Website

Although we have a new look, you can still find all the old stuff at Gramene's Archive.

Genomes Release Notes

• New genomes

  1. Ostreococcus lucimarinus (a green alga)
  2. Leersia perrieri (a wild grass)
  3. Oryza rufipogon (brownbeard rice)
  4. Oryza longistaminata (a wild rice)
  5. Theobroma cacao (cocoa)
  6. Brassica oleracea (the brassica C genome)

• Updated genomes

  1. Updated assembly and gene build for O. barthii (wild rice)
  2. Chloroplast genomes added to the triticeae genomes: Hordeum vulgare (barley), Aegilops tauschii (Tausch's goatgrass), Triticum aestivum (bread wheat) and Triticum urartu (an einkorn wheat)
  3. Mitochondrial genome added to Triticum aestivum (bread wheat)

• New & updated pathways (Plant Reactome)

  1. New auxin signaling pathway in rice
  2. Updated 9 amino acid pathways by incorporating recent literature and genes & compartment re-assignments.
     • arginine biosynthesis I
     • arginine biosynthesis II
     • glutamate biosynthesis I
     • glutamate biosynthesis V
     • glutamine biosynthesis I
     • alanine biosynthesis II
     • alanine biosynthesis III
     • glutamate biosynthesis IV
     • lysine biosynthesis VI
  3. New & updated orthology-based projections of rice pathways to 17 of the 39 completely sequenced plant genomes hosted by Gramene

• New data

  1. Split gene predictions for 37 plant genomes
  2. ncRNA annotation for Triticum aestivum (bread wheat)
  3. Probes from the Affymetrix barley genome array aligned to Hordeum vulgare (barley)
  4. Zea mays (maize) variation data based on Panzea release 2.7
  5. Sorghum bicolor (sorghum) variation data from Mace et al (2013)
  6. Triticum aestivum (bread wheat) variation data from Axiom, iSelect and KASP array sets
  7. Two transcriptome datasets from diploid einkorn wheat (Triticum monococcum cv DV92 and G3116), generated by Jaiswal's Lab, have been aligned to barley, bread wheat and Triticum urartu genomes using STAR
  8. TriFLDB full-length cDNA sequences aligned to bread wheat genome
  9. Whole genome alignments for bread wheat against barley

• Updated data

  1. Updated gene-trees across 37 species (Ostreococcus lucimarinus and Oryza longistaminata were not included in gene tree construction in the present release)
  2. Updated gene, sequence and variation BioMarts
  3. Updated GO term and gene name projection from Arabidopsis thaliana to all dicots

Genomes Core

Ensembl Variation

Compara

Gene Trees

• The EnsemblCompara GeneTree database was updated to include bread wheat gene models. A total of 56,134 GeneTree families were constructed comprising 1,242,576 individual genes (1,394,452 input proteins) from 38 plant genomes (and 5 non-plant outgroups).

• The OGE Compara tree was not updated. Last update was done in release 38 (August 2013). Note: The OGE Compara tree was pulled out from the website since they were build on the obsolete MSU6 genome assembly.

Potential gene annotation artifacts

Split gene analysis was done for the 38 fully sequenced plant reference genomes in Gramene release 42. This analysis includes information on 5 new genomes, compared to the last split gene split done in release 41. For a complete list, see Gramene's FTP site. Summary statistics follow.

Split genes by species

Synteny

No new synteny data was generated for this release. Last update was done in release 39 (October 2013).

WGA and other nucleotide alignments

1. DNA-DNA alignments between bread wheat and Oryza sativa, bread wheat and Brachypodium distachyon, and barley and the wild wheat progenitors (Triticum urartu and Aegilops tauschii).

2. RNA-Seq data aligned to bread wheat, as well as to its wild progenitors.

3. Wheat UniGene clusters sequences aligned to bread wheat, as well as to its wild progenitors.

Protein Annotation, Go, Xref

No updates in this release. Last update done in release 40 (January 2014).

Mart

New Plant Gene and Plant Variation Marts

Pathway Release Notes

Plant Reactome

• A new pathway on auxin signaling in rice has been released.

• The following amino acid pathways have been revised by incorporating recent literature and genes & compartment re-assignments: arginine biosynthesis I, arginine biosynthesis II, glutamate biosynthesis I, glutamate biosynthesis V, glutamine biosynthesis I, alanine biosynthesis II, alanine biosynthesis III, glutamate biosynthesis IV and lysine biosynthesis VI. Lysine biosynthesis VI is the new featured pathway on the Plant Reactome homepage.

• In this release we have also implemented orthology-based projections of rice pathways to 17 other species.

Projection Statistics

"Cyc" Pathways

• No updates on this release

Ontologies Release Notes

No updates in this release. Last update done in release 31 (May 2010). Below is a summary of the ontologies data.

See also the detailed Ontology Module statistics report.

Infrastructure

Web Services

Gramene's web services page documents many ways to directly connect to and analyze our databases.

Programmatic access to Gramene is now available through the RESTful Ensembl API.

Public MySQL Server

Gramene provides direct MySQL access to our core Ensembl databases for each of our sequenced genomes as well our databases for markers, sequences, genes, QTL and ontologies. To connect, use the following:

mysql -hgramenedb.gramene.org -pgramene