The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding

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dc.bibliographicCitation.titleHorticulture Researchen
dc.contributor.authorGrimplet, Jérômees_ES
dc.contributor.authorShi, Xiaoyaes_ES
dc.contributor.authorCao, Shuoes_ES
dc.contributor.authorWang, Xues_ES
dc.contributor.authorHuang, Xiyanges_ES
dc.contributor.authorWang, Yuees_ES
dc.contributor.authorLiu, Zhongjiees_ES
dc.contributor.authorLiu, Wenwenes_ES
dc.contributor.authorLeng, Xiangpenges_ES
dc.contributor.authorPeng, Yanlinges_ES
dc.contributor.authorWang, Nanes_ES
dc.contributor.authorWang, Yiwenes_ES
dc.contributor.authorMa, Zhiyaoes_ES
dc.contributor.authorXu, Xiaodonges_ES
dc.contributor.authorZhang, Fanes_ES
dc.contributor.authorZhong, Haixiaes_ES
dc.contributor.authorWang, Yies_ES
dc.contributor.authorZhang, Kekunes_ES
dc.contributor.authorVelt, Amandinees_ES
dc.contributor.authorAvia, Komlanes_ES
dc.contributor.authorHoltgräwe, Danielaes_ES
dc.contributor.authorMatus, José Tomáses_ES
dc.contributor.authorWare, Doreenes_ES
dc.contributor.authorWu, Xinyues_ES
dc.contributor.authorWang, Haiboes_ES
dc.contributor.authorLiu, Chonghuaies_ES
dc.contributor.authorFang, Yulinges_ES
dc.contributor.authorRustenholz, Camillees_ES
dc.contributor.authorCheng, Zongminges_ES
dc.contributor.authorXiao, Huaes_ES
dc.contributor.authorZhou, Yongfenges_ES
dc.coverage.spatialCiencia Vegetal
dc.date.accessioned2023-04-11T11:04:05Z
dc.date.available2023-04-11T11:04:05Z
dc.date.issued2023es_ES
dc.date.updated2023-04-10T08:41:22Z
dc.description.abstractGrapevine is one of the most economically important crops worldwide. However, the previous versions of the grapevine reference genome consisted of thousands of fragments with missing centromeres and telomeres, which limited the accessibility of the repetitive sequences, the centromeric and telomeric regions, and the inheritance of important agronomic traits in these regions. Here, we assembled a telomere-to-telomere (T2T) gap-free reference genome for the pinot noir cultivar (PN40024) using the PacBio HiFi long reads. The T2T reference genome (PN_T2T) was 69 Mb longer with 9026 more genes identified than the 12X.v2 version (Canaguier et al., 2017). We annotated 67% repetitive sequences, 19 centromeres and 36 telomeres, and incorporated gene annotations of previous versions into the PN_T2T. We detected a total of 377 gene clusters, which showed associations with complex traits, such as aroma and disease resistance. Even though the PN40024 sample had been selfed for nine generations, we still found nine genomic hotspots of heterozygous sites associated with biological processes, such as the oxidation-reduction process and protein phosphorylation. The fully annotated complete reference genome, therefore, provides important resources for grapevine genetics and breeding.en
dc.description.otherViticulture
dc.description.otherT2T
dc.description.othergap-fre
dc.description.othergene cluster
dc.description.othercentromere
dc.description.othertelomere
dc.description.sponsorshipThis work was supported by the National Natural Science Fund for Excellent Young Scientists Fund Program (Overseas) to Yongfeng Zhou, the National Key Research and Development Program of China(grant2019YFA0906200), the Agricultural Science and Technology Innovation Program (CAAS-ZDRW202101), the Shenzhen Science and Technology Program (grant KQTD2016113010482651), the BMBF funded de.NBI Cloud within the German Network for Bioinformatics Infrastructure (de.NBI). We thank Bianca Frommer, Marie Lahaye, David Navarro-Payá, Marcela K. Tello-Ruiz and Kapeel Chougule for their help in analyzing the RNA-Seq data and in running the gene annotation pipeline. This study is also based upon work from COST Action CA17111 INTEGRAPE and form COST Innovators Grant IG17111 GRAPEDIA, supported by COST (European Cooperation in Science and Technology).es_ES
dc.description.statusPublishedes_ES
dc.identifier.citationHorticulture Research, 2023
dc.identifier.issn20527276
dc.identifier.urihttp://hdl.handle.net/10532/6401
dc.language.isoenes_ES
dc.relation.doihttps://doi.org/10.1093/hr/uhad061es_ES
dc.relation.urihttps://www.researchgate.net/publication/369811205_The_complete_reference_genome_for_grapevine_Vitis_vinifera_L_genetics_and_breeding#fullTextFileContentes_ES
dc.rightsAtribución-NoComercial-SinDerivadas 3.0 España
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/3.0/es/
dc.subject.agrovocViticultura
dc.subject.agrovocEndogamia
dc.subject.agrovocSecuencia genética
dc.subject.agrovocVid
dc.titleThe complete reference genome for grapevine (Vitis vinifera L.) genetics and breedingen
dc.typeJournal Contribution*
dc.type.refereedRefereedes_ES
dc.type.specifiedArticlees_ES

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