Whole genome sequencing of grapevine, Vitis labrusca, reveals a majorexpansion of the NLR resistance gene family

Efficiently utilizing the wild genetic diversity is the key to sustainable crop improvement and achieving high quality cultivars. Cultivated grape (Vitis vinifera) is one of the most economically important fruit crops, which is wildly used to produce wine, juice, raisins, and fresh fruit. Vitis labrusca is one of the ~28 native grapevine species in North America and has been wildly used to produce hybrid grapevine cultivars, such as Concord, because of many beneficial traits, including disease resistance and cold tolerance. We sequenced and assembled the V. labrusca genome, which is the most continuous grape reference genome to date, with a contig N50 of 2.5 Mb. Based on V. vinifera (PN40024) reference, we further established 19 pseudomolecules, which covered >90% of entire genome assembly, resulting in a genome sequence size of 502 Mb. We annotated 35,915 protein coding genes, which were clustered into 18,137 gene families, of which 92.9% were shared between V. labrusca and V. vinifera. We identified some V. labrusca gene families that were greatly expanded, including gene families involved in defense response, such as the NLR gene family. Further genomic analysis will reveal novel insights into grapevine evolution and domestication, grapevine disease resistance, and cold tolerance, which will inform future grapevine breeding efforts by targeting and integrating superior genetic material from V. labrusca and other wild species into cultivated grapevines.