De novo phased assembly of the Vitis riparia grape genome.
De novo phased assembly of the Vitis riparia grape genome.
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DOI：
10.1038/s41597-019-0133-3
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发表时间：
2019-07-19
期刊：
影响因子：
9.8
通讯作者：
Bert, Pierre-Francois
中科院分区：
文献类型：
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作者：
Girollet, Nabil;Rubio, Bernadette;Bert, Pierre-Francois
葡萄藤是世界上最重要的果树之一。为了更好地了解性状变异的遗传基础，促进新基因型的育种，我们对美国本土葡萄属滨葡萄的基因组进行了测序、组装和注释。滨葡萄是世界范围内用于砧木和接穗育种的主要物种之一。从葡萄属河岸植物获得总共164 Gb原始DNA读段，导致225 X覆盖深度。我们使用PacBio长读段生成了V.riparia葡萄从头的基因组组装，该长读段与10x Genomics Chromium连接读段一起定相。在染色体水平，产生500 Mb基因组，支架N50大小为1 Mb。超过34%的全基因组被鉴定为重复序列，并预测了37，207个蛋白质编码基因。这种基因组组装为葡萄藤多样化和适应性的比较基因组分析奠定了基础，并将为进一步的遗传分析和这一经济重要物种的育种提供坚实的资源。
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 164Gb 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 500Mb genome was generated with a scaffold N50 size of 1Mb. 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.