New and updated plant genomes and pathways datasets planned for the Gramene release #63 (July 2020)

Submitted by Sushma_Naithani on Wed, 05/13/2020 - 12:21

We wish and hope that in this difficult time of COVID-19 pandemic, all Gramene database users and their loved ones are doing well and keeping safe. Through this post, we would like to provide an intended list of new and updated datasets for the upcoming release #63 scheduled for July 2020. The data includes 27 new genomes with enriched gene annotations -often provided by the community-, and genetic variation data including variant effect prediction (VEP) for durum wheat, golden apple, and sunflower. The Plant Reactome pathway portal will include ten newly curated pathways on cell cycle and plant organ development and ten updated pathways. The users will also notice the removal of the amino-propanol biosynthesis pathway and merger and extension of UDP-L-arabinose biosynthesis I and II pathways. A total of 312 curated rice reference pathways and annotations will be projected for all the 27 new plant varities listed in the new genomes section.

Plant Genome Updates

New Genomes:
  1. Clementine (Citrus clementina): GCA_000493195.1
  2. Sweet cherry (Prunus avium): GCA_002207925.1, and community annotation
  3. Morning glory, a relative of sweet potato (Ipomoea triloba): GCA_003576645.1, and community annotation
  4. Saccharum spontaneum, a sugar-poor relative of sugarcane: GCA_003544955.1, and community annotation
  5. Pineapple (Ananas comosus): GCA_902162155.1, and annotation from Ray MIng’s lab at Univ. of Illinois 
  6. Braun's stonewort, an ecorticated streptophyte algae (Chara braunii): GCA_003427395.1
  7. Weeping lovegrass (Eragrostis curvula): GCA_007726485.1
  8. Golden apple (Malus domestica): GCA_002114115.1 and annotation from IRHS
  9. Wild olive tree: (Olea europaea sylvestris):  GCA_002742605.1 and annotation from GDB
  10. Pistachio (Pistacia vera): GCA_008641045.1, and annotation from BIGD
  11. Almond (Prunus dulcis): GCA_902201215.1
  12. Alpine rock-cress (Arabis alpina): GCA_000733195.1
  13. Cannabis or marijuana (Cannabis sativa, female): GCA_900626175.1
  14. Camelina, gold-of-pleasure or false flax (Camelina sativa): GCA_000633955.1
  15. Watermelon (Citrullus lanatus): GCA_000238415.2
  16. Cantaloupe or muskmelon, smooth-skinned (Cucumis melo): GCA_902497455.1
  17. A tropical water lily (Nymphaea colorata): GCA_008831285.1
  18. China or Chinese rose(also Bengal rose, crimson or beauty (Rosa chinensis): GCA_002994745.2
  19. Wild or green foxtail millet, green bristlegrass (Setaria viridis): GCA_005286985.1
  20. Five new bread wheat (Triticum aestivum) varieties: 
    • var. Cadenza: GCA_902810645.1
    • var. Claire: GCA_902810655.1
    • var. Paragon: GCA_902810665.1
    • var. Robigus: GCA_902810685.1
    • var. Weebill: GCA_902810675
  21. A new barley variety Golden Promise (Hordeum vulgare subsp. Vulgare): GCA_902500625.1
  22. A new cultivar of cacao tree Matina 1-6 (Theobroma cacao Matina 1-6): GCA_000403535.1 
Genetic variation data: 
  • Durum wheat SNP variants (35K, 90K, 820K and TaBW280K arrays)
  • Malus domestica (apple) SNP variants
  • Helianthus annuus (sunflower) SNP variants
Other Genome Updates
  • Update common gene names from Entrez to some barley genes
  • The Ensembl Compara Enredo-Pecan-Ortheus (EPO) pipeline was parameterized and used to compute a multiple genome alignment of 11 Oryza taxa
  • dN/dS analysis for plants will be discontinued

Plant Reactome updates 

New Pathways curated 
  • Cell Cycle
    • S phase
      • Synthesis of DNA
        • DNA replication initiation
        • DNA strand elongation
          • Lagging strand synthesis
          • Leading strand synthesis
        • DNA strand maturation
  • Root development
    • Primary root development
      • Primary root elongation
    • Crown root development
      • Crown root initiation
      • Crown root emergence
    • Lateral root development
      • Lateral root initiation
      • Lateral root emergence
 Revised Pathways
  • Photorespiration
  • Cardiolipin biosynthesis
  • Flower development
  • Floral bracts development
  • Primary root development
  • UDP-L-arabinose biosynthesis and transport 
  • Tran-zeatin (cytokinin) Biosynthesis
  • Gibberellin biosynthesis I
  • Vitamin E biosynthesis
  • Ascorbate biosynthesis

The Gramene database is co-produced by the project teams from the Cold Spring Harbor Laboratory and Oregon State University in collaboration with its international partners, EMBL-EBI’s Ensembl Plants, Uniprot, and Gene Expression Atlas, and the Human Reactome project. The project is funded by the National Science Foundation (IOS-1127112) and USDA-ARS (1907-21000-030-00D).

Stay safe and healthy!

Sincerely,
The Gramene Team
www.gramene.org