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https://www.readbyqxmd.com/read/27864136/the-underlying-mechanisms-of-genetic-innovation-and-speciation-in-the-family-corynebacteriaceae-a-phylogenomics-approach
#1
Xiao-Yang Zhi, Zhao Jiang, Ling-Ling Yang, Ying Huang
The pangenome of a bacterial species population is formed by genetic reduction and genetic expansion over the long course of evolution. Gene loss is a pervasive source of genetic reduction, and (exogenous and endogenous) gene gain is the main driver of genetic expansion. To understand the genetic innovation and speciation of the family Corynebacteriaceae, which cause a wide range of serious infections in humans and animals, we analyzed the pangenome of this family, and reconstructed its phylogeny using a phylogenomics approach...
November 15, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/27861551/genomes-of-gardnerella-strains-reveal-an-abundance-of-prophages-within-the-bladder-microbiome
#2
Kema Malki, Jason W Shapiro, Travis K Price, Evann E Hilt, Krystal Thomas-White, Trina Sircar, Amy B Rosenfeld, Gina Kuffel, Michael J Zilliox, Alan J Wolfe, Catherine Putonti
Bacterial surveys of the vaginal and bladder human microbiota have revealed an abundance of many similar bacterial taxa. As the bladder was once thought to be sterile, the complex interactions between microbes within the bladder have yet to be characterized. To initiate this process, we have begun sequencing isolates, including the clinically relevant genus Gardnerella. Herein, we present the genomic sequences of four Gardnerella strains isolated from the bladders of women with symptoms of urgency urinary incontinence; these are the first Gardnerella genomes produced from this niche...
2016: PloS One
https://www.readbyqxmd.com/read/27834372/the-pangenome-of-an-agronomically-important-crop-plant-brassica-oleracea
#3
Agnieszka A Golicz, Philipp E Bayer, Guy C Barker, Patrick P Edger, HyeRan Kim, Paula A Martinez, Chon Kit Kenneth Chan, Anita Severn-Ellis, W Richard McCombie, Isobel A P Parkin, Andrew H Paterson, J Chris Pires, Andrew G Sharpe, Haibao Tang, Graham R Teakle, Christopher D Town, Jacqueline Batley, David Edwards
There is an increasing awareness that as a result of structural variation, a reference sequence representing a genome of a single individual is unable to capture all of the gene repertoire found in the species. A large number of genes affected by presence/absence and copy number variation suggest that it may contribute to phenotypic and agronomic trait diversity. Here we show by analysis of the Brassica oleracea pangenome that nearly 20% of genes are affected by presence/absence variation. Several genes displaying presence/absence variation are annotated with functions related to major agronomic traits, including disease resistance, flowering time, glucosinolate metabolism and vitamin biosynthesis...
November 11, 2016: Nature Communications
https://www.readbyqxmd.com/read/27829029/inferring-gene-networks-for-strains-of-dehalococcoides-highlights-conserved-relationships-between-genes-encoding-core-catabolic-and-cell-wall-structural-proteins
#4
Cresten B Mansfeldt, Gretchen W Heavner, Annette R Rowe, Boris Hayete, Bruce W Church, Ruth E Richardson
The interpretation of high-throughput gene expression data for non-model microorganisms remains obscured because of the high fraction of hypothetical genes and the limited number of methods for the robust inference of gene networks. Therefore, to elucidate gene-gene and gene-condition linkages in the bioremediation-important genus Dehalococcoides, we applied a Bayesian inference strategy called Reverse Engineering/Forward Simulation (REFS™) on transcriptomic data collected from two organohalide-respiring communities containing different Dehalococcoides mccartyi strains: the Cornell University mixed community D2 and the commercially available KB-1® bioaugmentation culture...
2016: PloS One
https://www.readbyqxmd.com/read/27826029/cytolethal-distending-toxin-producing-escherichia-coli-o157-h43-strain-t22-represents-a-novel-evolutionary-lineage-within-the-o157-serogroup
#5
Domonkos Sváb, Balázs Bálint, Gergely Maróti, István Tóth
Enterohemorrhagic Escherichia coli (EHEC) O157:H7/NM strains are significant foodborne pathogens intensively studied, while other sero- and pathotypes of the O157 serogroup only began to receive more attention. Here we report the first genome sequence of a cytolethal distending toxin (CDT-V) producing E. coli O157:H43 strain (T22) isolated from cattle. The genome consists of a 4.9Mb chromosome assembled into three contigs and one plasmid of 82.4kb. Comparative genomic investigations conducted with the core genomes of representative E...
November 5, 2016: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/27819663/two-fundamentally-different-classes-of-microbial-genes
#6
Yuri I Wolf, Kira S Makarova, Alexander E Lobkovsky, Eugene V Koonin
The evolution of bacterial and archaeal genomes is highly dynamic and involves extensive horizontal gene transfer and gene loss(1-4). Furthermore, many microbial species appear to have open pangenomes, where each newly sequenced genome contains more than 10% ORFans, that is, genes without detectable homologues in other species(5,6). Here, we report a quantitative analysis of microbial genome evolution by fitting the parameters of a simple, steady-state evolutionary model to the comparative genomic data on the gene content and gene order similarity between archaeal genomes...
November 7, 2016: Nature Microbiology
https://www.readbyqxmd.com/read/27734920/bacterial-intra-species-gene-loss-occurs-in-a-largely-clocklike-manner-mostly-within-a-pool-of-less-conserved-and-constrained-genes
#7
Evgeni Bolotin, Ruth Hershberg
Gene loss is a major contributor to the evolution of bacterial gene content. Gene loss may occur as a result of shifts in environment leading to changes in the intensity and/or directionality of selection applied for the maintenance of specific genes. Gene loss may also occur in a more neutral manner, when gene functions are lost that were not subject to strong selection to be maintained, irrespective of changes to environment. Here, we used a pangenome-based approach to investigate patterns of gene loss across 15 bacterial species...
October 13, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27697167/advances-in-the-genomics-and-metabolomics-of-dairy-lactobacilli-a-review
#8
Ewelina Stefanovic, Gerald Fitzgerald, Olivia McAuliffe
The Lactobacillus genus represents the largest and most diverse genera of all the lactic acid bacteria (LAB), encompassing species with applications in industrial, biotechnological and medical fields. The increasing number of available Lactobacillus genome sequences has allowed understanding of genetic and metabolic potential of this LAB group. Pangenome and core genome studies are available for numerous species, demonstrating the plasticity of the Lactobacillus genomes and providing the evidence of niche adaptability...
February 2017: Food Microbiology
https://www.readbyqxmd.com/read/27663497/accnet-accessory-genome-constellation-network-comparative-genomics-software-for-accessory-genome-analysis-using-bipartite-networks
#9
Val F Lanza, Fernando Baquero, Fernando de la Cruz, Teresa M Coque
MOTIVATION: AccNET (Accessory genome Constellation Network) is a Perl application that aims to compare accessory genomes of a large number of genomic units, both at qualitative and quantitative levels. Using the proteomes extracted from the analysed genomes, AccNET creates a bipartite network compatible with standard network analysis platforms. AccNET allows merging phylogenetic and functional information about the concerned genomes, thus improving the capability of current methods of network analysis...
September 23, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27638249/pangenome-and-phylogenomic-analysis-of-the-pathogenic-actinobacterium-rhodococcus-equi
#10
Elisa Anastasi, Iain MacArthur, Mariela Scortti, Sonsiray Alvarez, Steeve Giguère, Jose A Vazquez-Boland
We report a comparative study of 29 representative genomes of the animal pathogen Rhodococcus equi The analyses showed that R. equi is genetically homogeneous and clonal, with a large core genome accounting for ≈80% of an isolates' gene content. An open pangenome, even distribution of accessory genes among the isolates, and absence of significant core-genome recombination, indicated that gene gain/loss is a main driver of R. equi genome evolution. Traits previously predicted to be important in R. equi physiology, virulence and niche adaptation were part of the core genome...
September 16, 2016: Genome Biology and Evolution
https://www.readbyqxmd.com/read/27634541/pangenome-and-immuno-proteomics-analysis-of-acinetobacter-baumannii-strains-revealed-the-core-peptide-vaccine-targets
#11
Afreenish Hassan, Anam Naz, Ayesha Obaid, Rehan Zafar Paracha, Kanwal Naz, Faryal Mehwish Awan, Syed Aun Muhmmad, Hussnain Ahmed Janjua, Jamil Ahmad, Amjad Ali
BACKGROUND: Acinetobacter baumannii has emerged as a significant nosocomial pathogen during the last few years, exhibiting resistance to almost all major classes of antibiotics. Alternative treatment options such as vaccines tend to be most promising and cost effective approaches against this resistant pathogen. In the current study, we have explored the pan-genome of A. baumannii followed by immune-proteomics and reverse vaccinology approaches to identify potential core vaccine targets...
2016: BMC Genomics
https://www.readbyqxmd.com/read/27552639/genomic-composition-and-dynamics-among-methanomicrobiales-predict-adaptation-to-contrasting-environments
#12
Patrick Browne, Hideyuki Tamaki, Nikos Kyrpides, Tanja Woyke, Lynne Goodwin, Hiroyuki Imachi, Suzanna Bräuer, Joseph B Yavitt, Wen-Tso Liu, Stephen Zinder, Hinsby Cadillo-Quiroz
Members of the order Methanomicrobiales are abundant, and sometimes dominant, hydrogenotrophic (H2-CO2 utilizing) methanoarchaea in a broad range of anoxic habitats. Despite their key roles in greenhouse gas emissions and waste conversion to methane, little is known about the physiological and genomic bases for their widespread distribution and abundance. In this study, we compared the genomes of nine diverse Methanomicrobiales strains, examined their pangenomes, reconstructed gene flow and identified genes putatively mediating their success across different habitats...
August 23, 2016: ISME Journal
https://www.readbyqxmd.com/read/27536275/pangenome-evidence-for-higher-codon-usage-bias-and-stronger-translational-selection-in-core-genes-of-escherichia-coli
#13
Shixiang Sun, Jingfa Xiao, Huiyong Zhang, Zhang Zhang
Codon usage bias, as a combined interplay from mutation and selection, has been intensively studied in Escherichia coli. However, codon usage analysis in an E. coli pangenome remains unexplored and the relative importance of mutation and selection acting on core genes and strain-specific genes is unknown. Here we perform comprehensive codon usage analyses based on a collection of multiple complete genome sequences of E. coli. Our results show that core genes that are present in all strains have higher codon usage bias than strain-specific genes that are unique to single strains...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27477789/study-of-six-patients-with-complete-f9-deletion-characterized-by-cytogenetic-microarray-role-of-the-sox3-gene-in-intellectual-disability
#14
Y Jourdy, N Chatron, M L Carage, M Fretigny, S Meunier, C Zawadzki, V Gay, C Negrier, D Sanlaville, C Vinciguerra
BACKGROUND: Large deletions encompassing both the complete F9 gene and contiguous genes have been detected in patients with severe hemophilia B (HB). Some of these patients present other clinical features, such as intellectual disability (ID). OBJECTIVES/METHODS: In this study, we characterized six unrelated large deletions encompassing F9, by cytogenetic microarray analysis (CMA), to investigate genotype/phenotype correlation. RESULTS: Five of the six patients included in this study presented ID associated with HB...
August 1, 2016: Journal of Thrombosis and Haemostasis: JTH
https://www.readbyqxmd.com/read/27420027/association-mapping-reveals-novel-serpentine-adaptation-gene-clusters-in-a-population-of-symbiotic-mesorhizobium
#15
Stephanie S Porter, Peter L Chang, Christopher A Conow, Joseph P Dunham, Maren L Friesen
The genetic variants that underlie microbial environmental adaptation are key components of models of microbial diversification. Characterizing adaptive variants and the pangenomic context in which they evolve remains a frontier in understanding how microbial diversity is generated. The genomics of rhizobium adaptation to contrasting soil environments is ecologically and agriculturally important because these bacteria are responsible for half of all current biologically fixed nitrogen, yet they live the majority of their lives in soil...
July 15, 2016: ISME Journal
https://www.readbyqxmd.com/read/27189983/pangenome-evolution-in-the-marine-bacterium-alteromonas
#16
Mario López-Pérez, Francisco Rodriguez-Valera
We have examined a collection of the free-living marine bacterium Alteromonas genomes with cores diverging in average nucleotide identities ranging from 99.98% to 73.35%, i.e., from microbes that can be considered members of a natural clone (like in a clinical epidemiological outbreak) to borderline genus level. The genomes were largely syntenic allowing a precise delimitation of the core and flexible regions in each. The core was 1.4 Mb (ca. 30% of the typical strain genome size). Recombination rates along the core were high among strains belonging to the same species (37...
2016: Genome Biology and Evolution
https://www.readbyqxmd.com/read/27114887/genome-sequencing-and-analysis-of-the-first-complete-genome-of-lactobacillus-kunkeei-strain-mp2-an-apis-mellifera-gut-isolate
#17
Freddy Asenjo, Alejandro Olmos, Patricia Henríquez-Piskulich, Victor Polanco, Patricia Aldea, Juan A Ugalde, Annette N Trombert
Background. The honey bee (Apis mellifera) is the most important pollinator in agriculture worldwide. However, the number of honey bees has fallen significantly since 2006, becoming a huge ecological problem nowadays. The principal cause is CCD, or Colony Collapse Disorder, characterized by the seemingly spontaneous abandonment of hives by their workers. One of the characteristics of CCD in honey bees is the alteration of the bacterial communities in their gastrointestinal tract, mainly due to the decrease of Firmicutes populations, such as the Lactobacilli...
2016: PeerJ
https://www.readbyqxmd.com/read/27087830/bloom-filter-trie-an-alignment-free-and-reference-free-data-structure-for-pan-genome-storage
#18
Guillaume Holley, Roland Wittler, Jens Stoye
BACKGROUND: High throughput sequencing technologies have become fast and cheap in the past years. As a result, large-scale projects started to sequence tens to several thousands of genomes per species, producing a high number of sequences sampled from each genome. Such a highly redundant collection of very similar sequences is called a pan-genome. It can be transformed into a set of sequences "colored" by the genomes to which they belong. A colored de Bruijn graph (C-DBG) extracts from the sequences all colored k-mers, strings of length k, and stores them in vertices...
2016: Algorithms for Molecular Biology: AMB
https://www.readbyqxmd.com/read/27042991/dna-repair-genes-in-the-megavirales-pangenome
#19
REVIEW
Romain Blanc-Mathieu, Hiroyuki Ogata
The order 'Megavirales' represents a group of eukaryotic viruses with a large genome encoding a few hundred up to two thousand five hundred genes. Several members of Megavirales possess genes involved in major DNA repair pathways. Some of these genes were likely inherited from an ancient virus world and some others were derived from the genomes of their hosts. Here we examine molecular phylogenies of key DNA repair enzymes in light of recent hypotheses on the origin of Megavirales, and propose that the last common ancestors of the individual families of the order Megavirales already possessed DNA repair functions to achieve and maintain a moderately large genome and that this repair capacity gradually increased, in a family-dependent manner, during their recent evolution...
June 2016: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/26999001/strain-level-microbial-epidemiology-and-population-genomics-from-shotgun-metagenomics
#20
Matthias Scholz, Doyle V Ward, Edoardo Pasolli, Thomas Tolio, Moreno Zolfo, Francesco Asnicar, Duy Tin Truong, Adrian Tett, Ardythe L Morrow, Nicola Segata
Identifying microbial strains and characterizing their functional potential is essential for pathogen discovery, epidemiology and population genomics. We present pangenome-based phylogenomic analysis (PanPhlAn; http://segatalab.cibio.unitn.it/tools/panphlan), a tool that uses metagenomic data to achieve strain-level microbial profiling resolution. PanPhlAn recognized outbreak strains, produced the largest strain-level population genomic study of human-associated bacteria and, in combination with metatranscriptomics, profiled the transcriptional activity of strains in complex communities...
May 2016: Nature Methods
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