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Whole-genome draft assembly of Populus tremula x P. alba clone INRA 717-1B4

hal.structure.identifierJohann Heinrich von Thünen Institut
dc.contributor.authorMADER, Malte
hal.structure.identifierEtude du Polymorphisme des Génomes Végétaux [EPGV]
dc.contributor.authorLE PASLIER, Marie-Christine
hal.structure.identifierEtude du Polymorphisme des Génomes Végétaux [EPGV]
dc.contributor.authorBOUNON, Rémi
hal.structure.identifierEtude du Polymorphisme des Génomes Végétaux [EPGV]
dc.contributor.authorBERARD, Aurélie
hal.structure.identifierEtude du Polymorphisme des Génomes Végétaux [EPGV]
dc.contributor.authorFAIVRE-RAMPANT, Patricia
hal.structure.identifierJohann Heinrich von Thünen Institut
dc.contributor.authorFLADUNG, Matthias
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
hal.structure.identifierUnité de recherche Amélioration, Génétique et Physiologie Forestières [AGPF]
dc.contributor.authorLEPLÉ, Jean-Charles
hal.structure.identifierJohann Heinrich von Thünen Institut
dc.contributor.authorKERSTEN, Birgit
dc.date.issued2016
dc.identifier.issn0037-5349
dc.description.abstractEnPopulus trichocarpa and P. deltoides are the only Populus species known to date to have a publicly available nuclear genome sequence that has been assembled to chromosomes and annotated (https://phytozome.jgi.doe.gov/). Here we focus on the clone INRA 717-1B4, a female P. tremula x P. alba (P. x canescens) interspecific hybrid that is universally used by scientists worldwide as a tree model in transgenic experiments. The already available INRA 717-1B4 nuclear genomic resource (v1.1 of sPta717 at http://aspendb.uga.edu/index.php/databases/spta-717-genome) presents only INRA 717-1B4 genomic regions with high similarity to the P. trichocarpa genomic reference sequences. We assembled draft genomic scaffolds by a combination of de novo assembly with reference-based assembly using 30x resequencing NGS data (Illumina MiSeq® and Ion Torrent Ion PGM™) of INRA 717-1B4. In total, 419,969 scaffolds of length larger than 500 bp were generated. The mean length of the scaffolds is 2,166 bp and the size of the largest scaffold 84,573 bp. The N50 contig length is 3,850 bp when considering contigs larger than 1,000 bp. Probably due to the high level of heterozygosity of this interspecific hybrid, the accumulated scaffold length is with 0.9 GB about twice the expected size of the haploid nuclear genome. DNA sequences of the genomic scaffolds of INRA 717-1B4 are publicly available for Blast analyses and download via the new INRA web portal at https://urgi.versailles.inra.fr/Species/Forest-trees/Populus/Clone-INRA-717-1B4/. This new genomic sequence resource will complement the already available INRA 717-1B4 resources and will facilitate the future optimization of genetic transformation experiments to discover gene function.
dc.language.isoen
dc.publisherWalter De Gruyter
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/
dc.subjectINRA 717-1B4
dc.subjectP. x canescens
dc.subjectpoplars
dc.subject.ennext generation sequencing
dc.subject.engenome assembly
dc.subject.enscaffolds
dc.subject.enmodel tree
dc.title.enWhole-genome draft assembly of Populus tremula x P. alba clone INRA 717-1B4
dc.typeArticle de revue
dc.identifier.doi10.1515/sg-2016-0019
dc.subject.halSciences du Vivant [q-bio]
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale
bordeaux.journalSilvae Genetica
bordeaux.page74-79
bordeaux.volume65
bordeaux.issue2
bordeaux.peerReviewedoui
hal.identifierhal-02637979
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02637979v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Silvae%20Genetica&rft.date=2016&rft.volume=65&rft.issue=2&rft.spage=74-79&rft.epage=74-79&rft.eissn=0037-5349&rft.issn=0037-5349&rft.au=MADER,%20Malte&LE%20PASLIER,%20Marie-Christine&BOUNON,%20R%C3%A9mi&BERARD,%20Aur%C3%A9lie&FAIVRE-RAMPANT,%20Patricia&rft.genre=article


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