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/releasenotes20.html.
Data and statistics are located at
ftp://ftp.gramene.org/pub/gramene/release20/data/
The next release is anticipated in May.
Sincerely,
The Gramene Database
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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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This release includes:
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Website features:
The new layout of the website has been successful with users. Remember
that the Gramene logo is your
link to the Gramene Home Page, and the species pages can be accessed
through the images on the footer.
New users may find it useful to use the Site Map (listed under "help")
to review the website layout.
FAQ's have changed format, and can now be searched through a link at the
*bottom left* of the FAQ page.
To submit a question to the FAQ, send a question via the "feedback" link
at the top of every page,
or use the mailing list (www.gramene.org/mailarch/
<http://dev.gramene.org/mailarch/>). The FAQ page
will be simplified eventually, but for now users should simply select
the module they have a question for,
or use the search option at the bottom left of the page.
New species page for wheat
(www.gramene.org/triticum/triticum_intro.html) There has also been
some restructuring of the species pages, with a new species homepage
(www.gramene.org/species/index.html), with links to a general cereal
introduction and statistics.
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Genomes Release Notes
New Genomes Data
* Mapping to the Oryza sativa (japonica) genome of 14,589 rice
SSR tags obtained from gramene markers database.
* Mapping to the Oryza sativa (japonica) genome of 5,416 rice
QTLs anchored by boundary markers
* Updated 504 full-length Zea mays clones deposited with GenBank
as of 26-Jan-2006 in Maize Accessioned BAC Browser
* Mapping to the full-length Zea mays clones of the 61 sets of
sequences that are mapped to
rice TIGR v3 assembly. These 61 datasets include many datasets that are
already mapped to Maize clones
and many new datasets that are mapped to Maize clones for the 1st time.
For a complete list, go to the in silicon
mapping summary
(www.gramene.org/documentation/Alignment_docs/to_Maize/summary.html).
Some of these new sequence sets are
*Maize_BACends: 10,4007 out of 472,700 sequences were mapped
*Maize_wgs_JGI: 222,255 out of 1,124,441 sequences were mapped
*Maize_ArrayGenes_NSF58K: 2,910 out of 57,452 sequences were
mapped.
New Genomes Features
*Zea mays accessioned clones ContigView.
**The alignment feature coordinates representation changed in
this release,
and is consistant with the coordinates representation in rice genome
browser
**The alignment block coordinates no longer follow the BLAT
output format, where the query coordinates are
from the point of view of the reverse strand when the match is on the
reverse strand. The query coordinates
are always on the forward strand.
**All the coordinates are 1-based.
*Track names changed to be consistant with Oryza sativa genome browser
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BLAST Release Notes
The following databases have been added;
* Maize - cDNAs (FGENESH gene models)
* Maize - Peptides (FGENESH gene models)
* Maize - Clones (GenBank)
The following databases have been updated;
* All species - UniProtKB (SPTr) Peptides
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Maps Release Notes
In this build, we present one new genetic map each from barley and
rice, and a new rice QTL map.
Additional QTL have also been added to four existing rice QTL maps.
Nearly 3,000 maize genes have
been positioned on the maize bin map. The map of the rice TIGR assembly
has been updated to reflect
all the latest features mapped to the rice genome, which should
synchronize the CMap and Ensembl
versions of the map.
New Genetic Maps
* Barley-Barley consensus 2003
* Rice-CIAT SSR 2006
New QTL Map
* Rice-CNHAU Zhenshan97/ H94 DH SSR QTL 2005
Updated Maps
* QTL Added
o Rice-TKU Asominori/IR24 RI RFLP QTL 1996
o Rice-TTU IR58821/IR52561 RI AFLP QTL 2002
o Rice-NDSU EM93-1//EM93-1/SS18-2 BC1 SSR QTL 2004
o Rice-CNHZAU Zhenshan97/Minghui63 RI QTL 2002
* Features Added and Updated
o Rice-GR TIGR Assm IRGSP Seq 2005
o Maize Bins
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Markers Release Notes
The markers database has been updated with an additional 1,745,793
markers, most notably 1,099,874
genomic survey sequences from maize and related species. It now contains
a total of 6,293,401 markers
from more than 180 species.
Marker breakdown by species:
Barley (Hordeum spp.)--535,720
Maize (Zea spp.)--2,622,201
Oat (Avena spp.)--8,215
Rice (Oryza spp.)--1,651,823
Rye (Secale spp.)--13,262
Sorghum (Sorghum spp.)-- 312,845
Sugarcane (Saccharum spp.)--339,657
Wheat (Triticum spp. + Aegilops spp.) 798,051
Other 38,154
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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.
In this release we have:
* Total number of proteins: 76,512
* Proteins from SWISS-PROT: 2,304
* Proteins from TrEMBL: 74,208
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Ontologies Release Notes
* Ontologies: Various ontologies and their associations were
updated. For more details on
different types of ontologies please visit the ontology home page.
The ontologies provided are:
**Gene Ontology:
**Plant Ontology:
**Gramene Plant Growth Stage Ontology:
** Trait Ontology:
**Gramene Taxonomy Ontology:
**Environment Ontology: The Environment Ontology now provides
associations to genes,
proteins and EST libraries from rice
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Genes and Alleles Release Notes
Continually growing, Gramene release 20 presents a reorganized gene
search interface over the
last release. In addition to the generic search, the users can use
keyword to search the Genes database.
The search can be restricted to any one field, such as gene symbol, gene
name, chromosome number,
ontology terms (trait ontology, plant structure, growth stage, gene
ontology, environment ontology),
GenBank accession and Gramene protein accession. If necessary, the users
also can do a search in
all these fields.
As a collaboration and integration effort between Gramene and
MaizeGDB, 6,676 newly imported
maize genes from MaizeGDB have been integrated into the Gramene Genes
database. Together with
1,525 rice genetically identified genes, the total number of genes in
the Genes database has reached 8,201.
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 10,147 QTL identified
for numerous agronomic
traits in rice, maize, barley, oat, wheat, pearl millet, foxtail millet
and wild rice.
A significant improvement in this release is the integration of rice
QTL to the rice genome. Following
the protocol developed in our database, 5,416 rice QTL with directly
associated markers on the
genome have been anchored to the rice genome. This will allow users to
access a specific genome
region corresponding to a QTL or to browse QTL by searching for traits
on the rice genome browser.
In addition, 276 newly curated rice QTLs from the recent publications
have been add to the database.
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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Claire Hebbard
Gramene Outreach Coordinator
G15 Bradfield Hall
Cornell University
Ithaca, NY 14853
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