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High-quality SNPs from genic regions highlight introgression patterns among European white oaks (Quercus petraea and Q. robur)

hal.structure.identifierJinan University [Guangzhou]
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLANG, Tiange
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorABADIE, Pierre
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLÉGER, Valérie
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorDECOURCELLE, Thibaut
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
hal.structure.identifierPleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
dc.contributor.authorFRIGERIO, Jean-Marc
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorBURBAN, Christian
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorBODENES, Catherine
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorGUICHOUX, Erwan
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLE PROVOST, Grégoire
hal.structure.identifierGéosciences Rennes [GR]
dc.contributor.authorROBIN, Cécile
hal.structure.identifierJapan International Research Center for Agricultural Sciences [JIRCAS]
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorTANI, Naoki
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLÉGER, Patrick
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLEPOITTEVIN, Camille
hal.structure.identifierInstituto Nacional de Tecnología Agropecuaria [INTA]
dc.contributor.authorEL MUJTAR, Veronica
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorHUBERT, François
hal.structure.identifierAgriculture Victoria [AgriBio]
dc.contributor.authorTIBBITS, Josquin
hal.structure.identifierInstituto de Biologia Experimental e Tecnológica [IBET]
hal.structure.identifierPolska Akademia Nauk = Polish Academy of Sciences = Académie polonaise des sciences [PAN]
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorPAIVA, Jorge
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
hal.structure.identifierPleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
dc.contributor.authorFRANC, Alain
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorRASPAIL, Frédéric
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorMARIETTE, Stéphanie
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorREVIRON, Marie-Pierre
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorPLOMION, Christophe
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorKREMER, Antoine
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorDESPREZ-LOUSTAU, Marie-Laure
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorGARNIER‐GÉRÉ, Pauline
dc.date.issued2021
dc.identifier.issn2803-9971
dc.description.abstractEnIn the post-genomics era, non-model species like most Fagaceae still lack operational diversity resources for population genomics studies. Sequence data were produced from over 800 gene fragments covering ~530 kb across the genic partition of European oaks, in a discovery panel of 25 individuals from western and central Europe (11 Quercus petraea, 13 Q. robur, one Q. ilex as an outgroup). Regions targeted represented broad functional categories potentially involved in species ecological preferences, and a random set of genes. Using a high-quality dedicated pipeline, we provide a detailed characterization of these genic regions, which included over 14500 polymorphisms, with ~12500 SNPs −218 being triallelic-, over 1500 insertion-deletions, and ~200 novel di- and tri-nucleotide SSR loci. This catalog also provides various summary statistics within and among species, gene ontology information, and standard formats to assist loci choice for genotyping projects. The distribution of nucleotide diversity (θπ) and differentiation (FST) across genic regions are also described for the first time in those species, with a mean n θπ close to ~0.0049 in Q. petraea and to ~0.0045 in Q. robur across random regions, and a mean FST ~0.13 across SNPs. The magnitude of diversity across genes is within the range estimated for long-term perennial outcrossers, and can be considered relatively high in the plant kingdom, with an estimate across the genome of 41 to 51 million SNPs expected in both species. Individuals with typical species morphology were more easily assigned to their corresponding genetic cluster for Q. robur than for Q. petraea, revealing higher or more recent introgression in Q. petraea and a stronger species integration in Q. robur in this particular discovery panel. We also observed robust patterns of a slightly but significantly higher diversity in Q. petraea, across a random gene set and in the abiotic stress functional category, and a heterogeneous landscape of both diversity and differentiation. To explain these patterns, we discuss an alternative and non-exclusive hypothesis of stronger selective constraints in Q. robur, the most pioneering species in oak forest stand dynamics, additionally to the recognized and documented introgression history in both species despite their strong reproductive barriers. The quality of the data provided here and their representativity in terms of species genomic diversity make them useful for possible applications in medium-scale landscape and molecular ecology projects. Moreover, they can serve as reference resources for validation purposes in larger-scale resequencing projects. This type of project is preferentially recommended in oaks in contrast to SNP array development, given the large nucleotide variation and the low levels of linkage disequilibrium revealed.
dc.language.isoen
dc.publisherPeer Community In
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/
dc.subject.enSanger amplicon resequencing
dc.subject.enIntrogression
dc.subject.enSpecies differentiation
dc.subject.enQ petraea
dc.subject.enQuercus robur
dc.subject.enFunctional candidate genes
dc.subject.enSNPs
dc.title.enHigh-quality SNPs from genic regions highlight introgression patterns among European white oaks (Quercus petraea and Q. robur)
dc.typeArticle de revue
dc.identifier.doi10.1101/388447
dc.subject.halSciences de l'environnement/Biodiversité et Ecologie
bordeaux.journalPeer Community In Forest & Wood Sciences
bordeaux.page1-33
bordeaux.peerReviewedoui
hal.identifierhal-01985021
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-01985021v1
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