Legacy News - Rice Genome Annotation Project
The following is a list of older Rice Genome Annotation Project updates These updates may refer to web pages or resources that no longer exist on the current site.
- The Buell Lab has moved to the University of Georgia! The new URL for the Rice Genome Annotation Project (RGAP) website is rice.uga.edu.
- A paper describing the unified Os-Nipponbare-Reference-IRGSP-1.0 pseudomolecules and MSU Rice Genome Annotation Project Release 7 has been published in the journal Rice:
- Kawahara, Y., de la Bastide, M., Hamilton J. P., Kanamori, H., McCombie, W. R., Ouyang, S., Schwartz, D. C., Tanaka, T., Wu, J., Zhou, S., Childs, K. L., Davidson, R. M., Lin, H., Quesada-Ocampo, L., Vaillancourt, B., Sakai, H., Lee, S. S., Kim, J., Numa, H., Itoh, T., Buell, C. R., Matsumoto, T. 2013. Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice 6:4.
- The GFF3 and brief info files were updated on the FTP site. The update corrects issues with the UTR feature type and several cases where the mRNA coordinates were incorrect. The sequence files and other features in the GFF3 files were not changed.
- Release 7 of the MSU Rice Genome Annotation Project is available.
- This release is based on a new pseudomolecule assembly (Os-Nipponbare-Reference-IRGSP-1.0) made in collaboration with the Agrogenomics Research Center at the National Institute of Agrobiological Sciences, Tsukuba, Japan. This set of pseudomolecules unifies the previous MSU with the IRGSP/RAP effort.
- Genome browser has been updated with 81 tracks of data.
- Gene coexpression analysis has been performed on 15 different publically available gene expression data sets. The data have been analyzed to identify modules of highly coexpressed genes. The procedure used and the experiments that have been analyzed are described on the Gene Coexpression Analysispage.
- Three new search pages have been prepared to allow researchers to examine the gene coexpression data: Gene Expression Plot, Gene Correlation Search Within a Module and Gene Correlation Search Within an Experiment
- The gene annotation report pages have been updated to display gene coexpression annotations
- Updates have been made to the MSU Rice Genome Annotation Project (RGAP) website. The style of the entire project website has been modernized. All pages remain, but the layout and color scheme have been updated. The menu bar has been reorganized to be more simple and logical.
- The software that drives the Rice Genome Browser has been updated to the version 1.70. This update provides a more customizable browser experience for users. It also allows the display of RNA-seq data in "wiggle" tracks.
- A track of predicted rRNA loci has been added to the Rice Genome Browser.
- Tracks displaying alignments of Brachypodium distachyon and Zea mays gene alignments and tracks showing the top three best hits of Brachypodium distachyon and Zea mays gene models to rice gene models have been added to the Rice Genome Browser.
- "Wiggle" tracks showing the relative abundance and location of RNA-Seq reads from three libraries are viewable in the Rice Genome Browser.
- BAC sequences from chromosome 3 of Oryza barthii have been aligned to the Oryza sativa pseudomolecules, and those alignments are viewable in the Rice Genome Browser.
- The gene report pages have been updated to include model genome ortholgous gene group information from the Arabidopsis thaliana, rice, sorghum, poplar and grape gene sets.
- The gene report pages have been updated to include Poaceae ortholgous gene group information from the Brachypodium distachyon, rice, sorghum and maize gene sets.
- The Rice Genome Facts page has been updated with the latest statistics of the rice nucleotide sequences in GenBank and rice related publications in PubMed.
- 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.
- 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.
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This work is supported by grants (DBI-0321538/DBI-0834043) from the National Science Foundation and funds from the Georgia Research Alliance, Georgia Seed Development, and University of Georgia.