EGFV, Bordeaux Sciences Agro - INRA - Université de Bordeaux, ISVV, 210 chemin de Leysotte, 33882, Villenave d'Ornon, France.
IFV, Institut Français de la Vigne et du Vin, Domaine de l'Espîguette, 30240, Le Grau du Roi, France.
Sci Data. 2019 Jul 19;6(1):127. doi: 10.1038/s41597-019-0133-3.
Grapevine is one of the most important fruit species in the world. In order to better understand genetic basis of traits variation and facilitate the breeding of new genotypes, we sequenced, assembled, and annotated the genome of the American native Vitis riparia, one of the main species used worldwide for rootstock and scion breeding. A total of 164 Gb raw DNA reads were obtained from Vitis riparia resulting in a 225X depth of coverage. We generated a genome assembly of the V. riparia grape de novo using the PacBio long-reads that was phased with the 10x Genomics Chromium linked-reads. At the chromosome level, a 500 Mb genome was generated with a scaffold N50 size of 1 Mb. More than 34% of the whole genome were identified as repeat sequences, and 37,207 protein-coding genes were predicted. This genome assembly sets the stage for comparative genomic analysis of the diversification and adaptation of grapevine and will provide a solid resource for further genetic analysis and breeding of this economically important species.
葡萄是世界上最重要的水果物种之一。为了更好地了解性状变异的遗传基础，并促进新基因型的培育，我们对美国本土葡萄属植物河岸葡萄进行了测序、组装和注释，该物种是全世界用于砧木和接穗培育的主要品种之一。我们从河岸葡萄中获得了总共 164GB 的原始 DNA 读取量，覆盖率达到了 225 倍。我们使用 PacBio 长读序列对 V. riparia 葡萄进行了从头组装，并与 10x Genomics Chromium 连接读取进行了相位处理。在染色体水平上，生成了一个 500MB 的基因组，支架 N50 大小为 1MB。整个基因组的 34%以上被鉴定为重复序列，预测了 37207 个蛋白质编码基因。该基因组组装为葡萄的多样化和适应性的比较基因组分析奠定了基础，并将为该具有重要经济价值的物种的进一步遗传分析和培育提供坚实的资源。
