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A phase-resolved, chromosome-scale de novo assembly of the diploid 'Regina' sweet cherry genome.

hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorLE DANTEC, Loïck
hal.structure.identifierEcophysiologie et Génomique Fonctionnelle de la Vigne [UMR EGFV]
dc.contributor.authorGIROLLET, Nabil
hal.structure.identifierLaboratoire des Interactions Plantes Microbes Environnement [LIPME]
dc.contributor.authorGOUZY, Jérôme
hal.structure.identifierLaboratoire des Interactions Plantes Microbes Environnement [LIPME]
dc.contributor.authorSALLET, Erika
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorDONKPEGAN, Armel
hal.structure.identifierPhase Genomics [Seattle]
dc.contributor.authorSULLIVAN, Shawn
hal.structure.identifierPhase Genomics [Seattle]
dc.contributor.authorMANGELSON, Hayley
hal.structure.identifierPhase Genomics [Seattle]
dc.contributor.authorLANGFORD, Kyle
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorFOUCHÉ, Mathieu
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorQUERO-GARCIA, Jose
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorDIRLEWANGER, Elisabeth
dc.date.conference2020-12-09
dc.description.abstractEnSweet cherry (Prunus avium L.) is a diploid species with an estimated genome size of 338 MB (Arumuganathan et al. 1991). It is mostly selfincompatible, and therefore has a heterozygous genetic background. We have sequenced the genome of the 'Regina' sweet cherry variety, which is a late blooming cultivar. Here we present whole-chromosomes assembly and phasing using a combination of long read sequencing, proximity ligation (HiC) data and GBS markers.Regina PacBio long reads were de novo assembled using FALCON UNZIP. A first assembly using optical mapping and high density genetic linkage maps with GBS data resulted in a genome of 264,8 Mb (78,4 % of estimated genome size) distributed on 8 linkage groups with a scaffold N50~6Mb (Regina V1). A new assembly (ReginaV2) combining Falcon Unzip assembly of PacBio long reads, proximity ligation (HiC) data and GBS markers has been done with Falcon Phased and the Proximo pipeline of Phase Genomics. It produced complete, fully phased, diploid chromosome scale scaffolds with a genome coverage of~90%, a N50 of~37 Mb and a complete BUSCO score of 95,6%. Structural and functional annotations of Regina V2 are in progress. Obtaining these phased chromosomes will allow very detailed studies of the allelic effects on the traits studied, in particular by making it possible to study the allelic expressions of candidate genes.
dc.language.isoen
dc.subjectAmélioration des plantes
dc.subject.ensweet cherry
dc.subject.enPrunus Avium L
dc.subject.enRegina
dc.subject.engenome
dc.title.enA phase-resolved, chromosome-scale de novo assembly of the diploid 'Regina' sweet cherry genome.
dc.typeAutre communication scientifique (congrès sans actes - poster - séminaire...)
dc.subject.halSciences du Vivant [q-bio]/Génétique/Génétique des plantes
dc.subject.halSciences du Vivant [q-bio]
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale
bordeaux.countryES
bordeaux.conference.cityBarcelone
bordeaux.peerReviewednon
hal.identifierhal-03318885
hal.version1
hal.invitednon
hal.proceedingsnon
hal.conference.end2020-12-18
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-03318885v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.au=LE%20DANTEC,%20Lo%C3%AFck&GIROLLET,%20Nabil&GOUZY,%20J%C3%A9r%C3%B4me&SALLET,%20Erika&DONKPEGAN,%20Armel&rft.genre=conference


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