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NodMutDB: a database for genes and mutants involved in symbiosis

C. Mao, J. Qiu, C. Wang, T. C. Charles, B. W. S. Sobral
2005 Bioinformatics  
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

Anke Becker, Melanie J. Barnett, Delphine Capela, Michael Dondrup, Paul-Bertram Kamp, Elizaveta Krol, Burkhard Linke, Silvia Rüberg, Kai Runte, Brenda K. Schroeder, Stefan Weidner, Svetlana N. Yurgel (+4 others)
2009 Journal of Biotechnology  
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

Marco Galardini, Alessio Mengoni, Matteo Brilli, Francesco Pini, Antonella Fioravanti, Susan Lucas, Alla Lapidus, Jan-Fang Cheng, Lynne Goodwin, Samuel Pitluck, Miriam Land, Loren Hauser (+12 others)
2011 BMC Genomics  
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

Hansheng Zhao, Mao Li, Kechi Fang, Wenfeng Chen, Jing Wang, Alejandra Bravo
2012 PLoS ONE  
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

C. F. Tian, Y. J. Zhou, Y. M. Zhang, Q. Q. Li, Y. Z. Zhang, D. F. Li, S. Wang, J. Wang, L. B. Gilbert, Y. R. Li, W. X. Chen
2012 Proceedings of the National Academy of Sciences of the United States of America  
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

C. Amadou, G. Pascal, S. Mangenot, M. Glew, C. Bontemps, D. Capela, S. Carrere, S. Cruveiller, C. Dossat, A. Lajus, M. Marchetti, V. Poinsot (+8 others)
2008 Genome Research  
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

Antonio Camilo da Silva Filho, Roberto Tadeu Raittz, Dieval Guizelini, Camilla Reginatto De Pierri, Diônata Willian Augusto, Izabella Castilhos Ribeiro dos Santos-Weiss, Jeroniza Nunes Marchaukoski
2018 Frontiers in Genetics  
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