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A High Quality Draft Assembly of the Diploid 'Regina' Sweet Cherry Genome

hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorLE DANTEC, Loick
dc.contributor.authorGIROLLET, Nabil
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorFOUCHE, Mathieu
hal.structure.identifierLaboratoire des interactions plantes micro-organismes [LIPM]
dc.contributor.authorGOUZY, Jerome
hal.structure.identifierInteractions plantes-microorganismes et santé végétale
dc.contributor.authorSALLET, Erika
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorQUERO-GARCIA, José
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorBARRENECHE, Teresa
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorWENDEN, Bénédicte
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorDIRLEWANGER, Elisabeth
dc.date.conference2018-01-13
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 self-incompatible, and therefore has a heterozygous genetic background. We have sequenced and assembled the genome of the 'Regina' sweet cherry variety, which is a late blooming cultivar. Here we present a draft phased sweet cherry genome assembly using a combination of sequencing strategies (long reads sequencing with PacBio RSII and optical mapping with BioNano whole-genome maps). CONCLUSION. PacBio long reads were de novo assembled using FALCON assembler and phased using FALCON UNZIP. BioNano optical whole genome maps were used for further scaffolding. Our de novo genome assembly resulted in a genome of 279 Mb (83 % of estimated genome size), 92 scaffolds and a largest scaffold of 16,3 Mb. The assembly has high contiguity (contig N50 1,23Mb, scaffold N50 ~6Mb) and good completeness with 95,9% BUSCO genes complete (scaffolds+ unscaffolded contigs). We are now in the process of reconstructing the pseudo molecules using high density genetic linkage maps and GBS data. Structural annotation is on the way using the integrative EuGene platform with different sources of evidence available for gene prediction including transcriptomic data from Regina obtained previously in the lab (Unigene set and RNASeq).
dc.language.isoen
dc.title.enA High Quality Draft Assembly of the Diploid 'Regina' Sweet Cherry Genome
dc.typeAutre communication scientifique (congrès sans actes - poster - séminaire...)
dc.subject.halSciences du Vivant [q-bio]/Biochimie, Biologie Moléculaire/Génomique, Transcriptomique et Protéomique [q-bio.GN]
dc.subject.halInformatique [cs]/Bio-informatique [q-bio.QM]
bordeaux.countryUS
bordeaux.conference.citySan Diego
bordeaux.peerReviewedoui
hal.identifierhal-01865005
hal.version1
hal.invitednon
hal.proceedingsnon
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-01865005v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.au=LE%20DANTEC,%20Loick&GIROLLET,%20Nabil&FOUCHE,%20Mathieu&GOUZY,%20Jerome&SALLET,%20Erika&rft.genre=conference


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