title: A portal for rhizobial genomes: RhizoGATE integrates a Sinorhizobium meliloti genome annotation update with postgenome data.
abstract: Sinorhizobium meliloti is a symbiotic soil bacterium of the alphaproteobacterial subdivision. Like other rhizobia, S. meliloti induces nitrogen-fixing root nodules on leguminous plants. This is an ecologically and economically important interaction, because plants engaged in symbiosis with rhizobia can grow without exogenous nitrogen fertilizers. The S. meliloti-Medicago truncatula (barrel medic) association is an important symbiosis model. The S. meliloti genome was published in 2001, and the M. truncatula genome currently is being sequenced. Many new resources and data have been made available since the original S. meliloti genome annotation and an update was needed. In June 2008, we submitted our annotation update to the EMBL and NCBI databases. Here we describe this new annotation and a new web-based portal RhizoGATE. About 1000 annotation updates were made; these included assigning functions to 313 putative proteins, assigning EC numbers to 431 proteins, and identifying 86 new putative genes. RhizoGATE incorporates the new annotion with the S. meliloti GenDB project, a platform that allows annotation updates in real time. Locations of transposon insertions, plasmid integrations, and array probe sequences are available in the GenDB project. RhizoGATE employs the EMMA platform for management and analysis of transcriptome data and the IGetDB data warehouse to integrate a variety of heterogeneous external data sources.
authors.affiliation: Genetics and Systems Biology, Faculty of Biology, University of Freiburg, Freiburg, Germany. anke.becker@biologie.uni-freiburg.de
authors.forename: Anke
authors.initials: A
authors.lastname: Becker
authors.forename: Melanie J
authors.initials: MJ
authors.lastname: Barnett
authors.forename: Delphine
authors.initials: D
authors.lastname: Capela
authors.forename: Michael
authors.initials: M
authors.lastname: Dondrup
authors.forename: Paul-Bertram
authors.initials: PB
authors.lastname: Kamp
authors.forename: Elizaveta
authors.initials: E
authors.lastname: Krol
authors.forename: Burkhard
authors.initials: B
authors.lastname: Linke
authors.forename: Silvia
authors.initials: S
authors.lastname: Rüberg
authors.forename: Kai
authors.initials: K
authors.lastname: Runte
authors.forename: Brenda K
authors.initials: BK
authors.lastname: Schroeder
authors.forename: Stefan
authors.initials: S
authors.lastname: Weidner
authors.forename: Svetlana N
authors.initials: SN
authors.lastname: Yurgel
authors.forename: Jacques
authors.initials: J
authors.lastname: Batut
authors.forename: Sharon R
authors.initials: SR
authors.lastname: Long
authors.forename: Alfred
authors.initials: A
authors.lastname: Pühler
authors.forename: Alexander
authors.initials: A
authors.lastname: Goesmann
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D030541:Databases, Genetic; D016680:Genome, Bacterial; D019451:Information Management; D016247:Information Storage and Retrieval; D020407:Internet; D046913:Medicago truncatula; D046228:Microarray Analysis; D016962:Sinorhizobium meliloti / Q000235:genetics*; D014584:User-Computer Interface
chemical_list: D001426:Bacterial Proteins