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De novo assembled nuclear, chloroplast, and mitochondrial genomes show high intraspecific variation in the tropical rainforest species Symphonia globulifera

hal.structure.identifierInstituto de Ciencias Forestales [ICIFOR]
dc.contributor.authorOLSSON, Sanna
hal.structure.identifierUniversidad de Málaga [Málaga] = University of Málaga [Málaga]
dc.contributor.authorBAUTISTA, Rocío
hal.structure.identifierUniversidad de Málaga [Málaga] = University of Málaga [Málaga]
dc.contributor.authorCLAROS, M
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorHEUERTZ, Myriam
hal.structure.identifierEcologie des Forêts Méditerranéennes [URFM]
dc.contributor.authorSCOTTI, Ivan
dc.date.accessioned2025-10-02T02:01:35Z
dc.date.available2025-10-02T02:01:35Z
dc.date.issued2025-09-10
dc.identifier.issn2160-1836
dc.identifier.urihttps://oskar-bordeaux.fr/handle/20.500.12278/207703
dc.description.abstractEnSymphonia globulifera (Clusiaceae) has emerged as a model organism in tropical forest ecology and evolution due to its significant ecological role and complex biogeographical history. Originating from Africa, this species has independently colonized Caribbean, Central, and South America three times, becoming a key component of tropical ecosystems across these regions. Despite the ecological importance of S. globulifera and other tropical tree species, our understanding of their genomic architecture remains limited compared to temperate species. To bridge this gap, we present a comparative analysis of two de novo assembled nuclear genomes of S. globulifera—one from a South American individual and one from an African individual—and report newly assembled chloroplast and mitochondrial genomes. Initial assembly of the organelles was performed using GetOrganelle, and the results were compared with corresponding publicly available sequences from closely related Garcinia species. Our study introduces novel genomic resources, including an annotated nuclear draft genome based on Illumina short reads, the first chloroplast genome assembly for the genus, and a set of assembled mitochondrial gene sequences. Additionally, we provide a set of single-copy nuclear gene alignments identified by BUSCO as well as manually curated coding plastid genes, which will serve as valuable tools for future comparative analyses and phylogenetic studies. Our preliminary results based on chloroplast genes and limited sampling suggest that Garcinia might be nonmonophyletic. The detected differences in nuclear and organellar genomes reveal high intraspecific variation, emphasizing the importance of genome-wide sampling for understanding tropical tree evolution.
dc.description.sponsorshipGénétique écologique des arbres forestiers : interactions entre flux de gènes et variabilité environnementale dans la détermination de l'adaptation locale et du potentiel d'adaptation - ANR-12-ADAP-0007
dc.language.isoen
dc.publisherGenetics Society of America
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.subject.enphylogeny
dc.subject.enmarkers
dc.subject.enorganelles
dc.subject.engenomic diversity
dc.subject.engenome assembly
dc.subject.entropical trees
dc.title.enDe novo assembled nuclear, chloroplast, and mitochondrial genomes show high intraspecific variation in the tropical rainforest species Symphonia globulifera
dc.typeArticle de revue
dc.identifier.doi10.1093/g3journal/jkaf208
dc.subject.halSciences du Vivant [q-bio]/Génétique/Génétique des plantes
bordeaux.journalG3
bordeaux.hal.laboratoriesBioGeCo (Biodiversité Gènes & Communautés) - UMR 1202*
bordeaux.institutionUniversité de Bordeaux
bordeaux.institutionINRAE
bordeaux.peerReviewedoui
hal.identifierhal-05291758
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-05291758v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=G3&rft.date=2025-09-10&rft.eissn=2160-1836&rft.issn=2160-1836&rft.au=OLSSON,%20Sanna&BAUTISTA,%20Roc%C3%ADo&CLAROS,%20M&HEUERTZ,%20Myriam&SCOTTI,%20Ivan&rft.genre=article


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