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Dear Cereal Researchers, <br><br>
The Gramene database
(<a href="http://www.gramene.org">http://www.gramene.org</a>) emails its
registered users an announcement each time a new release is made. This
announcement includes information on new or updated data and software.
<br><br>
Sincerely, <br>
The Gramene Database <br><br>
***************************************************************** <br>
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. <br><br>
*****************************************************************
<br><br>
Gramene website features: <br><br>
<br>
Navigation Bar changes: <br>
"Genome Browser" link on the navigation bar replaced with
"Genomes". <br>
"CMap" link on the navigation bar replaced with
"Maps". <br>
"Protein" link on the navigation bar replaced with
"Proteins". <br>
"Ontology" link on the navigation bar replaced with
"Ontologies". <br>
"Gene" link on the navigation bar replaced with
"Genes". <br><br>
New and updated tutorials <br>
All tutorials have been updated. Tutorials are available in HTML, PDF or
PowerPoint versions to allow for different browser preferences. Many
slides have notes pages to improve explanations. <br>
Updated tutorials include Maps, Proteins, Ontologies, Genes, QTL and
Literature. <br>
Genomes and BLAST tutorials are two individual tutorials, whereas
previously Genome Browser and Blast were a single tutorial. <br>
New tutorials have been developed for Markers, GrameneMart (a tool in the
Genomes database), website navigation and an overview of the modules.
<br>
Two new exercises have been created to help users conduct an ontology
search and a comparison between species. <br><br>
********************* <br>
Genomes<br><br>
Mapping to the Oryza sativa (japonica) genome of Rice SAGE tags obtained
from MGOS (Magnaporthe Grisea Oryza Sativa Database). <br><br>
Mapping to the Oryza sativa (japonica) genome of BAC ends of the
following species, sequences provided by OMAP project. <br>
Oryza coarctata <br>
Oryza minuta <br><br>
Mapping to the Oryza sativa (japonica) genome of Maize whole genome shot
gun reads from JGI (Joint Genome Institute). <br><br>
Mapping to the Oryza sativa (japonica) genome of Maize genes/loci
sequences being assayed by the Panzea project, most sequences are maize
unigenes. <br><br>
Updated mapping of OMAP BAC ends for the following species. <br>
Oryza alta <br>
Oryza brachyantha <br><br>
Updated mapping of PUTs (putative unique transcripts) downloaded from
PlantGDB. <br>
Oryza sativa <br>
Hordeum vulgare <br>
Sorghum bicolor <br>
Triticum aestivum <br>
Zea mays <br><br>
Updated mapping of 3' Sorghum EST cluster from LGB(Laboratory of Genomics
and Bioinformatics) at University of Georgia. 3' cluster sorghum
Milestone version 3.0 replaced the 3' cluster sorghum Milestone version
2.0 <br><br>
Updated mapping of Ryegrass assembly by ViaLactia, the genomic sequences
used by the assembly were cloned from a GeneThresher methyl-filtered
library. <br><br>
1307 of the previously unmapped Rice MPSS (Massively Parallel Signature
Sequencing) oligo sequences were mapped to the Oryza sativa (japonica)
genome. <br><br>
33 of the previously unmapped Rice Oligos were mapped, these oligos are
from NSF Rice Oligonucleotide Array Project <br><br>
ContigView
<dl>
<dd>The alignment feature query coordinates changed in this release
<dl>
<dd>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.
<dd>All the coordinates are 1-based.
</dl>
<dd>Some track names changed, new names are more accurate, intuitive and
consistent.
<dd>A new track named "Rice_FSTtransposon" replaced 2 old
tracks "Rice_FST_Ds" and "Rice_FST_IS"
<dd>Oryza Sativa TE (transponsable element) track added at the bottom of
the detail view.
</dl>********************* <br>
BLAST<br>
<a name="BLAST"></a><br>
There is now a BLAST tutorial <br>
********************* <br>
Maps<a name="maps"></a>
<ul>
<li>In this build (v. 19) we present our initial release of the IRGSP
build 4.0 rice genome assembly, to which we have mapped the RFLP markers
from rice.
<li>We have also added three maps of the recently-released set of Class I
SSRs.
<li>New BAC end sequence from wild <i>Oryza</i> spp. has been added to
the map of the TIGR rice assembly; some other features have also been
updated on that map.
<li>Nine rice maps been updated with additional QTL and genes.
<li>One new QTL map for maize was also added.
</ul><br>
New Sequence and Physical Maps New QTL Map Updated Maps
<dl>
<dd>Rice-Gramene IRGSP Assm 2005
<dd>Rice-Cornell Class I SSR (TIGR) 2005
<dd>Rice-Cornell Class I SSR (IRGSP) 2005
<dd>Rice-Cornell Class I SSR (93-11) 2005
<dd>Maize Bins QTL 2005 <br><br>
</dl>Features Added and Updated
<dl>
<dd>Rice-GR TIGR Assm IRGSP Seq 2005 <br><br>
</dl>QTL Added
<dl>
<dd>Rice-IRRI Lemont/Teqing RI RFLP QTL 2001
<dd>Rice-JRGP Nipponbare/Kasalath RFLP QTL 2000
<dd>Rice-JKU Asominori/IR24 RI RFLP QTL 1996 <br><br>
</dl>Genes Added
<dl>
<dd>Rice-Cornell IR64/Azucena SSR 2001
<dd>Rice-Cornell BS125/2/BS125/WLO2 RFLP 2001
<dd>Rice-IGCN ZhaiYeQing 8/JingXi 17 1998
<dd>Rice-IRMI Integrated SSR 2003
<dd>Rice-JRGP Nipponbare/Kasalath RFLP 2000
<dd>Rice-Hokkaido Morphological 2000 <br><br>
</dl>********************* <br>
Markers<a name="markers"></a><br>
The marker database now contains a total of 4,547,608 markers from more
than 180 species. <br>
The database has been updated with an additional 13,519 Class I SSRs from
rice. <br>
We have added
<dl>
<dd>2,530,661 Genbank dbEST sequences from fifty species of Poaceae
as marker type "EST"
<dd>129,527 NCBI Unigene entries from six Poaceae species and 472,408
TIGR Gene Indexes from eight Poaceae species as marker type; "EST
Cluster"; and
<dd>91,074 GenBank DNA sequences from Poaceae flagged as mRNA (excluding
dbEST) entries from 162 species as marker type "mRNA" <br><br>
</dl>The results table once again shows any number of results, even if
more than 1,000 markers result from a query. The search results are
returned unsorted, however. Users may still sort the results by clicking
on column headings, but sorting a large number (> 1,000) of markers
will be slow. <br><br>
Marker breakdown by species: <br>
Species Markers <br>
Barley (Hordeum spp.)
<x-tab> </x-tab><x-tab>
</x-tab><x-tab>
</x-tab>535720<br>
Maize (Zea spp.)
<x-tab> </x-tab><x-tab>
</x-tab><x-tab>
</x-tab>1089433<br>
Oat (Avena spp.)
<x-tab> </x-tab><x-tab>
</x-tab><x-tab>
</x-tab>8215<br>
Rice (Oryza spp.)
<x-tab> </x-tab><x-tab>
</x-tab><x-tab>
</x-tab>1475049<br>
Rye (Secale spp.)
<x-tab> </x-tab><x-tab>
</x-tab><x-tab>
</x-tab>13260<br>
Sorghum (Sorghum spp.)
<x-tab> </x-tab><x-tab>
</x-tab>260634<br>
Sugarcane (Saccharum spp.)
<x-tab> </x-tab><x-tab>
</x-tab>339657<br>
Wheat (Triticum spp. + Aegilops spp.)
<x-tab> </x-tab>787493<br>
Other
<x-tab> </x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab>38147<br><br>
********************<br>
Proteins<a name="proteins"></a><br><br>
The Gramene protein database now provides curated information on
SP-Trembl entries from family Poaceae (Grasses) <br><br>
The protein database includes new and updated information on 68,123 gene
products drawn from SwissProt (2074) and SP-TREMBL (66,049). <br><br>
These proteins are annotated using Pfam, Prosite, TMHMM (for
transmembrane domains), TargetP and Predotar (plastid, mitochrondrial and
secretory pathway targeting) and Interpro categories. A total of 49,565
gene products are associated with 1,479 Gene Ontology terms. <br><br>
You can search the protein database for entries by using either the
SWISSPROT accession number / SPTrEMBL ID / Protein Sequence Identifier
(Protein_ID) / GI number / protein name / gene name / species / cultivar.
<br><br>
The entries for Aegilops, Triticum, Avena and Hordeum link back to
GrainGenes database. Similarly the proteins from maize link back to
the MaizeGDB. <br><br>
********************<br>
Ontologies<a name="ontologies"></a><br>
New: The ontology detail page now displays 'External references' and
'Comments' associated with a given ontology term. <br><br>
Gramene Taxonomy Ontology: NEW <br>
Total number of terms = 2204. A total of 68,122 proteins, 1488 genes,
9871 QTL and 163 mapset associations. <br><br>
Gene Ontology: Updated <br>
Total number of terms = 19,498. A total of 49,565 proteins and 21,369
Ensembl genes are associated with 1,479 Gene Ontology terms. <br><br>
Plant Ontology: Updated <br>
Total number of terms = 684. Includes associations to rice genes only
<br><br>
Gramene Plant Growth Stage Ontology: No updates <br>
Total number of terms = 236 <br>
The wheat, barley and oat growth stages have the same growth stage
ontology. <br><br>
Trait Ontology: Updated <br>
Total number of terms = 693. A total of 428 genes and 9871 QTL are
associated with the trait terms. <br><br>
Environment Ontology:Updated: <br>
Total number of terms = 490 <br><br>
The Ontology browser now displays the total number of objects
(QTL/phenotype gene/EnsEMBL gene/proteins/mapsets) associated with the
"term name". For example: genus "Oryza" has following
associations: <br>
64,137 data entries <br>
55,238 proteins from various Oryza species <br>
1488 genes <br>
7302 QTL <br>
109 map sets <br>
********************<br>
Genes and Alleles<br>
<a name="mutant"></a><br>
Continually growing, Gramene release 19 presents a reorganized gene
detail display page over the last release. Specifically, changes will be
noted for allele, germplasm, nucleotide and protein sequences, and the
associated features sections. Associated features included all trait
(Trait Ontology), growth stage (Plant Ontology), plant anatomy parts
(Plant Ontology), and gene ontology terms associated with a particular
gene. Links to the Gramene Ontology have been provided as well. <br><br>
For release 19, there were 151 genes curated and mapped on several rice
genetic maps to display as interpolated phenotypes. These map positions
were based on closely linked markers. All genes with gene symbols
beginning with the letters "A" through "N" and for
which information was available are included. <br><br>
The Gramene Genes Database contains 1,488 genes from rice which have been
characterized by phenotype. Among them, 425 genes have been fully
annotated with phenotypic descriptions, associations to trait, plant and
gene ontologies, map positions, alleles, phenotypic studies, germplasms,
sequences, gene products, and related public references. <br><br>
********************<br>
QTL<br><br>
There are 246 newly curated rice QTLs from recent publications that have
been added to the database. <br>
Collaborative and integrative efforts between Gramene and MaizeGDB
continue, and 1,215 newly imported maize QTLs from MaizeGDB have been
integrated into the Gramene QTL database. <br><br>
Trait Ontology (TO) terms have been integrated with definitions of the
associated traits of QTL. <br>
This will also allow the users to browse QTL by searching traits in the
Gramene Ontology Database. <br><br>
The Gramene QTL database includes a total of 9,871 QTL <br>
These QTL were identified for numerous agronomic traits in rice, maize,
barley, oat, wheat, pearl millet, foxtail millet and wild rice. <br><br>
<br>
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************************************************************************
<br>
Claire Hebbard<br>
Gramene Outreach Coordinator<br>
G15 Bradfield Hall<br>
Ithaca, NY 14853<br><br>
Cereals are mankind's most important source of calories. Gramene can
assist in research on agriculturally important features in rice, maize,
wheat and other grasses.</body>
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