Gramene Vitis PanGenome is released with 11 grapevine genomes

Vitis PanGenome Release 2.0

Released: September 17, 2021

Gramene's Vitis Pan-Genome (https://vitis.gramene.org) is a web portal for comparative plant genomics focused on grapevine varieties. In its second release, it provides access to 11 grape reference genomes, together with seven other species selected for comparative analysis. These include two versions of the partially inbred Pinot Noir reference (clone PN40024): Vitis vinifera (L.) ssp. vinifera PN40024 v3 [Jaillon et al (2007)] and V. vinifera (L.) ssp. vinifera PN40024 v4 [INTEGRAPE]. The remaining grapevine genomes include seven Vitis vinifera (L.) ssp. vinifera varieties: Cabernet Sauvignon (clone FPS08) [Massonnet et al (2020) & Chin et al (2016)], Carménère (clone FPS02) [Minio et al (2019)], Chardonnay (clone FPS04) [Zou et al (2019)], Concord (interspecific hybrid PI 588077) [Zou et al (2020)], Flame Seedless (clone Parlier) [Zou et al (2020)], Merlot (clone FPS15) [Massonnet et al (2020)], and Zinfandel (clone FPS03) [Vondras et al (2019)]; plus two Vitis vinifera spp. sylvestris varieties: C1-2 (Badouin et al, 2020) and DVIT3351.27 (a male individual carrying a Ren1+ locus collected from Armenia; [Massonnet et al (2020)]). In addition, six plant outgroup species (Japonica rice, B73 maize, Arabidopsis thaliana, grapevine, a vascular plant, and a single-celled green algae) plus Drosophila melanogaster were used to build 24,050 protein-coding gene family trees. These family trees were constructed with 594,645 input proteins from 553,999 individual genes; and include 8,881grapevine-specific trees. Gene expression and orthology-based pathway projections are available for version 3 of the PN40024 grape reference genome via the Vitis Pan-Genome search interface. Complementary pairwise DNA alignments and synteny maps, as well as genetic variation (nearly half million SNPs) is available for version 3 of the Pinot noir PN40024 reference in the Gramene website.

We are grateful to the grapevine research community, especially the VitisGen2 (https://www.vitisgen2.org; USDA NIFA SCRI 51181-26829) and the EU-COST action CA 17111 (http://www.integrape.eu) collaborators for generously sharing their data, making valuable contributions, and providing feedback on the site. The genomes sequenced by the VitisGen2 are also available at grapegenomics.com hosted by the Cantu Lab at the University of California in Davis. Funding for the Flame Seedless genome was provided by the California Table Grape Commission, and the Concord genome was sequenced and assembled by 10X Genomics. The genome assembly of the Cabernet sauvignon variety clone FPS08 was funded by E.&J. Gallo Winery and J. Lohr Vineyards and Wines. The genome assembly of the Carménère variety clone FPS02 was funded by the Chilean Economic Development Agency (CORFO; Project 13CEI2-21852), Viña Concha y Toro, and Viña San Pedro. The genome assembly of the Chardonnay variety clone FPS04 was funded by UC Davis Chile Life Sciences Innovation Center, Viña Concha y Toro, E. & J. Gallo Winery, J. Lohr Vineyards and Wines, Viña San Pedro, Louis P. Martini Endowment in Viticulture, and NSF Plant Genome Research grant #1741627. The genome assembly of the Merlot variety clone FPS15 was funded by UC Davis Chile Life Sciences Innovation Center, Viña Concha y Toro, and Viña San Pedro. The genome assembly of the Zinfandel variety clone FPS03 was funded by Louis P. Martini Endowment in Viticulture. The genome assembly of Vitis vinifera spp. sylvestris clone DVIT3351.27 was funded by NSF Plant Genome Research grant #1741627.

The genome databases were built in direct collaboration with the Gramene and Ensembl Plants projects. Gene expression and orthology-based pathway association available for the grapevine PN40024 reference v3 via the Search functionality, were facilitated through collaborations with the Expression Atlas, and the Plant Reactome databases. Core funding for the project was provided by the National Sciene Foundation (NSF IOS-1127112) and the Agricultural Research Service of the U.S. Department of Agriculture (USDA ARS 8062-21000-041-00D) to the Ware Lab at the Cold Spring Harbor Laboratory.