Gramene Release 21 May 2006

This release includes:.

Gramene website features:

Gramene Database:

For more information on the gramene modules, review the release notes (below) and the most recent Gramene Publications

Genomes Release Notes

New Genomes Data

New Genomes Features


Maps Release Notes

We have updated our annotated rice sequence to release 4 of the TIGR rice pseudomolecules. As in previous releases, Gramene has added its own annotations to the map, in the form of features such as RFLPs, SSRs, ESTs from rice as well as other species. This map was previously known as the "Gramene TIGR Pseudomolecule Assembly of IRGSP Sequence". To shorten the name, as well as emphasize Gramene's additions to the map, the name of the rice sequence map has been changed to "Rice-Gramene Annotated Nipponbare Sequence".

In addition to the updated sequence map, we have curated additional rice QTL which have been added to four existing QTL maps.

Updated Sequence Map Updated QTL maps
Rice-Gramene Annotated Nipponbare Seq 2006
[formerly known as Rice-GR TIGR Pseudomolecule Assembly of IRGSP Sequence 2005]

Markers Release Notes

The marker database now contains a total of 11,832,129 markers. Those markers previously classified into "BAC end sequence" and "Tos17" have been consolidated into "GSS", which contains all Poaceae genomic sequences.

Marker breakdown by type

Marker Type Markers
AFLP 950
Centromere 12
Clone 2,033,658
EST 3,675,691
EST Cluster 1,325,059
Gene 8,474
Gene Model 57,503
Gene Primer 19
GSS 4,605,001
mRNA 99,054
Primer 34
RAPD 135
RFLP 7,822
SSR 16,835
STS 65
Undefined 1,817

Marker breakdown by species

Species Markers
Barley (Hordeum spp.) 637,879
Maize (Zea spp.) 3,365,983
Oat (Avena spp.) 8,226
Rice (Oryza spp.) 4,395,144
Rye (Secale spp.) 4,91,841
Sorghum (Sorghum spp.) 1,401,556
Sugarcane (Saccharum spp.) 339,661
Wheat (Triticum spp. + Aegilops spp.) 1,062,830
Other 129,009

Proteins Release Notes

The Gramene protein database provides curated information on SP-Trembl entries from family Poaceae (Grasses). The annotations include Pfam, Prosite, TMHMM (for transmembrane domains), TargetP and Predotar (plastid, mitochrondrial and secretory pathway targeting) and Interpro assignments. Various ontologies such as Gene Ontology (GO), Plant Ontologies (PO+GRO) and Environment Ontology (EO) are used to provide functional characteristics.

Almost all the rice proteins encoded by plastid and mitochondrial genomes are annotated.


Ontologies Release Notes

Various ontologies and their associations were updated. For more details on different types of ontologies please visit the ontology home

The ontologies provided are:

Gramene taxonomy ontology now has associations to the species in marker database. e.g. Oryza (GR_tax:013655) has 19 species associated in marker db.

The marker libraries are now associated to Ontology terms from Plant structure (PO), cereal growth (GRO) and Environment ontologies (EO). e.g. plant structure leaf (PO:0009025) has 77 marker libraries, suggesting that individual entries from this library were expressed in the plant structure leaf.


Genes and Alleles Release Notes

Continually growing, Gramene release 21 presents a further improvement based on the previously reorganized gene search interface.

Content:

1657 of 1798 (92%) rice genes have literature references.

The genes present on rice plastid (157) and mitochondrial (59) genomes were added and curated.

Search improvements:

  1. Genes can searched by their types, not sequenced, CDS (Protein coding), rRNA (Ribosomal RNA), tRNA (Transfer RNA), Pseudogene (non-functional), and "Not classified".
  2. For those genes identified by classical genetics method but have no sequenced loci associated with them, please use the gene type 'Not sequenced'.
  3. Additional filters for 'has phenotype' can be applied to your gene searches. Selecting 'has phenotype' search those genes that have phenotypes.

A more detailed genes database statistics report can be found here.

QTL Release Notes

The Gramene QTL database includes a total of 10,495 QTL identified for numerous agronomic traits in rice, maize, barley, oat, wheat, pearl millet, foxtail millet and wild rice.

Almost 350 new rice QTLs related with low nitrogen tolerance, tissue culture performance, and other important traits in rice from recent publications have been curated and added to the database.

Another improvement in this release is the addition of links to the QTL that have been originally integrated from GrainGenes and MaizeGDB which will allow the users to go to the original databases to get more detailed information if necessary.

A more detailed QTL database statistics report can be found here.

Pathways Release Notes

The Pathway tool is a web based tool for viewing gene annotations mapped to various biochemical pathways in plants, rice (Oryza sativa) and Arabidopsis thaliana and bacteria E. coli. This tool also allows you to draw comparisons among the data sets from the above three species.

This is the version 1.0 of the rice pathways. The rice pathways are also called (RiceCyc) and are curated by Gramene. The rice genes and their annotation used in this analyses were based on release 4 of the TIGR's assembly of Oryza sativa japonica cv.Nipponbare genome sequenced by IRGSP.

Arabidopsis thaliana and E. coli pathways were imported from AraCyc (http://www.arabidopsis.org/tools/aracyc/) and EcoCyc (http://www.ecocyc.org/) project sites.

The RiceCyc ver 1.0 has following contents.

A peptides link to the gene model pages in rice genome. Similarly if the gene model has been mapped to a biochemical pathway it links to particular reaction in pathway database from the genome browser.

This tool also allows you to upload your own gene expression data on the pathways to visualize an overview of the cellular level expression profile. For more info please visit http://www.gramene.org/pathway/.


Diversity Release Notes

The Gramene Genetic Diversity database contains SSR allelic data for rice, SNP data for Wheat, and phenotypic, SSR and SNP data for maize. Allelic variation on loci of multiple germplasms of a species and genome-wide allelic variation of germplasms can be viewed by searching for locus/marker name, germplasm name or accession number.

Wheat and maize data was obtained from their respective genome projects. For rice, the data was obtained from a paper published by the McCouch rice group.


On this release,

For a more detailed summary of the datasets, click here.

Please continue to visit the Gramene Diversity Home Page as we continue to develop our data sources and analysis software tools.