The Vitis PanGenome, a web portal for comparative plant genomics focused on grapevine varieties, has released its second version. It provides access to 11 grape reference genomes, together with seven other species selected for comparative analysis. 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 is 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.
We would like to thank 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 National Science Foundation 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 National Science Foundation Plant Genome Research grant #1741627.
- Eleven grape reference genomes including two versions of the partially inbred Pinot Noir reference (clone PN40024): Vitis vinifera (L.) ssp. vinifera Pinot noir PN40024 v3 and Vitis vinifera (L.) ssp. vinifera Pinot noir PN40024 v4. The remaining grapevine genomes include seven Vitis vinifera (L.) ssp. vinifera varieties: Cabernet Sauvignon (clone FPS08), Carménère (clone FPS02), Chardonnay (clone FPS04), Concord (interspecific hybrid PI 588077), Flame Seedless (clone Parlier), Merlot (clone FPS15), and Zinfandel (clone FPS03); 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).
- Six plant outgroup species (Japonica rice, B73 maize, Arabidopsis thaliana, grapevine, a vascular plant, and a single-celled green algae) and Drosophila melanogaster were used to build 24,050 protein-coding gene family trees.
- Our comparative genomics collection includes a total of 24,050 phylogenetic trees, of which 8,881 are grapevine specific. These family trees were constructed with 594,645 input proteins from 553,999 individual genes. Pairwise DNA alignments and synteny maps are available for version 3 of the Pinot noir PN40024 reference in the Gramene website.
- Gene expression and orthology-based pathway projections are available for version 3 of the PN40024 grape reference genome via the Search interface.
Gene Trees. A total of 24,050 protein-coding gene family trees were constructed using the peptide encoded by the canonical transcript (i.e., a representative transcript for a given gene) for each of 553,999 individual genes (594,645 input proteins) from 17 plant genomes.
Whole-Genome Alignments. 76 pairwise genomic alignments are available for version 3 of the Pinot noir PN40024 reference assembly in the Gramene website. New alignments across the grape genomes will be made available here in future releases.
Synteny. Eight synteny maps are available for version 3 of the Pinot noir PN40024 reference assembly in the Gramene website. New synteny maps across the grape genomes will be made available here in future releases.
Genetic variation is available for version 3 of the Pinot noir PN40024 reference assembly in the Gramene website for will be available in future releases. Genetic variation data sets will be made availale here in future releases.
Gene expression data for the PN40024 grape v3 genome reference was curated and processed through the EMBL-EBI Expression Atlas. The set consists of 10 studies with baseline expression (REFS?) and 23 baseline studies (REFS?).
266 orthology-based grape pathways associated with 1,074 grapevine PN40024 v3 genes. These were projected from curated Japonica rice pathways and are linked to Gramene’s Plant Reactome.
| Species | Classification | Note | Assembly | Literature reference | Accession | Expression | Phylogenetic Trees | Pathways | BioProject or Genomics Data Source |
|---|---|---|---|---|---|---|---|---|---|
| Vitis vinifera L. ssp. vinifera Pinot noir PN40024 v3 | Eudicotyledons | Dicot reference | IGGP_12x (V3) | Jaillon et al (2007) | GCA_000003745.2 | Search only | Y | Search only | - |
| Vitis vinifera L. ssp. vinifera Pinot noir PN40024 v4 | Eudicotyledons | Dicot reference | v1 (V4) | INTEGRAPE | PN40024_40X_REF_AnnoV2 | - | Y | - | - |
| Vitis vinifera L. ssp. vinifera Cabernet Sauvignon clone FPS08 | Eudicotyledons | Cabernet_Sauvignon | Massonnet et al (2020) & Chin et al (2016) | VvCabSauv08_v1 | - | Y | - | PRJNA593045, Data, PRJNA316730, PRJNA433195 & Cantu Lab | |
| Vitis vinifera L. ssp. vinifera Carménère clone FPS02 | Eudicotyledons | Carmenere | Minio et al (2019) | VvCarFPS02VCR702_v1 | - | Y | - | PRJNA517468, Cantu Lab | |
| Vitis vinifera L. ssp. vinifera Chardonnay clone FPS04 | Eudicotyledons | Chardonnay | Zou et al (2019) | VvChar04_v1 | - | Y | - | PRJNA550461 | |
| Vitis vinifera L. ssp. vinifera interspecific crossing Concord PI588077 | Eudicotyledons | 10x201806 | Zou et al (2020) | 10x201806 | - | Y | - | PRJNA281110 | |
| Vitis vinifera L. ssp. vinifera Flame Seedless clone Parlier | Eudicotyledons | pacbio201806 | Zou et al (2020) | - | Y | - | PRJNA281110 | ||
| Vitis vinifera L. ssp. vinifera Merlot clone FPS15 | Eudicotyledons | Merlot | Massonnet et al (2020) | VITVvi_vMerlFPS15_v1.1 | - | Y | - | PRJNA593045, Data | |
| Vitis vinifera L. ssp. vinifera Zinfandel clone FPS03 | Eudicotyledons | Zinfandel | Vondras et al (2019) | VvZin03_v1 | - | Y | - | PRJNA527006 & Cantu Lab | |
| Vitis vinifera L. ssp. sylvestris C1-2 (Badouin et al, 2020) | Eudicotyledons | Sylvestris_C1-2 | Badouin et al (2020) | Sylvestris_C1-2 | - | Y | - | PRJEB37020 | |
| Vitis vinifera L. ssp. sylvestris DVIT3351.27 (Ren1 male) | Eudicotyledons | Sylvestris_DVIT3351.27 | Massonnet et al (2020) | VITVvi_sDVIT3351.27_v1.1 | - | Y | - | PRJNA593045, Data |
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