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/1822/65852 |
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 PeninsulaAdaptation, PhysiologicalAnimalsBeesDNA, IntergenicExonsGene FrequencyGene OntologyGenetic Association StudiesGenetics, PopulationGenomicsHaplotypesMalePolymorphism, Single NucleotidePortugalSelection, GeneticSpainWhole Genome SequencingGenome, InsectCiências Naturais::Ciências BiológicasScience & TechnologyThe 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.John C. Patton, Phillip San Miguel, Paul Parker, Rick Westerman, University of Purdue, resequenced the 87 whole genomes of IHBs. Jose Rufino provided computational resources at IPB. Analyses were performed using the computational resources at the Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX), Uppsala University. DH was supported by a PhD scholarship (SFRH/BD/84195/2012) from the Portuguese Science Foundation (FCT). MAP is a member of and receives support from the COST Action FA1307 (SUPER-B). This work was supported by FCT through the programs COMPETE/QREN/EU (PTDC/BIA-BEC/099640/2008) and the 2013-2014 BiodivERsA/FACCE-JPI (joint call for research proposals, with the national funders FCT, Portugal, CNRS, France, and MEC, Spain) to MAP.Nature ResearchUniversidade do MinhoHenriques, DoraWallberg, AndreasChávez-Galarza, JulioJohnston, J SpencerWebster, Matthew T.Pinto, Maria Alice20182018-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/65852engHenriques, D., Wallberg, A., Chávez-Galarza, J. et al. Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula. Sci Rep 8, 11145 (2018). https://doi.org/10.1038/s41598-018-29469-52045-232210.1038/s41598-018-29469-530042407https://www.nature.com/articles/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:RCAAP2023-07-21T11:55:34Zoai:repositorium.sdum.uminho.pt:1822/65852Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T18:45:06.122140Repositório 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, Physiological Animals Bees DNA, Intergenic Exons Gene Frequency Gene Ontology Genetic Association Studies Genetics, Population Genomics Haplotypes Male Polymorphism, Single Nucleotide Portugal Selection, Genetic Spain Whole Genome Sequencing Genome, Insect Ciências Naturais::Ciências Biológicas Science & Technology |
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, Maria Alice |
author_role |
author |
author2 |
Wallberg, Andreas Chávez-Galarza, Julio Johnston, J Spencer Webster, Matthew T. Pinto, Maria Alice |
author2_role |
author author author author author |
dc.contributor.none.fl_str_mv |
Universidade do Minho |
dc.contributor.author.fl_str_mv |
Henriques, Dora Wallberg, Andreas Chávez-Galarza, Julio Johnston, J Spencer Webster, Matthew T. Pinto, Maria Alice |
dc.subject.por.fl_str_mv |
Adaptation, Physiological Animals Bees DNA, Intergenic Exons Gene Frequency Gene Ontology Genetic Association Studies Genetics, Population Genomics Haplotypes Male Polymorphism, Single Nucleotide Portugal Selection, Genetic Spain Whole Genome Sequencing Genome, Insect Ciências Naturais::Ciências Biológicas Science & Technology |
topic |
Adaptation, Physiological Animals Bees DNA, Intergenic Exons Gene Frequency Gene Ontology Genetic Association Studies Genetics, Population Genomics Haplotypes Male Polymorphism, Single Nucleotide Portugal Selection, Genetic Spain Whole Genome Sequencing Genome, Insect Ciências Naturais::Ciências Biológicas Science & Technology |
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 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/1822/65852 |
url |
http://hdl.handle.net/1822/65852 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Henriques, D., Wallberg, A., Chávez-Galarza, J. et al. Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula. Sci Rep 8, 11145 (2018). https://doi.org/10.1038/s41598-018-29469-5 2045-2322 10.1038/s41598-018-29469-5 30042407 https://www.nature.com/articles/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.publisher.none.fl_str_mv |
Nature Research |
publisher.none.fl_str_mv |
Nature Research |
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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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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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) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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