Announcing Gramene Release 21

Thu May 11 16:50:05 EDT 2006

Dear Cereal Researchers,

The Gramene database (www.gramene.org)
emails its registered users an announcement each time a new release is
made. This announcement includes information on new or updated data and
software at Gramene.

For the current release notes (shown below), visit
www.gramene.org/documentation/release_notes/releasenotes.html.

Data and statistics are located at
ftp://ftp.gramene.org/pub/gramene/release21/data/statistics

Sincerely,

The Gramene Database Team

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This work is funded by the National Science Foundation (NSF) and the
USDA-Agricultural Research Service, and was previously funded by the USDA
Initiative for Future Agriculture and Food Systems (IFAFS). We are thankful
to numerous collaborators and contributors for help in curation and for
sharing their datasets and tools.
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May 2006

Gramene Release 21

New Gramene website features:

NEW! Introduction of two new modules, Pathways and Diversity

New species pages. Some pages are still being worked on for
completion, but there is now information for every species
listed. They can be accessed by clicking on the species images
at the bottom of the page.

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Gramene Release Notes

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Genomes

New Genomes Data

	*Genome assembly: The rice genome browser has been updated with
	release 4 of the TIGR Rice Pseudomolecules and Genome Annotation
	including TIGR gene annotation.

	*Chromosomes: Mitochrondrion and chloroplast chromosomes and
	associated annotations have been added to the browser.

	*Browser Tracks: Many datasets were enriched and updated,
	they include:

	   1- 8 EST datasets of various species, updated with NCBI Genbank records
	   2- 13 BACend_OMAP datasets, updated with NCBI Genbank, 3 OMAP
	   species are new in this build (RiceGranulata, RiceOfficinalis, RiceRidleyi)
	   3- 5 ESTcluster_TIGR datasets from TIGR ftp site (TIGR GIs)
	   4- 5 ESTcluster_PlantGDB from PlantGDB website
	   5- Other updated datasets include:
	        Rice_CDS (updated from Genbank)
	        RiceJaponica_cDNA_KOME (updated from Genbank)
	        Maize_BACend (updated from Genbank)
	        Rice_FstTransposon (updated from Genbank)
	        Rice_FST-TDNA (updated from Genbank)
	        Rice_FSTtos17 (updated from Genbank)
	        Rice_BAC (these are Genbank Rice BAC/clones not used by Rice Assembly)
            Due to 3rd party data processing delays,
    		the following tracks are omitted, but will be reinstated in the next 
release;
                                 Rice_ArrayOligo_NSF20K
                                 Rice_MPSStag_Meyers
                                 Rice_SAGEtag_MGOS
                                 Rice_TE

* SNP Data: Approx. 4M Oryza sativa SNPs from dbSNP
	version 125 (http://www.ncbi.nlm.nih.gov/projects/SNP) have
	been mapped to the rice genome assembly. The consequence of
	each SNP (synonymous, non-synonymous, UTR etc) on affected
	gene model transcripts have been annotated.

* Xref mapping: The following external database identifiers for
	Oryza sativa have been mapped directly to the rice gene models
	via dna/protein homology;
		SwissProt/TrEMBL,
		RefSeq,
		TIGR Gene Indices.
		The following identifiers have also been mapped;
		NCBI Genes,
		Gramene GenesDB entries,
		Gramene Pathway entries.

*New Genomes Features

       **Xref mapping: The GeneView pages now display
	cross-reference links to external identifiers that have
	been mapped. These appear in the 'Similarity Matches'
	section. See, for example, LOC_Os01g56810
	(http://www.gramene.org/Oryza_sativa/geneview?gene=LOC_Os01g56810).

       **SNP display: Features in the SNP track of the
	ContigView display are now color coded according to their
	consequence w.r.t. overlapping gene models. This color
	coding extends to the GeneSNPDisplay so that it is easy
	to find, for example, which SNPs affect the peptide
	sequence of the gene (i.e. non-synonymous genes). See, for example,
	LOC_Os01g01510
	(http://www.gramene.org/Oryza_sativa/genesnpview?db=core&gene=LOC_Os01g01510). 

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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".

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

* We have curated additional rice QTL which have been added to four 
existing QTL maps.
           Rice-JRGP Koshihikari/Kasalath RIL RFLP QTL 2003
           Rice-Integrated IR64/Azucena DH QTL
           Rice-CNHZAU Zhenshan97/Minghui63 RI QTL 2002
           Rice-Aberdeen Bala/Azucena 2002

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Markers

	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

	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

	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

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Proteins

	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.

	Total number of proteins: 76745
	Proteins from SWISS-PROT: 2367
	Proteins from TrEMBL: 74378

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

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Ontologies

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

The ontologies provided are:
	*Gene Ontology
	*Plant Ontology
	*Gramene Plant Growth Stage Ontology
	*Trait Ontology
	*Gramene Taxonomy Ontology
	*Environment Ontology

	**Gramene taxonomy ontology now has associations to the
	species in marker database. e.g. Oryza
	(http://www.gramene.org/db/ontology/search_term?id=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
	(http://www.gramene.org/db/ontology/search_term?id=PO:0009025)
	has 77 marker libraries, suggesting that individual entries from
	this library were expressed in the plant structure leaf.

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Genes and Alleles Release Notes

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

Content:
	*  Rice -- 1798 (260 New genes)
	*  Maize -- 6676
	*  Total -- 8474

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 all rice plastid genes by visiting
	http://www.gramene.org/db/genes/search_gene?query=plastid&search_field=chromosome&gene_type_id=&species=1 

	*Search all rice mitochondrial genes by visiting
	http://www.gramene.org/db/genes/search_gene?query=mito*&search_field=chromosome&gene_type_id=&species=1 

Search improvements:
	Genes can searched by their types, not sequenced, CDS
	(Protein coding), rRNA (Ribosomal RNA), tRNA (Transfer RNA),
	Pseudogene (non-functional), and "Not classified".

	For those genes identified by classical genetics method but
	have no sequenced loci associated with them, please use
	the gene type 'Not sequenced'.

	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 
at 	ftp://ftp.gramene.org/pub/gramene/release20/data/statistics/gene_statistics

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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 
at 	ftp://ftp.gramene.org/pub/gramene/release20/data/statistics/qtl_statistics.

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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.
	Pathways: 316
	Enzymatic Reactions: 1687
	Transport Reactions: 5
	Polypeptides: 43172
	Protein Complexes: 4
	Enzymes: 10387
	Transporters: 62
	Compounds: 1265

	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/.

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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. See the abstract
	at http://www.gramene.org/db/literature/pub_search?ref_id=11020.

With this release,
	Rice: 234 germplasms; 169 SSR markers.
	Wheat: 48 germplasms; 3802 SNP markers.
	Maize: 2793 germplasms; 520 SSR and 897 SNP markers.

	For a more detailed summary of the datasets, see
	http://www.gramene.org/diversity/summary.html

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

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For more information on the gramene modules, review the
	most recent Gramene Publications:

	Gramene: A genomics and genetics resource for rice.
	Rice Genetics Newsletter, 2006, Vol. 22, No. 1. 9-16.
	(http://www.shigen.nig.ac.jp/rice/rgn/vol22/v01.html)

	Gramene: Sowing the seeds of genomics research.
	eCALSconnect, March 2006, Vol. 12-3.
	(http://cals.cornell.edu/cals/public/comm/pubs/ecalsconnect/vol12-3/features/gramene.cfm) 

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Claire Hebbard
Gramene Outreach Coordinator
G15 Bradfield Hall
Ithaca, NY 14853
USA

www.gramene.org