Journal ArticleDOI
Population genomics of the symbiotic plasmids of sympatric nitrogen-fixing Rhizobium species associated with Phaseolus vulgaris.
Olga M. Pérez Carrascal,David VanInsberghe,Soledad Juárez,Martin F. Polz,Pablo Vinuesa,Víctor González +5 more
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TLDR
In this paper, the genomes of 33 strains isolated from the rhizosphere and root nodules of a particular bean variety grown in the same agricultural plot were sequenced and compared, and it was found that the Rhizobium species coexist with low genetic recombination across their core genomes.Abstract:
Cultivated common beans are the primary protein source for millions of people around the world who subsist on low-input agriculture, enabled by the symbiotic N2 -fixation these legumes perform in association with rhizobia. Within a single agricultural plot, multiple Rhizobium species can nodulate bean roots, but it is unclear how genetically isolated these species remain in sympatry. To better understand this issue, we sequenced and compared the genomes of 33 strains isolated from the rhizosphere and root nodules of a particular bean variety grown in the same agricultural plot. We found that the Rhizobium species we observed coexist with low genetic recombination across their core genomes. Accessory plasmids thought to be necessary for the saprophytic lifestyle in soil show similar levels of genetic isolation, but with higher rates of recombination than the chromosomes. However, the symbiotic plasmids are extremely similar, with high rates of recombination and do not appear to have co-evolved with the chromosome or accessory plasmids. Therefore, while Rhizobium species are genetically isolated units within the microbial community, a common symbiotic plasmid allows all Rhizobium species to engage in symbiosis with the same host in a single agricultural plot.read more
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SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Population Genomics of Early Events in the Ecological Differentiation of Bacteria
B. J. Shapiro,Jonathan Friedman,Otto X. Cordero,Sarah P. Preheim,Sonia Timberlake,Gitta Szabó,Martin F. Polz,Eric J. Alm +7 more
TL;DR: This paper showed that in two recently diverged populations of ocean bacteria, ecological differentiation has occurred akin to a sexual mechanism: a few genome regions have swept through subpopulations in a habitat-specific manner, accompanied by gradual separation of gene pools as evidenced by increased habitat specificity of the most recent recombinations.
Journal ArticleDOI
Rhizobia: from saprophytes to endosymbionts.
TL;DR: Rhizobia are some of the best-studied plant microbiota, which must exist in soil and compete with other members of the microbiota before infecting legumes and forming N2-fixing bacteroids.
Journal ArticleDOI
Multidisciplinary approaches for studying rhizobium-legume symbioses.
George C. diCenzo,Maryam Zamani,Alice Checcucci,Marco Fondi,Joel S. Griffitts,Turlough M. Finan,Alessio Mengoni +6 more
TL;DR: This review summarizes many of the research strategies that have been employed in the study of rhizobia and the unique knowledge gained from these diverse tools, with a focus on genome- and systems-level approaches.
Journal ArticleDOI
Horizontal operon transfer, plasmids, and the evolution of photosynthesis in Rhodobacteraceae
TL;DR: This work investigates the evolution of phototrophy in 105 genome-sequenced Rhodobacteraceae and provides the first unequivocal evidence for the horizontal transfer of the photosynthesis gene cluster (PGC).
References
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Journal ArticleDOI
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Stephen F. Altschul,Thomas L. Madden,Alejandro A. Schäffer,Jinghui Zhang,Zheng Zhang,Webb Miller,David J. Lipman +6 more
TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
Journal ArticleDOI
MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0
TL;DR: An advanced version of the Molecular Evolutionary Genetics Analysis software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis, is released, which enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny.
Journal ArticleDOI
MUSCLE: multiple sequence alignment with high accuracy and high throughput
TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
Brief Communication MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0
TL;DR: The Molecular Evolutionary Genetics Analysis (MEGA) software as discussed by the authors provides facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis, including the inference of timetrees.
Journal ArticleDOI
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.
TL;DR: This work presents some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees.
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