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September 2, 2009
June 3, 2009
- Release 6.1 of the MSU Rice Genome Annotation Project is available.
- A small set of genes (33) that had been classified as TE-related but that had been annotated by Community Annotators as being non-TE functional genes are no longer classified as being TE-related.
- In Release 6.0, 121 TE-related genes were not properly flagged as TE-related. Those genes have been reclassified as being TE-related.
- The all.TE_related, orthologous_groups, rice_segmental_duplication_100kb, rice_segmental_duplication_500kb, and the complete set of "TU_model_brief_info" files have been updated on our ftp site. All other files on the ftp site are identical to the release 6.0 files.
- The JGI Sorghum bicolor gene set has become available. The gene ortholog analyses have been performed again, and they now include the proteins from Sorghum bicolor in addition to the protein sequences from Arabidopsis thaliana, Oryza sativa, Populus trichocarpa and Vitis vinifera. The results from this new analysis can be searched from the Orthologous Groups Query Page.
- The JGI Sorghum bicolor gene set has been aligned to the rice pseudomolecules. Those results can be viewed in the rice genome browser.
- The JGI Sorghum bicolor proteome has been aligned to the rice proteome. Best hits and reciprocal best hits were determined. Those results can also be viewed in the rice genome browser.
January 30, 2009
- Release 6.0 of the MSU Rice Genome Annotation Project is available.
- The pseudomolecules have been reconstructed. Improved BAC sequences that have become available at Genbank/EMBL/DDBJ have been incorporated into the pseudomolecules. Improvements have been made to the pseudomolecules based on the optical mapping work of Zhou et al. (2007). Sequences from the Syngenta rice genome sequencing project have also been used to reduce and fill gaps. Syngenta sequences that did not match existing pseudomolecule sequences and that were not incorporated into the regular pseudomolecules have been assembled into an unanchored sequences pseudomolecule - ChrSy.
- Updates to the structural and functional annotation of loci and gene models have been made.
- All tracks on the Rice Genome Browser have been updated and new tracks have been added to the Rice Genome Browser. Plant Transcript Assembly alignments have been removed. PUTs from PlantGDB have been added. Alignments of the protein sequences from arabidopsis, poplar and grapevine genes to the pseudomolecules are now available as browser tracks. MULEs have now been annotated along all 12 chromosomes. There are a total of 60 tracks available on the Rice Genome Browser.
- Orthologous gene relationships between rice, arabidopsis, poplar and grapevine have been predicted with OrthoMCL, and these data can be searched or viewed in the Rice Genome Browser.
- For some loci, gene models (alternative splice isoforms) have been deprecated because transcript evidence no longer supports those alternative transcripts.
- Nuclear insertions of the organellar genomes have been annotated.
- Pack MULEs identified by Hanada et al. 2009 have been annotated on all chromosomes.
June 16, 2008
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The Rice Genome Annotation Project has moved from TIGR/JCVI to Michigan State University. The new url from the website is http://rice.plantbiology.msu.edu.
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The Release 5 rice pseudomolecules and annotation are the same as those that were formerly hosted at TIGR. We are currently working on Release 6 and plan to release it in Fall 2008.
January 24, 2007
- The Rice Genome Browser has been updated and contains 62 tracks of annotation. These tracks have been updated to contain the latest evidence and datasets.
- Gene model structure has been improved for 33,882 gene models (28,706 genes) with ~ 1.2 million of EST and/or full length cDNA evidence using the PASA program. A portion of models has been manually curated using the expression evidence and comparative genomics studies.
- The rice gene expression Anatomy Viewer/Digital Northern and Tissue Specific Expression page have been updated.
- The rice community annotation has been carried out, and the results have been integrated into the annotation database.
- Locus names have been assigned to chloroplast and mitochondrial genes.
- A new protein function category, conserved hypothetical protein, has been introduced for proteins only matching to proteins without known function in other organisms.
- The maize genetic maps used to generate the rice/maize synteny information have been updated. We now provide alignments of the cIBM 2005 and the IBM2 2005 Neighbor maps to the rice pseudomolecules.
- Gene name assignment has been changed slightly. Hypothetical proteins that align with hypothetical or an uncharacterized proteins are now called conserved hypothetical proteins.
- A track of small RNAs has been added to the Rice Genome Browser. Small RNAs from the Cereal Small RNAs Database have been mapped to the pseudomolecules.
November 2, 2006
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The Rice Genome Browser has been updated.
- The results from InterProScan searches have been added as a new track in
the browser.
- Oryza protein sequences from SwissProt were aligned to the rice
pseudomolecules, and these data have been added as an additional track in the
browser.
- The latest set of available Flanking Sequence Tags (FST) have been incorporated
into the FST track in the browser.
October 17, 2006
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New Community Annotations have been added. Annotation from 23 gene families with a
total of 454 genes has been provided by rice researchers. The newest
contributions are:
- Annotation for twenty eight glutaredoxin genes has been added.
- Annotation for thirteen indole-3-acetic-acid synthetase genes has been added.
August 5, 2006
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The Rice Genome Browser has been updated.
- Tracks representing alignments of
sequences from the TIGR Gene Indices have been removed.
- Tracks representing
alignments with the TIGR Plant Transcript
Assemblies have been added.
- A track of Interim Structural Gene Models as determined by PASA2 using
the latest FL-cDNA and EST evidence has been added. These models will serve as
the basis of the models in the version 5 release, but this data set has not yet been finalized.
- A new track of EST Read Pairs has been added. These data are derived from
the ~750,000 read pairs that were generated by KOME. Those EST read pairs that
aligned to the rice pseudomolecules in the proper orientation and in proximity to each other are displayed.
- A new expression track of Rice MPSS tags has been
added.
- The tracks for Agilent, Affymetrix, Yale and NSF expression oligos have
all been updated.
- The Protein Evidence track that shows the alignments of TIGR
niaa proteins to the rice pseudomolecules has been updated with more stringent
alignments.
- The track showing the
alignment of Pack MULEs identified by Juretic et al. has been renamed
"Pack MULEs (McGill)".
- The Flanking Sequence Tags track has been updated.
May 17, 2006
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A track showing the alignment of Kasalath and OMap rice BAC-ends has been added
to the Rice Genome Browser.
April 26, 2006
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Four new tracks have been added to the Rice Genome Browser:
- Alignments of Zea mays genomic sequences.
- Alignments of Sorghum bicolor genomic sequences
- Alignments of Arabidopsis thaliana genomic sequences
- NSF 45k Rice Oligo Microarray probes
- One track has been updated on the Rice Genome Browser:
March 13, 2006
February 17, 2006
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TIGR will be hosting its annual 5-day Annotation Workshop from June 26-30th. This workshop provides a comprehensive training in all aspects of the annotation of the rice genome. While this workshop focuses on rice, the fundamentals are broadly applicable to higher plant genomes. This workshop is geared towards biologically oriented graduate students and post-doctoral researchers who are interested in bioinformatics. Go to the Training Opportunities page to obtain more information and feel free to e-mail Matthew Campbell (campbell@tigr.org) with any questions.
January 12, 2006
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