A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Filters
NodMutDB: a database for genes and mutants involved in symbiosis
2005
Bioinformatics
Preserved Fulltext
We have developed a relational database, NodMutDB (Nodulation Mutant Database), to provide a comprehensive resource for depositing, organizing and retrieving information on symbiosis-related genes, mutants ...
NodMutDB brings together new studies and existing mutant-based literature to facilitate our understanding of how genes function in symbiotic processes in both Rhizobia and their host plants. ...
Daniel Kahn at INRA-CNRS, France for making NodMutDB gene/mutant links available at the international S.meliloti genome project Toulouse website. ...
doi:10.1093/bioinformatics/bti427
pmid:15817696
fatcat:xt2warfgcbcknogvdf2z4op5fu
A portal for rhizobial genomes: RhizoGATE integrates a Sinorhizobium meliloti genome annotation update with postgenome data
2009
Journal of Biotechnology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
In June 2008, we submitted our annotation update to the EMBL and NCBI databases. Here we describe this new annotation and a new webbased portal RhizoGATE. ...
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. ...
Acknowledgements The work was funded by grants 031U213D and 0313805A from Bundesministerium für Bildung und Forschung, Germany in the framework of the GenoMik and GenoMik Plus Competence Networks. ...
doi:10.1016/j.jbiotec.2008.11.006
pmid:19103235
pmcid:PMC2656595
fatcat:5yq6kaesxfeanpyarri4wcupxy
Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti
2011
BMC Genomics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2015; you can also visit the original URL.
The file type is application/pdf.
Notably, the symbiosis inefficient AK83 lacked several genes required for microaerophilic growth inside nodules, while several genes for accessory functions related to competition, plant invasion and bacteroid ...
We found 65 interesting orthologous groups of genes that were present only in the accessory genome, consequently responsible for phenotypic diversity and putatively involved in plant-bacterium interaction ...
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. ...
doi:10.1186/1471-2164-12-235
pmid:21569405
pmcid:PMC3164228
fatcat:nyh7mzapvfc2pdn7d2pyc7hdom
In Silico Insights into the Symbiotic Nitrogen Fixation in Sinorhizobium meliloti via Metabolic Reconstruction
2012
PLoS ONE
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
The predicted SNFrequired essential genes will facilitate understanding of the key functions in SNF and help identify key genes and design experiments for further validation. ...
There were 19.8% (112) of the 565 metabolic genes included in iHZ565 predicted to be essential for efficient SNF in bacteroids under the in silico microaerobic and nutrient sharing condition. ...
Acknowledgments We thank Changfu Tian and Yunzeng Zhang for comments and suggestions on earlier drafts of the manuscript.
Author Contributions ...
doi:10.1371/journal.pone.0031287
pmid:22319621
pmcid:PMC3272708
fatcat:j4xl46oay5gzdnvtlutylljsve
Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations
2012
Proceedings of the National Academy of Sciences of the United States of America
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
Recently we reported that soybean nodules were dominated by Sinorhizobium at sampling sites with alkaline-saline soil conditions, whereas Bradyrhizobium were widely distributed and dominated in neutral ...
Young, and three anonymous reviewers for their valuable comments on the manuscript. ...
Based on extensive research on published genetics studies of the rhizobium-legume symbiosis, we collected 561 symbiosis genes (Table S3 ) from the literature and Nodulation Mutant Database (NodMutDB) ...
doi:10.1073/pnas.1120436109
pmid:22586130
pmcid:PMC3365164
fatcat:clcrylhp7rf2beqgm3xeljbpgy
Genome sequence of the -rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia
2008
Genome Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
Altogether, specific regions in C. taiwanensis compared with C. eutrophus cover 1.02 Mb and are enriched in genes associated with symbiosis or virulence in other bacteria. ...
We did not find any gene that was both common and specific to all rhizobia, thus suggesting that a unique shared genetic strategy does not support symbiosis of rhizobia with legumes. ...
Acknowledgments We thank Michael Chandler and Patricia Siguier for sharing expertise on insertion sequence elements, and Thomas Faraut, François Enault, and Jérome Gouzy for helpful discussions. ...
doi:10.1101/gr.076448.108
pmid:18490699
pmcid:PMC2527706
fatcat:7hzlnsax3fh3hppoe7c3zi3dwi
Comparative Analysis of Genomic Island Prediction Tools
2018
Frontiers in Genetics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
We copied only the amino acid sequences from the coding sequence and constructed a multi-FASTA file for each predictor. ...
Escherichia coli CFT073 was used as a control and considered as the gold standard because its islands were previously curated in vitro. ...
Project for support. ...
doi:10.3389/fgene.2018.00619
pmid:30631340
pmcid:PMC6315130
fatcat:6ogdmnylpbd5dgm6cxw3ywjy4q