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Development of genomic tools in a widespread tropical tree, Symphonia globulifera L.f.: a new low-coverage draft genome, SNP and SSR markers

hal.structure.identifierCentro de Investigacion Forestal [INIA-CIFOR]
dc.contributor.authorOLSSON, Sanna
hal.structure.identifierDepartamento de Biología Molecular y Bioquímica, and Plataforma Andaluza de Bioinformática
dc.contributor.authorSEOANE ZONJIC, Pedro
hal.structure.identifierDepartamento de Biología Molecular y Bioquímica, and Plataforma Andaluza de Bioinformática
dc.contributor.authorBAUTISTA, Rocío
hal.structure.identifierDepartamento de Biología Molecular y Bioquímica, and Plataforma Andaluza de Bioinformática
dc.contributor.authorCLAROS, M. Gonzalo
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
hal.structure.identifierCentro de Investigacion Forestal [INIA-CIFOR]
dc.contributor.authorGONZALEZ MARTINEZ, Santiago
hal.structure.identifierEcologie des Forêts Méditerranéennes [URFM]
dc.contributor.authorSCOTTI, Ivan
hal.structure.identifierEcologie des Forêts Méditerranéennes [URFM]
dc.contributor.authorSCOTTI-SAINTAGNE, Caroline
hal.structure.identifierFaculté des Sciences, Evolutionary Biology and Ecology
dc.contributor.authorHARDY, Olivier J.
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
hal.structure.identifierCentro de Investigacion Forestal [INIA-CIFOR]
dc.contributor.authorHEUERTZ, Myriam
dc.date.issued2016
dc.identifier.issn1755-098X
dc.description.abstractEnPopulation genetic studies in tropical plants are often challenging because of limited information on taxonomy, phylogenetic relationships and distribution ranges, scarce genomic information and logistic challenges in sampling. We describe a strategy to develop robust and widely applicable genetic markers based on a modest development of genomic resources in the ancient tropical tree species Symphonia globulifera L. f. (Clusiaceae), a keystone species in African and Neotropical rainforests. We provide the first low-coverage (11X) fragmented draft genome sequenced on an individual from Cameroon, covering 1.027 Gbp or 67.5% of the estimated genome size. Annotation of 565 scaffolds (7.57 Mbp) resulted in the prediction of 1,046 putative genes (231 of them containing a complete ORF) and 1523 exact simple sequence repeats (SSRs, microsatellites). Aligning a published transcriptome of a French Guiana population against this draft genome produced 923 high quality single nucleotide polymorphisms (SNPs). We also preselected genic SSRs in silico that were conserved and polymorphic across a wide geographical range, thus reducing marker development tests on rare DNA samples. Out of 23 SSRs tested, 19 amplified and 18 were successfully genotyped in four S. globulifera populations from South America (Brazil and French Guiana) and Africa (Cameroon and São Tomé island, FST=0.34). Most loci showed only population-specific deviations from Hardy-Weinberg proportions, pointing to local population effects (e.g., null alleles). The described genomic resources are valuable for evolutionary studies in Symphonia and for comparative studies in plants. The methods are especially interesting for widespread tropical or endangered taxa with limited DNA availability.
dc.language.isoen
dc.publisherWiley/Blackwell
dc.subjectsymphonia globulifera
dc.subjectarbre tropical
dc.subjecttranscriptome
dc.subjectpolymorphisme nucléotidique simple (SNP)
dc.subjectmarqueur génétique
dc.subjectséquençage du génome
dc.subjectmarqueur ssr
dc.subjectmarqueur microsatellite
dc.subjectamérique du sud
dc.subjectafrique
dc.subject.enmicrosatellites
dc.subject.ensingle nucleotide polymorphisms
dc.subject.entranscriptomic
dc.subject.endraft genome
dc.subject.enclusiaceae
dc.subject.enmicrosatellite repeats
dc.title.enDevelopment of genomic tools in a widespread tropical tree, Symphonia globulifera L.f.: a new low-coverage draft genome, SNP and SSR markers
dc.typeArticle de revue
dc.identifier.doi10.1111/1755-0998.12605
dc.subject.halSciences de l'environnement/Biodiversité et Ecologie
dc.description.sponsorshipEuropeSpatially explicit mechanisms of Recent EVOLution in an African biodiversity hotspot
bordeaux.journalMolecular Ecology Resources
bordeaux.pagenp
bordeaux.volumeon-line
bordeaux.issue4
bordeaux.peerReviewedoui
hal.identifierhal-01512127
hal.version1
hal.popularnon
hal.audienceNon spécifiée
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-01512127v1
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