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horizontal gene transfers

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https://www.readbyqxmd.com/read/29786161/evidence-for-horizontal-gene-transfer-and-separation-of-effector-recognition-from-effector-function-revealed-by-analysis-of-effector-genes-shared-between-cape-gooseberry-and-tomato-infecting-formae-speciales-of-fusarium-oxysporum
#1
Jaime Simbaqueba, Ann-Maree Catanzariti, Carolina González, David A Jones
RNAseq reads from cape-gooseberry plants (Physalis peruviana) infected with Fusarium oxysporum f. sp. physali (Foph) were mapped against the lineage-specific transcriptome of Fusarium oxysporum f. sp. lycopersici (Fol) to look for putative effector genes. Homologues of Fol SIX1 (designated SIX1a and SIX1b), SIX7, SIX10, SIX12, SIX15 and Ave1 were identified. The near identity of the Foph and Fol SIX7, SIX10 and SIX12 genes and their intergenic regions suggest that this gene cluster may have undergone recent lateral transfer...
May 22, 2018: Molecular Plant Pathology
https://www.readbyqxmd.com/read/29779502/multi-locus-phylogenetics-of-the-midichloria-endosymbionts-reveals-variable-specificity-of-association-with-ticks
#2
M Buysse, O Duron
Candidatus Midichloria mitochondrii is a maternally inherited bacterium of ticks with a unique intra-mitochondrial lifestyle. Here, we investigate on the evolutionary history of these associations and the degree of Midichloria-tick specificity. While previous surveys used the 16S rRNA gene as an exclusive molecular marker, we rather developed a multi-locus typing method based on four more variable housekeeping genes (groEL, rpoB, dnaK and ftsZ) and on one flagellum gene (fliC) present in Midichloria genomes...
May 21, 2018: Parasitology
https://www.readbyqxmd.com/read/29778228/the-highly-heterogeneous-methylated-genomes-and-diverse-restriction-modification-systems-of-bloom-forming-microcystis
#3
Liang Zhao, Yulong Song, Lin Li, Nanqin Gan, Jerry J Brand, Lirong Song
The occurrence of harmful Microcystis blooms is increasing in frequency in a myriad of freshwater ecosystems. Despite considerable research pertaining to the cause and nature of these blooms, the molecular mechanisms behind the cosmopolitan distribution and phenotypic diversity in Microcystis are still unclear. We compared the patterns and extent of DNA methylation in three strains of Microcystis, PCC 7806SL, NIES-2549 and FACHB-1757, using Single Molecule Real-Time (SMRT) sequencing technology. Intact restriction-modification (R-M) systems were identified from the genomes of these strains, and from two previously sequenced strains of Microcystis, NIES-843 and TAIHU98...
May 2018: Harmful Algae
https://www.readbyqxmd.com/read/29778183/high-genetic-diversity-of-extended-spectrum-%C3%AE-lactamases-producing-escherichia-coli-in-feces-of-horses
#4
Syndia Sadikalay, Yann Reynaud, Stéphanie Guyomard-Rabenirina, Mélanie Falord, Célia Ducat, Laetitia Fabre, Simon Le Hello, Antoine Talarmin, Séverine Ferdinand
Extended-spectrum beta-lactamases (ESBLs), especially those of the CTX-M type, represent a major public health problem throughout the world. Although the carriage of ESBL-producing Enterobacteriaceae (EPE) in feces of horses is now well recognized, little is known about the diversity of EPE after treatment of horses with antibiotics. We undertook this study to assess and follow the diversity of EP Escherichia coli isolated from horses after antibiotic treatment for an infection. Fecal samples from two horses treated and two that were untreated were tested for the presence of EPE on different days...
June 2018: Veterinary Microbiology
https://www.readbyqxmd.com/read/29775685/phenotypic-and-genetic-resistance-traits-in-pseudomonas-aeruginosa-strains-infecting-cystic-fibrosis-patients-a-french-cohort-study
#5
Nathalie Courtois, Yvan Caspar, Max Maurin
Pseudomonas aeruginosa is responsible for chronic respiratory tract colonisation and acute exacerbations in cystic fibrosis (CF) patients. This Gram-negative bacterium often develops multidrug resistance, which represents a therapeutic challenge. Our objective was to characterize the phenotypic and genetic β-lactam resistance traits of P. aeruginosa strains isolated from CF patients followed at Grenoble Alpes university hospital. The susceptibility to β-lactam compounds of 123 P. aeruginosa strains collected from the lower respiratory tract of 45 CF patients, between 2010 and 2014, was evaluated...
May 15, 2018: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/29775460/genus-wide-comparison-of-pseudovibrio-bacterial-genomes-reveal-diverse-adaptations-to-different-marine-invertebrate-hosts
#6
Anoop Alex, Agostinho Antunes
Bacteria belonging to the genus Pseudovibrio have been frequently found in association with a wide variety of marine eukaryotic invertebrate hosts, indicative of their versatile and symbiotic lifestyle. A recent comparison of the sponge-associated Pseudovibrio genomes has shed light on the mechanisms influencing a successful symbiotic association with sponges. In contrast, the genomic architecture of Pseudovibrio bacteria associated with other marine hosts has received less attention. Here, we performed genus-wide comparative analyses of 18 Pseudovibrio isolated from sponges, coral, tunicates, flatworm, and seawater...
2018: PloS One
https://www.readbyqxmd.com/read/29773850/comparative-genomic-analysis-of-acinetobacter-spp-plasmids-originating-from-clinical-settings-and-environmental-habitats
#7
Ileana P Salto, Gonzalo Torres Tejerizo, Daniel Wibberg, Alfred Pühler, Andreas Schlüter, Mariano Pistorio
Bacteria belonging to the genus Acinetobacter have become of clinical importance over the last decade due to the development of a multi-resistant phenotype and their ability to survive under multiple environmental conditions. The development of these traits among Acinetobacter strains occurs frequently as a result of plasmid-mediated horizontal gene transfer. In this work, plasmids from nosocomial and environmental Acinetobacter spp. collections were separately sequenced and characterized. Assembly of the sequenced data resulted in 19 complete replicons in the nosocomial collection and 77 plasmid contigs in the environmental collection...
May 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29773659/modeling-leaderless-transcription-and-atypical-genes-results-in-more-accurate-gene-prediction-in-prokaryotes
#8
Alexandre Lomsadze, Karl Gemayel, Shiyuyun Tang, Mark Borodovsky
In a conventional view of the prokaryotic genome organization, promoters precede operons and RBS sites with Shine-Dalgarno consensus precede genes. However, recent experimental research suggesting a more diverse view motivated us to develop an algorithm with improved gene-finding accuracy. We describe GeneMarkS 2, an ab initio algorithm that uses a model derived by self-training for finding species-specific (native) genes, along with an array of pre-computed "heuristic" models designed to identify harder-to-detect genes (likely horizontally transferred)...
May 17, 2018: Genome Research
https://www.readbyqxmd.com/read/29772393/unexpected-mechanisms-of-resistance-in-dutch-pseudomonas-aeruginosa-isolates-collected-during-fourteen-years-of-surveillance
#9
P D Croughs, C H W Klaassen, J van Rosmalen, D M Maghdid, S A Boers, J P Hays, W H F Goessens
Pseudomonas aeruginosa is one of the most important causes of infection in the intensive care unit. It is intrinsically resistant to many antibiotics and easily acquires additional resistance genes via horizontal gene transfer of mobile genetic elements. In the present study, 1,528 P. aeruginosa isolates, obtained from a Dutch national surveillance program between the years 1998 and 2011, were analyzed for the presence of Extended Spectrum β-Lactamase (ESBL) genes blaCTX-M , blaSHV , blaTEM , blaBEL , blaPER , blaVEB , blaOXA-10 and metallo-β-Lactamase (MBL) genes blaIMP , blaVIM and blaNDM ...
May 14, 2018: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/29769695/genomic-and-functional-characterisation-of-incx3-plasmids-encoding-bla-shv-12-in-escherichia-coli-from-human-and-animal-origin
#10
Apostolos Liakopoulos, Jeanet van der Goot, Alex Bossers, Jonathan Betts, Michael S M Brouwer, Arie Kant, Hilde Smith, Daniela Ceccarelli, Dik Mevius
The blaSHV-12 β-lactamase gene is one of the most prevalent genes conferring resistance to extended-spectrum β-lactams in Enterobacteriaceae disseminating within and between reservoirs, mostly via plasmid-mediated horizontal gene transfer. Yet, studies regarding the biology of plasmids encoding blaSHV-12 are very limited. In this study, we revealed the emergence of IncX3 plasmids alongside IncI1α/γ in blaSHV-12 in animal-related Escherichia coli isolates. Four representative blaSHV-12 -encoding IncX3 plasmids were selected for genome sequencing and further genetic and functional characterization...
May 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29769342/cotesia-congregata-bracovirus-circles-encoding-ptp-and-ankyrin-genes-integrate-into-the-dna-of-parasitized-manduca-sexta-hemocytes
#11
Germain Chevignon, Georges Periquet, Gabor Gyapay, Nathalie Vega-Czarny, Karine Musset, Jean-Michel Drezen, Elisabeth Huguet
Polydnaviruses (PDVs) are essential for the parasitism success of tens of thousands of species of parasitoid wasps. PDVs are present in wasp genomes as proviruses, which serve as template for the production of double stranded circular viral DNA carrying virulence genes that are injected into lepidopteran hosts. PDV circles do not contain genes coding for particle production hence impeding viral replication in caterpillar hosts during parasitism. Here we investigated the fate of PDV circles of Cotesia congregata bracovirus during parasitism of the tobacco hornworm, Manduca sexta , by the wasp Cotesia congregata Sequences sharing similarities with Host integration Motifs (HIM) involved in integration into DNA of Microplitis demolitor bracovirus (MdBV) circles, could be identified in 12 CcBV circles, which encode PTP and VANK gene families involved in host immune disruption...
May 16, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29760209/complex-control-of-a-genomic-island-governing-biofilm-and-rugose-colony-development-in-vibrio-vulnificus
#12
Daniel M Chodur, Dean A Rowe-Magnus
V. vulnificus is a potent opportunistic human pathogen that contaminates the human food-chain by asymptomatically colonizing seafood. Expression of the 9-gene brp exopolysaccharide locus mediates surface adherence and is controlled by the secondary signaling molecule c-di-GMP and the regulator BrpT. Here, we show that c-di-GMP and BrpT also regulate the expression of an adjacent 5-gene cluster that includes the cabABC operon, brpT and another VpsT-like transcriptional regulator, brpS The expression of the 14 genes spanning the region increased with elevated intracellular c -di-GMP levels in a BrpT-dependent manner, save brpS , which was positively regulated by c-di-GMP and repressed by BrpT...
May 14, 2018: Journal of Bacteriology
https://www.readbyqxmd.com/read/29760148/bacterial-silver-resistance-gained-by-cooperative-interspecies-redox-behavior
#13
Michael Muller
Silver has emerged as an important therapeutic option for wound infections in recent years due to its broad spectrum antimicrobial activity. The silver cation (Ag+ ), but not the bulk metal (Ag0 ), is highly toxic for most microorganisms although resistance due to genetic modification or horizontal gene transfer does occur. Pseudomonas aeruginosa , however, achieves silver resistance by producing the redox active metabolite pyocyanin that reduces Ag+ to non-toxic Ag0 Pyocyanin also possess broad spectrum antimicrobial activity...
May 14, 2018: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29759900/detection-of-the-type-iii-secretion-system-and-its-phylogenetic-and-symbiotic-characterization-in-peanut-bradyrhizobia-isolated-from-guangdong-province-china
#14
Huaqin Ruan, Meijuan Hu, Jingyu Chen, Xue Li, Ting Li, Yongxiu Lai, En Tao Wang, Jun Gu
The distribution of rhcRST and rhcJ-C1 fragments located in different loci of the type III secretion system (T3SS) gene cluster in the peanut-nodulating bradyrhizobia isolated from Guangdong Province, China was investigated by PCR-based sequencing. T3SS was detected in approximately one-third of the peanut bradyrhizobial strains and the T3SS-harboring strains belonging to different Bradyrhizobium genomic species. Diverse T3SS groups corresponding to different symbiotic gene types were defined among the 23 T3SS-harboring strains...
April 8, 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29753892/next-generation-sequencing-reveals-packaging-of-host-rnas-by-brome-mosaic-virus
#15
N Shrestha, P H Weber, S V Burke, W Wysocki, M R Duvall, J J Bujarski
Although RNA viruses evolved the mechanisms of specific encapsidation, miss-packaging of cellular RNAs has been reported in such RNA virus systems as flock house virus or cucumber necrosis virus. To find out if brome mosaic virus (BMV), a tripartite RNA virus, can package cellular RNAs, BMV was propagated in barley and in Nicotiana benthamiana hosts, purified by cesium chloride (CsCl) gradient ultracentrifugation followed by nuclease treatment to remove any contaminating cellular (host) RNAs. The extracted virion RNA was then sequenced by using next-generation sequencing (NGS RNA-Seq) with the Illumina protocol...
May 10, 2018: Virus Research
https://www.readbyqxmd.com/read/29752561/searching-whole-genome-sequences-for-biochemical-identification-features-of-emerging-and-reemerging-pathogenic-corynebacterium-species
#16
André S Santos, Rommel T Ramos, Artur Silva, Raphael Hirata, Ana L Mattos-Guaraldi, Roberto Meyer, Vasco Azevedo, Liza Felicori, Luis G C Pacheco
Biochemical tests are traditionally used for bacterial identification at the species level in clinical microbiology laboratories. While biochemical profiles are generally efficient for the identification of the most important corynebacterial pathogen Corynebacterium diphtheriae, their ability to differentiate between biovars of this bacterium is still controversial. Besides, the unambiguous identification of emerging human pathogenic species of the genus Corynebacterium may be hampered by highly variable biochemical profiles commonly reported for these species, including Corynebacterium striatum, Corynebacterium amycolatum, Corynebacterium minutissimum, and Corynebacterium xerosis...
May 11, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29751066/keeping-it-together-absence-of-genetic-variation-and-dna-incorporation-by-the-predatory-bacteria-micavibrio-aeruginosavorus-and-bdellovibrio-bacteriovorus-during-predation
#17
Shilpi Gupta, Alexander Lemenze, Robert J Donnelly, Nancy D Connell, Daniel E Kadouri
The use of predatory bacteria as a potential live therapeutic to control human infection is gaining increased attention. Earlier work with Micavibrio spp. and Bdellovibrio spp. has demonstrated the ability of these predators to control drug-resistant Gram-negative pathogens, Tier-1 select agents and biofilms. Additional studies also confirmed that introducing high doses of the predators into animals does not negatively impact animal well-being and might assist in reducing bacterial burden in vivo. The survival of predators requires extreme proximity to the prey cell, which might bring about horizontal transfer of genetic material, such as genes encoding for pathogenic genetic islands that would indirectly facilitate the spread of genetic material to other organisms...
May 8, 2018: Research in Microbiology
https://www.readbyqxmd.com/read/29746697/adaptation-of-s-cerevisiae-to-fermented-food-environments-reveals-remarkable-genome-plasticity-and-the-footprints-of-domestication
#18
Jean-Luc Legras, Virginie Galeote, Frédéric Bigey, Carole Camarasa, Souhir Marsit, Thibault Nidelet, Isabelle Sanchez, Arnaud Couloux, Julie Guy, Ricardo Franco-Duarte, Marcet-Houben Marina, Toni Gabaldon, Dorit Schuller, José Paulo Sampaio, Sylvie Dequin
The budding yeast Saccharomyces cerevisiae can be found in the wild and is also frequently associated with human activities. Despite recent insights into the phylogeny of this species, much is still unknown about how evolutionary processes related to anthropogenic niches have shaped the genomes and phenotypes of S. cerevisiae. To address this question, we performed population-level sequencing of 82 S. cerevisiae strains from wine, flor, rum, dairy products, bakeries and the natural environment (oak trees). These genomic data enabled us to delineate specific genetic groups corresponding to the different ecological niches and revealed high genome content variation across the groups...
May 8, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29745854/the-performance-of-coalescent-based-species-tree-estimation-methods-under-models-of-missing-data
#19
Michael Nute, Jed Chou, Erin K Molloy, Tandy Warnow
BACKGROUND: Estimation of species trees from multiple genes is complicated by processes such as incomplete lineage sorting, gene duplication and loss, and horizontal gene transfer, that result in gene trees that differ from each other and from the species phylogeny. Methods to estimate species trees in the presence of gene tree discord due to incomplete lineage sorting have been developed and proved to be statistically consistent when gene tree discord is due only to incomplete lineage sorting and every gene tree includes the full set of species...
May 8, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29745213/-bacterial-quorum-sensing-cooperation-and-cheating
#20
Bai Min Lai, Mei Zhen Wang, Dong Sheng Shen
Quorum sensing (QS), a cell-to-cell communication, regulates a variety of social beha-viors, such as biofilm formation, public goods produce and gene horizontal transfer of bacteria. In the process of quorum sensing, public goods could be utilized by any members in the population, which was termed as cooperation. Notably, public goods also could be shared by the individuals who could not produce them, which was termed as cheating. Once cheaters come up, they possibly maintain equilibrium with cooperators, meanwhile they also possibly induce the collapse of population due to their rapid growth and shortage of public goods...
May 18, 2017: Ying Yong Sheng Tai Xue Bao, the Journal of Applied Ecology
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