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Epstein B.,University of Minnesota | Branca A.,University of Minnesota | Branca A.,University of Munster | Mudge J.,National Center for Genome Resources | And 9 more authors.
PLoS Genetics | Year: 2012

The symbiosis between rhizobial bacteria and legume plants has served as a model for investigating the genetics of nitrogen fixation and the evolution of facultative mutualism. We used deep sequence coverage (>100×) to characterize genomic diversity at the nucleotide level among 12 Sinorhizobium medicae and 32 S. meliloti strains. Although these species are closely related and share host plants, based on the ratio of shared polymorphisms to fixed differences we found that horizontal gene transfer (HGT) between these species was confined almost exclusively to plasmid genes. Three multi-genic regions that show the strongest evidence of HGT harbor genes directly involved in establishing or maintaining the mutualism with host plants. In both species, nucleotide diversity is 1.5-2.5 times greater on the plasmids than chromosomes. Interestingly, nucleotide diversity in S. meliloti but not S. medicae is highly structured along the chromosome - with mean diversity (θπ) on one half of the chromosome five times greater than mean diversity on the other half. Based on the ratio of plasmid to chromosome diversity, this appears to be due to severely reduced diversity on the chromosome half with less diversity, which is consistent with extensive hitchhiking along with a selective sweep. Frequency-spectrum based tests identified 82 genes with a signature of adaptive evolution in one species or another but none of the genes were identified in both species. Based upon available functional information, several genes identified as targets of selection are likely to alter the symbiosis with the host plant, making them attractive targets for further functional characterization. © 2012 Epstein et al. Source


Epstein B.,University of Minnesota | Epstein B.,Washington State University | Sadowsky M.J.,University of Minnesota | Sadowsky M.J.,BioTechnology Institute | Tiffin P.,University of Minnesota
Genome Biology and Evolution | Year: 2014

Structural variation, including variation in gene copy number and presence or absence of genes, is a widespread and important source of genomic variation. We used whole-genome DNA sequences from 48 strains of Sinorhizobium (recently renamed Ensifer), including 20 strains of Sinorhizobium melilotiand 12 strains of S. medicae thatwere the focus of the analyses, to study the fitness effects of new structural variants created by duplication and horizontal gene transfer. We find that derived duplicated and horizontally transferred (HT) genes segregate at lower frequency than synonymous and nonsynonymous nucleotide variants in S. meliloti and S. medicae. Furthermore, the relative frequencies of different types of variants are more similar inS. medicaethan in S. meiloti, the specieswith the larger effective population size. These results are consistent with the hypothesis that most duplications and HT genes have deleterious effects. Diversity of duplications, as measured by segregating duplicated genes per gene, is greater than nucleotide diversity, consistent with a high rate of duplication. Our results suggest that the vast majority of structural variants found among closely related bacterial strains are short-lived and unlikely to be involved in species-wide adaptation. © 2014 The Author(s). Source


Bos K.I.,University of Tubingen | Harkins K.M.,Arizona State University | Herbig A.,University of Tubingen | Coscolla M.,Swiss Tropical and Public Health Institute | And 30 more authors.
Nature | Year: 2014

Modern strains of Mycobacterium tuberculosis from the Americas are closely related to those fromEurope, supporting the assumption that human tuberculosis was introduced post-contact1. This notion, however, is incompatible with archaeological evidence of pre-contact tuberculosis in the New World2. Comparative genomics of modern isolates suggests that M. tuberculosis attained its worldwide distribution following human dispersals out of Africa during the Pleistocene epoch3, although this has yet to be confirmed with ancient calibration points. Here we present three 1,000-year-oldmycobacterial genomesfromPeruvianhuman skeletons, revealing that amember of the M. tuberculosis complex caused human disease before contact.The ancient strains are distinct fromknownhuman-adapted forms and are most closely related to those adapted to seals and sea lions. Two independent dating approaches suggest a most recent common ancestor for the M. tuberculosis complex less than 6,000 years ago, which supports a Holocene dispersal of the disease. Our results implicate sea mammals as having played a role in transmitting the disease to humans across the ocean. © 2014 Macmillan Publishers Limited. All rights reserved. Source


Trademark
Biotechnology Institute | Date: 2016-03-08

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Imperiale B.R.,Reference Laboratory | Cataldi A.A.,BioTechnology Institute | Morcillo N.S.,Reference Laboratory
International Journal of Tuberculosis and Lung Disease | Year: 2011

SETTING: Dr Cetrangolo Hospital, Buenos Aires Province, Argentina. OBJECTIVE: To evaluate a multiplex allele-specific polymerase chain reaction (MAS-PCR) to detect multidrugresistant tuberculosis (MDR-TB) clinical isolates and to describe the main mutations conferring resistance to isoniazid (INH) and rifampicin (RMP). DESIGN: Drug-resistant Mycobacterium tuberculosis clinical isolates were tested to detect mutations using MAS-PCR. The genes involved were katG, inhA promoter and rpoB. RESULTS: Among 193 clinical isolates included in the study, 52.6% of the INH-resistant isolates presented a mutation in the katG (315) gene, 28.1% in the inhAP (-15) and 3.0% in both. For the rpoB gene, 60% of the RMP-resistant isolates showed a mutation in codon 531, 17.5% in 526 and 2.5% in 516. Results were compared with those obtained by sequencing, and 100% concordance was obtained for the detection of the mutation in katG (315), 94.1% for inhAP (-15), and 97.8% for rpoB. The global concordance between both methods was 98%. CONCLUSIONS: The MAS-PCR system allowed the simultaneous and rapid detection of approximately 80.0% of the drug-resistant clinical isolates. This method could be used as a rapid and simple screening tool to detect drug-resistant TB in clinical practice. © 2011 The Union. Source

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