Selection following gene duplication shapes recent genome evolution in the pea aphid acyrthosiphon pisum

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  • dc.contributor.author Fernández, Rosa
  • dc.contributor.author Marcet Houben, Marina
  • dc.contributor.author Legeai, Fabrice
  • dc.contributor.author Richard, Gautier
  • dc.contributor.author Robin, Stéphanie
  • dc.contributor.author Wucher, Valentin
  • dc.contributor.author Pegueroles Queralt, Maria Cinta
  • dc.contributor.author Gabaldón Estevan, Juan Antonio, 1973-
  • dc.contributor.author Tagu, Denis
  • dc.date.accessioned 2020-10-20T05:53:23Z
  • dc.date.available 2020-10-20T05:53:23Z
  • dc.date.issued 2020
  • dc.description.abstract Ecology of insects is as wide as their diversity, which reflects their high capacity of adaptation in most of the environments of our planet. Aphids, with over 4,000 species, have developed a series of adaptations including a high phenotypic plasticity and the ability to feed on the phloem sap of plants, which is enriched in sugars derived from photosynthesis. Recent analyses of aphid genomes have indicated a high level of shared ancestral gene duplications that might represent a basis for genetic innovation and broad adaptations. In addition, there are a large number of recent, species-specific gene duplications whose role in adaptation remains poorly understood. Here, we tested whether duplicates specific to the pea aphid Acyrthosiphon pisum are related to genomic innovation by combining comparative genomics, transcriptomics, and chromatin accessibility analyses. Consistent with large levels of neofunctionalization, we found that most of the recent pairs of gene duplicates evolved asymmetrically, showing divergent patterns of positive selection and gene expression. Genes under selection involved a plethora of biological functions, suggesting that neofunctionalization and tissue specificity, among other evolutionary mechanisms, have orchestrated the evolution of recent paralogs in the pea aphid and may have facilitated host-symbiont cooperation. Our comprehensive phylogenomics analysis allowed us to tackle the history of duplicated genes to pave the road toward understanding the role of gene duplication in ecological adaptation.
  • dc.description.sponsorship R.F. was funded by a Juan de la Cierva-Incorporación Fellowship (Government of Spain, IJCI-2015-26627) and a Marie Skłodowska-Curie Fellowship (747607). T.G. acknowledges support from the Spanish Ministry of Economy, Industry, and Competitiveness (MEIC) for the EMBL partnership, and grants “Centro de Excelencia Severo Ochoa 2013–2017” SEV-2012-0208, and BFU2015-67107 cofunded by European Regional Development Fund (ERDF); from the CERCA Programme/Generalitat de Catalunya; from the Catalan Research Agency (AGAUR) SGR857, and grant from the European Union’s Horizon 2020 research and innovation program under the grant agreement ERC-2016-724173 and the Marie Sklodowska-Curie (Grant Agreement No. H2020-MSCA-ITN-2014-642095). D.T. was funded by “Severo Ochoa visiting scientific program” for a 6 months stay at the Center for Genomic Regulation—Barcelona—to start the project, supported as well by INRA SPE. Dr Roderic Guigo (CRG, Barcelona) is warmly acknowledged for his welcome in his lab. Dr Akiko Sugio, Dr Julie Jaquiéry, Dr Gaël Le Trionnaire, and Dr Jean-Christophe Simon (INRAE, UMR 1349 Igepp, Rennes, France) are acknowledged for access to unpublished data of RNA-Seq. Daktulosphaira vitifoliae data were provided by the Phylloxera Genome Project (https://bipaa.genouest.org/is/aphidbase/): funding for D. vitifoliae clone Pcf genomic sequencing was provided by INRA (AIP Bioresources) and BGI Biotech in the frame of i5k initiative. Parts of the transcriptomic resources were obtained within the 1KITE projects (Bernhard Misof, Bonn, Germany). The Acyrthosiphon pisum phylome can be accessed at PhylomeDB 4.0 under phylome number 441
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Fernández R, Marcet-Houben M, Legeai F, Richard G, Robin S, Wucher V et al. Selection following gene duplication shapes recent genome evolution in the pea aphid acyrthosiphon pisum. Mol Biol Evol. 2020 Sep 1; 37(9): 2601-2615. DOI: 10.1093/molbev/msaa110
  • dc.identifier.doi http://dx.doi.org/10.1093/molbev/msaa110
  • dc.identifier.issn 0737-4038
  • dc.identifier.uri http://hdl.handle.net/10230/45511
  • dc.language.iso eng
  • dc.publisher Oxford University Press (OUP)
  • dc.relation.ispartof Molecular Biology and Evolution. 2020 Sep 1;37(9):2601-15
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/747607
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/724173
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/642095
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/BFU2015-67107
  • dc.rights © Rosa Fernández et al. 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by/4.0/
  • dc.subject.other Duplicació cromosòmica
  • dc.subject.other Genoma -- Evolució
  • dc.subject.other Pugons
  • dc.title Selection following gene duplication shapes recent genome evolution in the pea aphid acyrthosiphon pisum
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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