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The aim of this Oryza sativa database was first to display sequence information resulting from the activities of our group, such as the T-DNA and Ds flanking sequence tags (FSTs) produced in the framework of the French genomics initiative Genoplante and the EU consortium Cereal Gene Tags. Later, we decided to link this information with related molecular data from external rice molecular resources (cDNA full length, Gene, EST, Markers, Expression data...). Genome Browser (Gbrowse), a Web-based application for displaying genomic annotations and other features, is the core of our database. The reference annotation layer consists in the 12 rice pseudomolecules released by the MSU (Version 6.1, June 2009). All the data are superposed as annotations layers and positioned with respect to these pseudomolecules. We developed a set of tools around GBrowse to retrieve as exhaustively as possible information related to queries with several starting points. These tools allow a molecular geneticist to readily find insertion lines (T-DNA, Tos17, Ds) in genes of interest and to retrieve all the associated annotations related to these sequences. |
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Breaking news Opening at Montpellier, France of the RicE FUnctional GEnomics (REFUGE) platform: an international hosting platform for elucidating gene function using rice as a model system. [More details] Archipelago version 4 - July 2009 is out-It contains 639 new pieces of information for 562 rice genes- 271 pieces of information are new as compared to previous release- This release includes data from Kaku et al (PNAS 2006) and Kimoto-Tomiyama et al (PMB 2003) dealing with rice response to chitin elicitor as well as data from Zhao et al (TAG 2008) dealing with genes responsive to the fngal pathogen Rhizoctonia solani. Rice Annotation Release 6.1 (June 2009) TAIR9 Genome Release (June 2009) All tracks on both Genome Browser had been updated. Archipelago version 3 - Update April 2009. More than 1000 informations relative to disease resistance were added to Archipelago. This represent more than 750 genes that were NOT previously known to be involved in disease resistance. This information comes from 8 recently published papers : - Umemura et al, Plant J 2009. This paper deals with : - Kondou et al, Plant J 2009. This paper deals with rice genes that were over-expressed in arabidopsis - Kottapalli et al, PPB 2007. This paper deals with resistant and susceptible rice infected with Xanthomonas - Lian et al, PMB 2006. This paper deals with genes that are mis-regulated after nitrogen deprivation - Shi and Wang, Gene 2008. This paper deals with resistant cultivar carrying Pi-9 infected by Magnaporthe - Stefens and Sauter, Plant Cell 2009. This paper deals with genes induced by ethylene and hydrogen peroxide - Ventelon-Debout et al, BMC Plant Biology 2008. This paper deals with genes expressed in rice infected by the RYMV. - Ding et al, Plant Physiol 2009. This papers deals with systematic Y2H approach of rice receptor-like kinases. We are pleased to inform you that Oxford Journals has published an update of OryGenesDB in Nucleic Acids Research. G. Droc ,C. Perin, S. Fromentin and P. Larmande. OryGenesDB 2008 update: database interoperability for functional genomics of rice. Nucl. Acids Res Advance Access published on November 26, 2008. |
| Researchers who wish to cite OryGenesDB website are encouraged to refer to our publications : G. Droc , M. Ruiz , P. Larmande , A. Pereira , P. Piffanelli , J. B. Morel , A. Dievart , B. Courtois , E. Guiderdoni , and C. Perin. OryGenesDB: a database for rice reverse genetics. Nucl. Acids Res. 34: D736-D740. |