasChávez-Galarza, JulioJohnston, J. SpencerWebster, Matthew T.Pinto, M. Alice2018-01-19T10:00:00Z20182018-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10198/18645engHenriques, Dora; Wallberg, Andreas; Chávez-Galarza, Julio; Johnston, J. Spencer; Webster, Matthew T.; Pinto, M. Alice (2018). Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula. Scientific Reports. ISSN 2045-2322. 8:12045-232210.1038/s41598-018-29469-5info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-11-21T10:42:50Zoai:bibliotecadigital.ipb.pt:10198/18645Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T23:09:02.487583Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula |
title |
Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula |
spellingShingle |
Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula Henriques, Dora Adaptation Genomics Local adaptation |
title_short |
Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula |
title_full |
Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula |
title_fullStr |
Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula |
title_full_unstemmed |
Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula |
title_sort |
Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula |
author |
Henriques, Dora |
author_facet |
Henriques, Dora Wallberg, Andreas Chávez-Galarza, Julio Johnston, J. Spencer Webster, Matthew T. Pinto, M. Alice |
author_role |
author |
author2 |
Wallberg, Andreas Chávez-Galarza, Julio Johnston, J. Spencer Webster, Matthew T. Pinto, M. Alice |
author2_role |
author author author author author |
dc.contributor.none.fl_str_mv |
Biblioteca Digital do IPB |
dc.contributor.author.fl_str_mv |
Henriques, Dora Wallberg, Andreas Chávez-Galarza, Julio Johnston, J. Spencer Webster, Matthew T. Pinto, M. Alice |
dc.subject.por.fl_str_mv |
Adaptation Genomics Local adaptation |
topic |
Adaptation Genomics Local adaptation |
description |
The availability of powerful high-throughput genomic tools, combined with genome scans, has helped identifying genes and genetic changes responsible for environmental adaptation in many organisms, including the honeybee. Here, we resequenced 87 whole genomes of the honeybee native to Iberia and used conceptually different selection methods (Samβada, LFMM, PCAdapt, iHs) together with in sillico protein modelling to search for selection footprints along environmental gradients. We found 670 outlier SNPs, most of which associated with precipitation, longitude and latitude. Over 88.7% SNPs laid outside exons and there was a significant enrichment in regions adjacent to exons and UTRs. Enrichment was also detected in exonic regions. Furthermore, in silico protein modelling suggests that several non-synonymous SNPs are likely direct targets of selection, as they lead to amino acid replacements in functionally important sites of proteins. We identified genomic signatures of local adaptation in 140 genes, many of which are putatively implicated in fitness-related functions such as reproduction, immunity, olfaction, lipid biosynthesis and circadian clock. Our genome scan suggests that local adaptation in the Iberian honeybee involves variations in regions that might alter patterns of gene expression and in protein-coding genes, which are promising candidates to underpin adaptive change in the honeybee. |
publishDate |
2018 |
dc.date.none.fl_str_mv |
2018-01-19T10:00:00Z 2018 2018-01-01T00:00:00Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10198/18645 |
url |
http://hdl.handle.net/10198/18645 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Henriques, Dora; Wallberg, Andreas; Chávez-Galarza, Julio; Johnston, J. Spencer; Webster, Matthew T.; Pinto, M. Alice (2018). Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula. Scientific Reports. ISSN 2045-2322. 8:1 2045-2322 10.1038/s41598-018-29469-5 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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RCAAP |
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RCAAP |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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1799135350795272192 |