Afficher la notice abrégée

Development of genomic resources for Nothofagus species using next-generation sequencing data

hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
hal.structure.identifierInstituto Nacional de Tecnología Agropecuaria [INTA]
dc.contributor.authorEL MUJTAR, Veronica
hal.structure.identifierInstituto Nacional de Tecnología Agropecuaria [INTA]
dc.contributor.authorGALLO, L.A.
hal.structure.identifierChinese Academy of Agricultural Sciences [CAAS]
dc.contributor.authorLANG, T.
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorGARNIER‐GÉRÉ, Pauline
dc.date.accessioned2022-10-12T13:03:38Z
dc.date.available2022-10-12T13:03:38Z
dc.date.issued2014
dc.identifier.issn1755-098X
dc.identifier.urihttps://oskar-bordeaux.fr/handle/20.500.12278/157617
dc.description.abstractEnUsing next-generation sequencing, we developed the first whole-genome resources for two hybridizing Nothofagus species of the Patagonian forests that crucially lack genomic data, despite their ecological and industrial value. A de novo assembly strategy combining base quality control and optimization of the putative chloroplast gene map yielded ~32 000 contigs from 43% of the reads produced. With 12.5% of assembled reads, we covered ~96% of the chloroplast genome and ~70% of the mitochondrial gene content, providing functional and structural annotations for 112 and 52 genes, respectively. Functional annotation was possible on 15% of the contigs, with ~1750 potentially novel nuclear genes identified for Nothofagus species. We estimated that the new resources (13.41 Mb in total) included ~4000 gene regions representing ~6.5% of the expected genic partition of the genome, the remaining contigs potentially being nongenic DNA. A high-quality single nucleotide polymorphisms resource was developed by comparing various filtering methods, and preliminary results indicate a strong conservation of cpDNA genomes in contrast to numerous exclusive nuclear polymorphisms in both species. Finally, we characterized 2274 potential simple sequence repeat (SSR) loci, designed primers for 769 of them and validated nine of 29 loci in 42 individuals per species. Nothofagus obliqua had more alleles (4.89) on average than N. nervosa (2.89), 8 SSRs were efficient to discriminate species, and three were successfully transferred in three other Nothofagus species. These resources will greatly help for future inferences of demographic, adaptive and hybridizing events in Nothofagus species, and for conserving and managing natural populations.
dc.language.isoen
dc.publisherWiley/Blackwell
dc.subject.en454 genome sequencing; hybridization; Nothofagus nervosa ; Nothofagus obliqua ; single nucleotide polymorphisms identification; species identification; SSR loci
dc.title.enDevelopment of genomic resources for Nothofagus species using next-generation sequencing data
dc.typeArticle de revue
dc.identifier.doi10.1111/1755-0998.12276
dc.subject.halSciences du Vivant [q-bio]
bordeaux.journalMolecular Ecology Resources
bordeaux.page1281-1295
bordeaux.volume14
bordeaux.hal.laboratoriesBioGeCo (Biodiversité Gènes & Communautés) - UMR 1202*
bordeaux.issue6
bordeaux.institutionUniversité de Bordeaux
bordeaux.institutionINRAE
bordeaux.peerReviewedoui
hal.identifierhal-02636859
hal.version1
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02636859v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Molecular%20Ecology%20Resources&rft.date=2014&rft.volume=14&rft.issue=6&rft.spage=1281-1295&rft.epage=1281-1295&rft.eissn=1755-098X&rft.issn=1755-098X&rft.au=EL%20MUJTAR,%20Veronica&GALLO,%20L.A.&LANG,%20T.&GARNIER%E2%80%90G%C3%89R%C3%89,%20Pauline&rft.genre=article


Fichier(s) constituant ce document

FichiersTailleFormatVue

Il n'y a pas de fichiers associés à ce document.

Ce document figure dans la(les) collection(s) suivante(s)

Afficher la notice abrégée