A portal for rhizobial genomes: RhizoGATE integrates a Sinorhizobium meliloti genome annotation update with postgenome data.
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.
Becker
Anke
A
Genetics and Systems Biology, Faculty of Biology, University of Freiburg, Freiburg, Germany. anke.becker@biologie.uni-freiburg.de
Barnett
Melanie J
MJ
Capela
Delphine
D
Dondrup
Michael
M
Kamp
Paul-Bertram
PB
Krol
Elizaveta
E
Linke
Burkhard
B
Rüberg
Silvia
S
Runte
Kai
K
Schroeder
Brenda K
BK
Weidner
Stefan
S
Yurgel
Svetlana N
SN
Batut
Jacques
J
Long
Sharon R
SR
Pühler
Alfred
A
Goesmann
Alexander
A
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
D001426:Bacterial Proteins