Gramene Release 22 August 2006

This release includes:.

Gramene website features:

Gramene Database:

Genomes Release Notes

New Genomes Data

New Genomes Features

The current Gramene Genome Bowsers are developed on top of ensembl-39. Compared with the last build based on ensembl-30, it has had a major redesign, both on the surface and 'under the bonnet'. Most of the dynamic pages (e.g. ContigView, GeneView) have only minor cosmetic changes - in addition to the new template and stylesheets, some links have been moved from the body of the view to the new side-bar.


Maps Release Notes

The Map Module has been updated to the latest CMap 0.16 release. There have been numerous changes to both the code base and user interface, which should improve query response times. Among the user interface improvements are:

Updated Sequence Map

New and Updated Physical Maps

New QTL Maps

Updated QTL Maps

Markers Release Notes

The marker database now contains a total of 11,932,099 markers from 217 species.

Marker breakdown by type

Marker Type Markers
AFLP 1,230
Centromere 12
Clone 2,390,592
EST 3,675,648
EST Cluster 1,325,059
FPC 1,701
Gene 8,673
Gene Model 5,7501
Gene Primer 19
GSS 4,312,690
Maize Bin 100
mRNA 98,737
OVERGO 15,575
Primer 62
RAPD 133
RFLP 19,643
SSR 16,885
STS 2,213
Undefined 5,621

Marker breakdown by species

Species Markers
Barley (Hordeum spp.) 638,042
Maize (Zea spp.) 4,044,148
Oat (Avena spp.) 8,232
Rice (Oryza spp.) 4,412,024
Rye (Secale spp.) 13,346
Sorghum (Sorghum spp.) 1,265,320
Sugarcane (Saccharum spp.) 339,661
Wheat (Triticum spp. + Aegilops spp.) 1,063,010
Other 148,316

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.

The improvements in release 22 include:


Ontologies Release Notes

Various ontologies and their associations to genes, gene models, proteins, QTL, markers and maps were updated. Below is a summary of the ontologies data.

Improvements on a term's detail page include:

  • Anchor links for "Term" and "Annotations". These provide quick browsing to the appropriate section on the same page.
  • Ordering. The list of species in annotations section is now pre-sorted alphabetically from left to right, then top to bottom.

    To view these improvements see http://www.gramene.org/db/ontology/search_term?id=GO:0044425 as an example.


    Genes and Alleles Release Notes

    Continually growing, Gramene release 22 presents a further improvement based on the previously reorganized gene search interface.

    Content: Number of genes

    In order to provide users with the ability to compare gene positions across various genetic and sequence maps, about 800 rice genes now have map positions on most commonly used genetic maps, the "Cornell BS125/2/BS125/WL02 RFLP 2001 Map", the "Cornell IR64/Azucena SSR 2001 Map", the "JRGP Nipponbare/Kasalath RFLP 2000 Map", and the "Hokkaido Morphological 2000 Map". Of these about 250 have mappings to the gene models found on sequence map "Gramene Annotated Nipponbare Sequence 2006". About 45% of the maize genes have been mapped to the "Maize Bins Map".

    The Gene details now provide mappings to the "Plant Growth and Development Stages" ontology provided by the Plant Ontology project. This is in addition to the already displayed "Cereal Plant Growth Stages" developed by us. For example go to the gene 'd1'.

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

    QTL Release Notes

    The Gramene QTL database now contains a total of 10,791 QTL identified for numerous agronomic traits in rice, maize, barley, oat, wheat, sorghum, pearl millet, foxtail millet and wild rice.

    Around 200 new rice QTLs related to yield and other important traits have been curated from recent publications and added to the database. These new QTLs have been mostly identified from genetic populations derived from inter-specific crosses between cultivated rice (Oryza sativa) and its wild rice relatives such as Oryza rufipogon and Oryza glaberrima. The identification of those QTLs will provide new avenues to increase the yield of rice.

    Another improvement in this release is the inclusion of sorghum QTLs, almost 100 of which where detected from sorghum inter-specific and intra-specific populations. Those QTLs are associated with several traits with agronomic importance such as grain weight, leaf senescence and maturity.

    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 version 1.1 of the rice pathways. These pathways (also called RiceCyc) are curated by Gramene. The rice genes and their annotation used in this analysis was 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 the AraCyc and EcoCyc project sites. Neither AraCyc nor EcoCyc have been updated in the August release of Gramene.

    RiceCyc version 1.1 has following contents.

    Since the 1.0 release, seven new pathways have been added to RiceCyc; these pathways were added based upon information available from AraCyc. These pathways mainly relate to Gibberellin and include GA12 biosynthesis; ent-kaurene biosynthesis; and gibberellin synthesis I, II and III. The NAD biosynthesis II from tryptophan has also been added; this is based on the fact that in eukaryotes this pathway starts with tryptophan. Additionally the super pathway of pantothenate and coenzyme A biosynthesis has also been added so as to take into account missing components of the pathway.

    Based upon information made available from the Nelson lab at Yale University new information related to NADP-dependent malic genes has been added to the dataset. If any groups have knowledge of genes that they feel should be added to the RiceCyc dataset please feel free to contact the Gramene curators. 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 visualise 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.


    On this release,

    Click here for database summary.