Horizontal gene transfer in glycosyl hydrolases inferred from codon usage in Escherichia coli and Bacillus subtilis

Garcı́a-Vallvé, Santiago; Palau, Jaume; Romeu, Antoni

doi:10.1093/oxfordjournals.molbev.a026203

Cited by 262 publications

(163 citation statements)

References 35 publications

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“…The extent to which horizontal gene transfer may occur for resource acquisition machinery among prokaryotes is unclear. Previous work suggests that horizontal gene transfer may significantly impact the evolution of chitin-degrading enzymes (Garcia-Vallve et al, 1999). However, adaptive transfer of genes is limited to those that can be transferred as a functional unit containing a complement of genes that are involved in processing a single resource molecule (Wiedenbeck and Cohan, 2011).…”

Section: Discussionmentioning

confidence: 99%

Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes

2013

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Understanding the relationship between prokaryotic traits and phylogeny is important for predicting and modeling ecological processes. Microbial extracellular enzymes have a pivotal role in nutrient cycling and the decomposition of organic matter, yet little is known about the phylogenetic distribution of genes encoding these enzymes. In this study, we analyzed 3058 annotated prokaryotic genomes to determine which taxa have the genetic potential to produce alkaline phosphatase, chitinase and b-N-acetyl-glucosaminidase enzymes. We then evaluated the relationship between the genetic potential for enzyme production and 16S rRNA phylogeny using the consenTRAIT algorithm, which calculated the phylogenetic depth and corresponding 16S rRNA sequence identity of clades of potential enzyme producers. Nearly half (49.2%) of the genomes analyzed were found to be capable of extracellular enzyme production, and these were non-randomly distributed across most prokaryotic phyla. On average, clades of potential enzymeproducing organisms had a maximum phylogenetic depth of 0.008004-0.009780, though individual clades varied broadly in both size and depth. These values correspond to a minimum 16S rRNA sequence identity of 98.04-98.40%. The distribution pattern we found is an indication of microdiversity, the occurrence of ecologically or physiologically distinct populations within phylogenetically related groups. Additionally, we found positive correlations among the genes encoding different extracellular enzymes. Our results suggest that the capacity to produce extracellular enzymes varies at relatively fine-scale phylogenetic resolution. This variation is consistent with other traits that require a small number of genes and provides insight into the relationship between taxonomy and traits that may be useful for predicting ecological function.

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Section: Discussionmentioning

confidence: 99%

Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes

2013

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“…Identifying evolution by HGT involves detailed study of the protein level, including orthologous analysis and confirmation of an inappropriate position in a phylogenetic tree (Smith et al 1992;Syvanen 1994). For example, we determined previously that the xynA gene from B. subtilis has been transferred, probably from an actinomyces bacterium (Garcia-Vallvé et al 1999).…”

Section: Discussionmentioning

confidence: 99%

“…That is, the bias in codon usage is species specific. Both parameters (G+C content and codon usage) have been used to determine the acquisition of genomic portions by HGT (Kaplan and Fine 1998;Garcia-Vallvé et al 1999. In this article, we have combined a set of statistical approaches to determine which genes significantly deviate from the mean G+C and/or from the average codon usage and to so identify recently transferred genes in 17 bacterial complete genomes and seven archaeal ones.…”

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confidence: 99%

Horizontal Gene Transfer in Bacterial and Archaeal Complete Genomes

Garcı́a-Vallvé

Romeu²,

Palau³

2000

Genome Research

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327

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“…SSR products were treated as presence or absence when calculating a similarity coefficient. The Jaccard coefficient was used to compute a similarity matrix using a server running the program DendroUPGMA (http:// genomes.urv.es/UPGMA/) (Garcia-Vallvé et al 1999). This matrix was used to construct a dendrogram using the program PhyloWidget (http://www.phylowidget.…”

Section: Ssr Primers and Pcr Assaysmentioning

confidence: 99%

Development of a core set of SSR markers for the characterization of Gossypium germplasm

Fang

Kohel

et al. 2012

Euphytica

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Molecular markers such as simple sequence repeats (SSR) are a useful tool for characterizing genetic diversity of Gossypium germplasm. Genetic profiles by DNA fingerprinting of cotton accessions can only be compared among different collections if a common set of molecular markers are used by different laboratories and/or research projects. Herein, we propose and report a core set of 105 SSR markers with wide genome coverage of at least four evenly distributed markers per chromosome for the 26 tetraploid cotton chromosomes. The core marker set represents the efforts of ten research groups involved in marker development, and have been systematically evaluated for DNA polymorphism on the 12 genotypes belonging to six Gossypium species [known collectively as the cotton marker database (CMD) panel]. A total of 35 marker bins in triplex sets were arranged from the 105 markers that were each labeled with one of the three fluorescent dyes (FAM, HEX, and NED). Results from this study indicated that the core marker set was robust in revealing DNA polymorphism either between and within species. Average value of polymorphism information content (PIC) among the CMD panel was 0.65, and that within the cultivated cotton Electronic supplementary material The online version of this article

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Horizontal gene transfer in glycosyl hydrolases inferred from codon usage in Escherichia coli and Bacillus subtilis

Cited by 262 publications

References 35 publications

Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes

Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes

Horizontal Gene Transfer in Bacterial and Archaeal Complete Genomes

Development of a core set of SSR markers for the characterization of Gossypium germplasm

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