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GreenPhylDB

http://greenphyl.cirad.fr/

Description :
Comparative genomics of rice and Arabidopsis thaliana

DRTF

http://drtf.cbi.pku.edu.cn/

Description :
DRTF contains 2025 putative transcription factors (TFs) in Oryza sativa L. ssp. indica and 2384 in ssp. japonica, distributed in 63 families, identified by computational prediction and manual curation. It includes detailed annotations of each TF including sequence features, functional domains, Gene Ontology assignment, chromosomal localization, EST and microarray expression information, as well as multiple sequence alignment of the DNA-binding domains for each TF family. The database can be browsed and searched with a user-friendly web interface. DRTF is available at http://drtf.cbi.pku.edu.cn

Aknowledgement :
This study was supported by domestic grants: 2003CB715900 (973), 90408015 (NSFC) and the 863 Programme.

References :
Gao, G., Zhong, Y., Guo, A., Zhu, Q., Tang, W., Zheng, W., Gu, X., Wei, L. and Luo, J. (2006) DRTF: a database of rice transcription factors. Bioinformatics 2006, 22(10):1286-1287.

Rice Gene Thresher

http://rice.kps.ku.ac.th:8080/RiceGeneThresherWeb2

Description :
Web-based Application for Mining Genes Underlying QTLs in Rice Genome

Rice Mutant Database

http://rmd.ncpgr.cn/

Description :
Rice mutant database

Gramene

http://www.gramene.org/ Gramene is a curated, open-source, data resource for comparative genome analysis in the grasses. Our goal is to facilitate the study of cross-species homology relationships using information derived from public projects involved in genomic and EST sequencing, protein structure and function analysis, genetic and physical mapping, interpretation of biochemical pathways, gene and QTL localization and descriptions of phenotypic characters and mutations.

BGI-RISe - Beijing Genomics Institute Rice Information System

http://rise.genomics.org.cn/

Description :
Rice is a major food staple for the world s population and serves as a model species in cereal genome research. The Beijing Genomics Institute (BGI) has long been devoting itself to sequencing, information analysis and biological research of the rice and other crop genomes. In order to facilitate the application of the rice genomic information and to provide a foundation for functional and evolutionary studies of other important cereal crops, we implemented our Rice Information System (BGI-RIS), the most up-to-date integrated information resource as well as a workbench for comparative genomic analysis. In addition to comprehensive data from Oryza sativa L. ssp. indica sequenced by BGI, BGI-RIS also hosts carefully curated genome information from Oryza sativa L. ssp. japonica and EST sequences available from other cereal crops. In this resource, sequence contigs of indica (93-11) have been further assembled into Mbp-sized scaffolds and anchored onto the rice chromosomes referenced to physical/genetic markers, cDNAs and BAC-end sequences. We have annotated the rice genomes for gene content, repetitive elements, gene duplications (tandem and segmental) and single nucleotide polymorphisms between rice subspecies. Designed as a basic platform, BGI-RIS presents the sequenced genomes and related information in systematic and graphical ways for the convenience of in-depth comparative studies.

Aknowledgement :
Most of this work was jointly sponsored by Chinese Academy of Sciences, Commission for Economy Planning, Ministry of Science and Technology and National Natural Science Foundation of China.

References :
1. Zhao, W., Wang, J., He, X., Huang, X., Jiao, Y., Dai, M., Wei, S., Fu, J., Chen, Y., Ren, X. et al. (2004) BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics. Nucleic Acids Res, 32, D377-D382.

RetrOryza

http://retroryza.fr/

Description :
With the availability of the complete genomic sequence of rice, the identification and annotation of LTR-Retrotransposons has become a necessity as they comprise an important part of plant genomes (1). RetrOryza is a database that aims at providing the research community with the most complete resource on LTR-retrotransposon for rice. We provide the full description of 242 families of retrotransposons which have been curated and functionally annotated, this includes the identification of the Primer Binding Site, the PolyPurine Tract, the Target Site Duplication and the region matching a polyprotein when posible. The web interface allows the database to be browsed in an user friendly manner and some services are made available, such as a tool allowing the search of LTR-retrotransposons in the neighborhood of a gene of interest (based on the TIGR pseudomolecule annotation). Another service is the possibility to annotate a raw genomic sequence from any rice variety. A gff file describing the precise annotation of all LTR-retrotransposons will be returned which can be opened with any annotation tool or spreadsheet application.

Aknowledgement :
C. Chaparro is funded by the ITEGE project (ANR-05-BLAN-0244-03). The work is supported by both ANR and CNRS.

References :
Chaparro C et. al. (2007). RetrOryza: a database of the rice LTR-retrotransposons. Nucleic Acids Res. 2007 Jan;35(Database issue):D66-70. Epub 2006 Oct 28.

Cereal Small RNA Database

http://sundarlab.ucdavis.edu/smrnas/

Description :
Small RNAs (smRNAs), which include microRNAs (miRNAs), small-interfering RNAS (siRNAs) and trans-acting siRNAs (ta-siRNAs) are ~19-24 nt RNAs that are important negative regulators of nucleotide sequences involved in development, homeostasis and in the maintenance of heterochromatic states. The Cereals Small RNA Database (CSRDB) is an integrated resource for small RNAs expressed in rice and maize that includes a genome browser and a smRNA-target relational database as well as relevant bioinformatic tools. The resource currently contains a preliminary dataset of 35,454 and 68,871 mapped smRNA sequence reads for rice and maize respectively. Future updates will include smRNA data derived from different tissues and conditions. The database is accessible online at http://sundarlab.ucdavis.edu/smrnas/.

Plant MPSS

http://mpss.udel.edu/

Description :
MPSS (Massively Parallel Signature Sequencing) is a sequencing-based technology that uses a unique method to quantify gene expression level, generating millions of short sequence tags per library. The Plant MPSS databases are the largest publicly available set of tag-based gene expression data. These databases provide MPSS data with a user-friendly interface for four organisms (Arabidopsis, rice, grape, and Magnaporthe grisea, the rice blast fungus). These data include mRNA data and we’re currently expanding a set of small RNA data. The databases are built on a common set of web interfaces and are equipped with various graphical and analytical tools that allow the user to retrieve and analyze the data. The sequencing depth provides a quantitative assessment of transcript abundance (i.e. the expression level of the corresponding gene), while greatly increasing the likelihood of discovering novel transcripts. The website, equipped with various graphical and analytical tools, is available at http://mpss.udel.edu

Aknowledgement :
We are grateful to David Lee and Huizhuan Wu for their contributions to earlier versions of several of our MPSS databases. Our collaborators who contributed plant materials, RNA or MPSS libraries include Drs. Venu Reddyvari-Channa and Guo-liang Wang of the Ohio State University (rice and Magnaporthe materials), Drs. Cheng Lu and Pam Green of the University of Delaware (small RNA materials), and Dr. Alberto Iandolino of the University of California-Davis (grape materials). This work was supported primarily by awards from the NSF Plant Genome Program (#0321437) and USDA (2005-35604-15326).

References :
1. Meyers, B.C., Lee, D.K., Vu, T.H., Tej, S.S., Edberg, S.B., Matvienko, M. and Tindell, L.D. (2004) Arabidopsis MPSS. An online resource for quantitative expression analysis. Plant Physiol., 135, 801-813.

POGs/PlantRBP

http://plantrbp.uoregon.edu/

Description :
POGs/PlantRBP (http://plantrbp.uoregon.edu/) is a relational database that integrates data from rice, Arabidopsis, and maize by placing the complete Arabidopsis and rice proteomes and available maize sequences into "putative orthologous groups" (POGs). Annotation efforts will focus on predicted RNA binding proteins (RBPs): i.e. those with known RNA binding domains or otherwise implicated in RNA function. POGs form the heart of the database, and were assigned using a mutual-best-hit-strategy after performing BLAST comparisons of the predicted Arabidopsis and rice proteomes. Each POG entry includes orthologs in Arabidopsis and rice, annotated with domain organization, gene models, phylogenetic trees, and multiple intracellular targeting predictions. A graphical display maps maize sequences on to their most similar rice gene model. The database can be queried using any combination of gene name, accession, domain, and predicted intracellular location, or using BLAST. Useful features of the database include the ability to search for proteins with both a specified domain content and intracellular location, the concurrent display of mutual best hits and phylogenetic trees which facilitates evaluation of POG assignments, the association of maize sequences with POGs, and the display of targeting predictions and domain organization for all POG members, which reveals consistency (or lack thereof) of those predictions.

Aknowledgement :
This work was supported by grant DBI-0421799 from the National Science Foundation.

Oryza Tag Line

http://urgi.versailles.inra.fr/OryzaTagLine/

Description :
To organize data resulting from the phenotypic characterization of a library of T-DNA insertion lines of rice (Oryza sativa L cv. Nipponbare), we developed the Oryza Tag Line database (http://genoplante-info.infobiogen.fr/OryzaTagLine/), a project supported by the French genomic initiative Génoplante. Today, this database describes 5,000 insertion lines. In the long term, the database will contain information about 46,000 insertion lines already produced. Generic features such as production records and seed stocks, as well as textual and pictorial information on GUS or GFP assays in specific organs or tissues, or morphophysiological alterations observed during field evaluation of the insertion lines are displayed. Forward genetic search is possible through a web interface where users can submit queries based on phenotypic alterations, reporter gene expression or keywords. We also propose to combine different types of queries in an advanced search page.

Aknowledgement :
The authors would like to thank collaborators that have generated all the biological data integrated into Oryza Tag Line, especially Isabelle Barnola, Corinne Petit and Murielle Portefaix. The authors thank Christine Tranchant and Fabienne Bourgis for their help during the database interface conception and evaluation; Franck Samson, Véronique Brunnaud, Alain Lecharny and Sébastien Aubourg for rice FLAGdb++ adaptation; Delphine Samson, Fabrice Legeai, Sébastien Reboux, Isabelle Luyten and Aymeric Duclert for delivering access to the database.

INE

http://rgp.dna.affrc.go.jp/giot/INE.html

Description :
The rice genome database INE (INtegrated rice genome Explorer) is a rice integrated database with a browser for all the genomic information that have been accumulated from the large-scale rice genome analysis including cDNA analysis, genetic mapping, physical mapping and the ongoing rice genome sequencing project. A total of 481 Mbp of rice genomic sequence data (as of Sept. 2004) from 3,454 PAC/BAC and newly constructed fosmid clones has been incorporated in the database as a result of an extensive effort of the International Rice Genome Sequencing Project (IRGSP) to accelerate the completion of gettingthe genome sequence. Since the IRGSP comes very near to the goal ofcompletion, INE, which serves as the central database of IRGSP, currently contains almost 370 Mbp of non-overlapping sequence corresponding to about 95% of the entire rice genome. The sequence data areintegrated with the genetic map, a YAC (yeast artificial chromosome)-based physical map, transcript map, PAC (P1-derived artificial chromosome) / BAC (bacterial artificial chromosome) contigs for each sequenced clone. This map-based information of the sequence data would be very useful in elucidating the structure and function of specific regions of the genome particularly those containing agronomically important genes.

In 2002, RGP has finished sequencing of chromosome 1, the longest chromosomein the genome (Sasaki et al. 2002), followed by the analysis of chromosome 4 by the NCGR of Chinese Academy of Sciences (Feng et al. 2002), and chromosome 10 by US rice genome sequencing consortium (2003). At present the remaining nine chromosomes are almost completedand the finished sequences from PAC/BAC/fosmid clones are incorporated in INE. INE is also linked to the sequence annotation information. RGP is assigned for sequencing and annotation of chromosomes 1,2,6,7,8, and 9. In 2003, sequences from the rice full-length cDNAs were presented (The rice full-length cDNA consortium, 2003). The mapped cDNAs are the powerful resources for model construction of the evidenced genes. RGP has revised the system of manual curation ofthe predicted genes with the emphasis on the mapped cDNAs. For almost all the PAC/BAC clones aligned in chromosomes 2, 7, 8, and most part of 9 and half of chromosome 6, results of the manual curationof the genome sequences for the precise prediction of gene domain are presented. The RGP is also proceeding the re- annotation in which the gene models are revised with the updated information. For theclones of other six chromosomes, that are chromosomes 3,4,5,10,11, and 12, results of rice automated annotation system (RiceGAAS, Sakata et al, 2002) are presented with the finished genome sequence. Thus INE will continue to provide a system for consolidating all thegenome sequence data accumulated by the IRGSP as well as all relevant information to be elucidated from analysis of the genome sequence. INE can be accessed at http://rgp.dna.affrc.go.jp/giot/INE.html.

Recent develoments :
1. Integration of the sequence data corresponding to 95% of rice genomefrom the international sequencing effort.
2. Completion of the sequencing for almost all the chromosomes and access to the sequence data.
3. Annotation data for all the PAC/BAC clones are displayed. Revision of thecuration system based on rice full-length cDNA sequences was performed and results of the curation are shown for all the clonesalignedin chromosomes 2,6,7,8, and 9.
4. Re-annotation of the chromosome 1 sequences are successively incorporated.

Aknowledgement :
INE was developed and maintained by a grant from the Ministry of Agriculture, Forestry and Fisheries of Japan (Rice Genome Project GS-1302).

References :
1. Sasaki et al. 2002. The genome sequence and structure of rice chromosome 1. Nature 420:312-316.
2. Feng et al. 2002. Sequence and analysis of rice chromosome 4. Nature 420:316-320.
3.The Rice chromosome 10 sequencing consortium. 2003. In-depth view of structure, activity, and evolution of rice chromosome 10. Science 300:1566-1569.
4. The rice full-length cDNA consortium 2003. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301:376-379.
5. Sakata et al. 2002. RiceGAAS: an automated annotation system and database for rice genome sequence. Nucleic Acids Research 30:98-102.

IRIS - International Rice Information System

http://www.iris.irri.org/

Description :
The International Rice Information System (IRIS, www.iris.irri.org) is the rice implementation of The International Crop Information System (ICIS, www.cgiar.org/icis), a database system for the management and integration of global information on genetic resources and crop improvement for any crop. Ambiguous germplasm identification, difficulty in tracing pedigree information and lack of integration between genetic resources, characterization, breeding, evaluation and utilization data have been identified as major constraints in developing knowledge intensive crop improvement programs. ICIS is being developed to address these constraints by genetic resource specialists, crop scientists and information technicians in several centers of the Consultative Group for International Agricultural Research (CGIAR) and in National Agricultural Research Systems. The Genealogy Management System (GMS) is the core database which ensures unique identification of germplasm, management of nomenclature (including homonyms and synonyms) and retention of all germplasm development information. The GMS links germplasm with characterization and evaluation data in the Data Management System, and a trait ontology with a controlled vocabulary ensures integration of information across different studies. New components are now being added to the database to handle the diversity of rice functional genomics data including genomic sequence data, molecular genetic data, expression data and proteomic information. Stand-alone programs and web interfaces offer specialist applications and customized views to researchers with different interests. Breeders’ applications facilitate crop improvement tasks, map view and gene view facilitate molecular biology and the mutant view provides a workbench for functional genomics. The evolving crop information system will be invaluable for all researchers working on all aspects of rice biology, who will benefit from access to the latest international information linked unambiguously to specific germplasm. Just as these scientists have participated in the global exchange of genetic resources through the CGIAR’s extensive networks, IRIS will allow them to benefit from, and participate in the development and deployment of new, knowledge-intensive, crop improvement systems that link information to the seeds being exchanged.

Recent develoments :
Commissioning of new WWW site at http://www.iris.irri.org

Aknowledgement :
The members of the International Crop Information Systems (ICIS; http://www.cgiar.org/icis) community.

References :
1. Juretic N, Bureau TE, Bruskiewich RM. Transposable element annotation of the rice genome. Bioinformatics. 2004 Jan 22;20(2):155-60.
2. Bruskiewich RM, Cosico AB, Eusebio W, Portugal AM, Ramos LM, Reyes MT, Sallan MA, Ulat VJ, Wang X, McNally KL, Sackville Hamilton R, McLaren CG. Linking genotype to phenotype: the International Rice Information System (IRIS). Bioinformatics. 2003;19 Suppl 1:i63-i65.

MOsDB

http://mips.gsf.de/proj/plant/jsf/rice/index.jsp

Description :
MOsDB (http://mips.gsf.de/proj/plant/jsf/rice/index.jsp) is a resource for publicly available sequences of the rice (Oryza sativa L.) genome. Our goal at MOsDB is to provide all available data about rice genes and genomics, including (in the future) mutant information and expression profiles.

At this moment, the MOsDB database includes current (updated on daily basis) published sequences and gene annotation information of two Oryza sativa subspecies: japonica and indica. Currenty (Jan. 2005), MOsDB houses over 60000 gene calls on the pseudomolecule assembly (12 chromosomes) as provided by TIGR (http://www.tigr.org/tdb/e2k1/osa1/index.shtml). When the International Rice Genome Sequencing Project (IRGSP) genome sequence and annotation becomes available, that will be included in parallel.

To browse data, the user can navigate in a genome-oriented way. Starting from a chromosome list, one can retrieve detailed information on the chromsosome as well as links to sequence and genetic elements. The genetic element list links to reports on the protein genes or other features on display. Sequences can be viewed and downloaded as HTML, XML, FASTA and GAMEXML (Apollo annotation tool compatible) format. To visualize and browse genetic elements on a specified chromosome or contig, a graphical interface, DBBrowser, was developed.

Easy access to the MOsDB data is also provided through web services (http://www.eu-plant-genome.net) for application-level access.

Aknowledgement :
Work on MOsDB database system is funded in the GABI project by the German Federal Ministry of Education and Research (BMBF) (0312270/4).

OryGenesDB

http://orygenesdb.cirad.fr/

Description :
Rice genes, T-DNA and Ds flanking sequence tags

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