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Pangenome

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https://www.readbyqxmd.com/read/28894437/evolution-of-stenotrophomonas-maltophilia-in-cystic-fibrosis-lung-over-chronic-infection-a-genomic-and-phenotypic-population-study
#1
Alfonso Esposito, Arianna Pompilio, Clotilde Bettua, Valentina Crocetta, Elisabetta Giacobazzi, Ersilia Fiscarelli, Olivier Jousson, Giovanni Di Bonaventura
Stenotrophomonas maltophilia has been recognized as an emerging multi-drug resistant opportunistic pathogen in cystic fibrosis (CF) patients. We report a comparative genomic and phenotypic analysis of 91 S. maltophilia strains from 10 CF patients over a 12-year period. Draft genome analyses included in silico Multi-Locus Sequence Typing (MLST), Single-Nucleotide Polymorphisms (SNPs), and pangenome characterization. Growth rate, biofilm formation, motility, mutation frequency, in vivo virulence, and in vitro antibiotic susceptibility were determined and compared with population structure over time...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28890711/horizontally-acquired-genes-are-often-shared-between-closely-related-bacterial-species
#2
Evgeni Bolotin, Ruth Hershberg
Horizontal gene transfer (HGT) serves as an important source of innovation for bacterial species. We used a pangenome-based approach to identify genes that were horizontally acquired by four closely related bacterial species, belonging to the Enterobacteriaceae family. This enabled us to examine the extent to which such closely related species tend to share horizontally acquired genes. We find that a high percent of horizontally acquired genes are shared among these closely related species. Furthermore, we demonstrate that the extent of sharing of horizontally acquired genes among these four closely related species is predictive of the extent to which these genes will be found in additional bacterial species...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28887423/forensic-human-identification-using-skin-microbiomes
#3
Sarah E Schmedes, August E Woerner, Bruce Budowle
The human microbiome contributes significantly to the genetic content of the human body. Genetic and environmental factors help shape the microbiome, and as such, the microbiome can be unique to an individual. Previous studies have demonstrated the potential to use microbiome profiling for forensic applications, however a method has yet to identify stable features of skin microbiomes that produce high classification accuracies for samples collected over reasonably long time intervals. A novel approach is described to classify skin microbiomes to their donors by comparing two features types, Propionibacterium acnes pangenome presence/absence features and nucleotide diversities of stable clade-specific markers...
September 8, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28878862/permanent-draft-genome-sequence-of-frankia-sp-nrrl-b-16219-reveals-the-presence-of-canonical-nod-genes-which-are-highly-homologous-to-those-detected-in-candidatus-frankia-dg1-genome
#4
Amir Ktari, Imen Nouioui, Teal Furnholm, Erik Swanson, Faten Ghodhbane-Gtari, Louis S Tisa, Maher Gtari
Frankia sp. NRRL B-16219 was directly isolated from a soil sample obtained from the rhizosphere of Ceanothus jepsonii growing in the USA. Its host plant range includes members of Elaeagnaceae species. Phylogenetically, strain NRRL B-16219 is closely related to "Frankia discariae" with a 16S rRNA gene similarity of 99.78%. Because of the lack of genetic tools for Frankia, our understanding of the bacterial signals involved during the plant infection process and the development of actinorhizal root nodules is very limited...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28826610/calling-chromosome-alterations-dna-methylation-statuses-and-mutations-in-tumors-by-simple-targeted-next-generation-sequencing-a-solution-for-transferring-integrated-pangenomic-studies-into-routine-practice
#5
Simon Garinet, Mario Néou, Bruno de La Villéon, Simon Faillot, Julien Sakat, Juliana P Da Fonseca, Anne Jouinot, Christophe Le Tourneau, Maud Kamal, Windy Luscap-Rondof, Valentina Boeva, Sebastien Gaujoux, Michel Vidaud, Eric Pasmant, Franck Letourneur, Jérôme Bertherat, Guillaume Assié
Pangenomic studies identified distinct molecular classes for many cancers, with major clinical applications. However, routine use requires cost-effective assays. We assessed whether targeted next-generation sequencing (NGS) could call chromosomal alterations and DNA methylation status. A training set of 77 tumors and a validation set of 449 (43 tumor types) were analyzed by targeted NGS and single-nucleotide polymorphism (SNP) arrays. Thirty-two tumors were analyzed by NGS after bisulfite conversion, and compared to methylation array or methylation-specific multiplex ligation-dependent probe amplification...
September 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28821232/genomic-transcriptomic-and-proteomic-approaches-towards-understanding-the-molecular-mechanisms-of-salt-tolerance-in-frankia-strains-isolated-from-casuarina-trees
#6
Rediet Oshone, Mariama Ngom, Feixia Chu, Samira Mansour, Mame Ourèye Sy, Antony Champion, Louis S Tisa
BACKGROUND: Soil salinization is a worldwide problem that is intensifying because of the effects of climate change. An effective method for the reclamation of salt-affected soils involves initiating plant succession using fast growing, nitrogen fixing actinorhizal trees such as the Casuarina. The salt tolerance of Casuarina is enhanced by the nitrogen-fixing symbiosis that they form with the actinobacterium Frankia. Identification and molecular characterization of salt-tolerant Casuarina species and associated Frankia is imperative for the successful utilization of Casuarina trees in saline soil reclamation efforts...
August 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28756981/congenital-undifferentiated-sarcoma-associated-to-bcor-ccnb3-gene-fusion
#7
Clara Alfaro-Cervello, Verónica Andrade-Gamarra, Gema Nieto, Lara Navarro, Susana Martín-Vañó, Juan Pablo García de la Torre, María Bengoa Caamaño, Mª Luisa García Mauriño, Rosa Noguera, Samuel Navarro
Small round cell sarcomas are aggressive bone and soft tissue tumors that predominantly affect children and young adults. A new group of sarcomas with a recurrent BCOR-CCNB3 gene fusion has been recently identified in previously unclassifiable small round cell sarcomas. BCOR-CCNB3 sarcomas share clinical and pathologic similarities with Ewing sarcoma, but show a stronger male predilection and less aggressiveness, as well as distinct gene expression profiling and pangenomic SNP array analyses. We report the unusual case of a congenital BCOR-CCNB3 retroperitoneal sarcoma in a female born at 34th gestational week, which was diagnosed in necropsy after 21hours of life...
July 14, 2017: Pathology, Research and Practice
https://www.readbyqxmd.com/read/28705964/draft-genome-sequences-of-seven-streptococcus-agalactiae-strains-isolated-from-camelus-dromedarius-at-the-horn-of-africa
#8
Julian Rothen, Tobias Schindler, Joël F Pothier, Mario Younan, Ulrich Certa, Claudia Daubenberger, Valentin Pflüger, Joerg Jores
We present draft whole-genome sequences of seven Streptococcus agalactiae strains isolated from Camelus dromedarius in Kenya and Somalia. These data are an extension to the group B Streptococcus (GBS) pangenome and might provide more insight into the underlying mechanisms of pathogenicity and antibiotic resistance of camel GBS.
July 13, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28682230/-genetics-and-epigenetics-of-suicidal-behaviors
#9
Emilie Olié, Philippe Courtet
With more than 10 000 deaths each year in France, suicide is a major public health problem. Despite many known risk factors, suicide prediction remains extremely difficult in daily clinical practice. The identification of biomarkers, including genetic and epigenetic factors, is needed in suicidology in order to better understand pathophysiology of such behaviors and to improve the screening of individuals at high suicidal risk. Numerous studies have reported candidate genes involved in serotonergic system, HPA axis and neurotrophic system...
2017: Biologie Aujourd'hui
https://www.readbyqxmd.com/read/28642379/complete-genome-sequence-of-staphylococcus-lutrae-atcc-700373-a-potential-pathogen-isolated-from-deceased-otters
#10
Iva A Veseli, Chenling Tang, Jean-François Pombert
Despite their relevance to human health, not all staphylococcal species have been characterized. As such, the potential zoonotic threats posed by uninvestigated species and their contribution to the staphylococcal pangenome are unclear. Here, we report the complete genome sequence of Staphylococcus lutrae ATCC 700373, a coagulase-positive species isolated from deceased otters.
June 22, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28637301/eden-evolutionary-dynamics-within-environments
#11
Philipp C Münch, Bärbel Stecher, Alice C McHardy
Summary: Metagenomics revolutionized the field of microbial ecology, giving access to Gb-sized datasets of microbial communities under natural conditions. This enables fine-grained analyses of the functions of community members, studies of their association with phenotypes and environments, as well as of their microevolution and adaptation to changing environmental conditions. However, phylogenetic methods for studying adaptation and evolutionary dynamics are not able to cope with big data...
June 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28625995/novel-antibiotic-resistance-determinants-from-agricultural-soil-exposed-to-antibiotics-widely-used-in-human-medicine-and-animal-farming
#12
Calvin Ho-Fung Lau, Kalene van Engelen, Stephen Gordon, Justin Renaud, Edward Topp
Antibiotic resistance has emerged globally as one of the biggest threats to human and animal health. Although the excessive use of antibiotics is recognized for accelerating the selection for resistance, there is a growing body of evidence suggesting that natural environments are "hotspots" for the development of both ancient and contemporary resistance mechanisms. Given that pharmaceuticals can be entrained onto agricultural land through anthropogenic activities, this could be a potential driver for the emergence and dissemination of resistance in soil bacteria...
June 16, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28611758/genome-wide-analyses-reveal-genes-subject-to-positive-selection-in-pasteurella-multocida
#13
Peili Cao, Dongchun Guo, Jiasen Liu, Qian Jiang, Zhuofei Xu, Liandong Qu
Pasteurella multocida, a Gram-negative opportunistic pathogen, has led to a broad range of diseases in mammals and birds, including fowl cholera in poultry, pneumonia and atrophic rhinitis in swine and rabbit, hemorrhagic septicemia in cattle, and bite infections in humans. In order to better interpret the genetic diversity and adaptation evolution of this pathogen, seven genomes of P. multocida strains isolated from fowls, rabbit and pigs were determined by using high-throughput sequencing approach. Together with publicly available P...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28594829/mendel-md-a-user-friendly-open-source-web-tool-for-analyzing-wes-and-wgs-in-the-diagnosis-of-patients-with-mendelian-disorders
#14
Raony G C C L Cardenas, Natália D Linhares, Raquel L Ferreira, Sérgio D J Pena
Whole exome and whole genome sequencing have both become widely adopted methods for investigating and diagnosing human Mendelian disorders. As pangenomic agnostic tests, they are capable of more accurate and agile diagnosis compared to traditional sequencing methods. This article describes new software called Mendel,MD, which combines multiple types of filter options and makes use of regularly updated databases to facilitate exome and genome annotation, the filtering process and the selection of candidate genes and variants for experimental validation and possible diagnosis...
June 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28593194/fine-scale-structure-analysis-shows-epidemic-patterns-of-clonal-complex-95-a-cosmopolitan-escherichia-coli-lineage-responsible-for-extraintestinal-infection
#15
David M Gordon, Sarah Geyik, Olivier Clermont, Claire L O'Brien, Shiwei Huang, Charmalie Abayasekara, Ashwin Rajesh, Karina Kennedy, Peter Collignon, Paul Pavli, Christophe Rodriguez, Brian D Johnston, James R Johnson, Jean-Winoc Decousser, Erick Denamur
The Escherichia coli lineage known as clonal complex 95 (CC95) is a cosmopolitan human-associated lineage responsible for a significant fraction of extraintestinal infections of humans. Whole-genome sequence data of 200 CC95 strains from various origins enabled determination of the CC95 pangenome. The pangenome analysis revealed that strains of the complex could be assigned to one of five subgroups that vary in their serotype, extraintestinal virulence, virulence gene content, and antibiotic resistance gene profile...
May 2017: MSphere
https://www.readbyqxmd.com/read/28560114/differentiation-of-bifidobacterium-longum-subspecies-longum-and-infantis-by-quantitative-pcr-using-functional-gene-targets
#16
Blair Lawley, Karen Munro, Alan Hughes, Alison J Hodgkinson, Colin G Prosser, Dianne Lowry, Shao J Zhou, Maria Makrides, Robert A Gibson, Christophe Lay, Charmaine Chew, Pheng Soon Lee, Khai Hong Wong, Gerald W Tannock
BACKGROUND: Members of the genus Bifidobacterium are abundant in the feces of babies during the exclusively-milk-diet period of life. Bifidobacterium longum is reported to be a common member of the infant fecal microbiota. However, B. longum is composed of three subspecies, two of which are represented in the bowel microbiota (B. longum subsp. longum; B. longum subsp. infantis). B. longum subspecies are not differentiated in many studies, so that their prevalence and relative abundances are not accurately known...
2017: PeerJ
https://www.readbyqxmd.com/read/28475226/molecular-cytogenetic-characterization-of-five-f8-complex-rearrangements-utility-for-haemophilia-a-genetic-counselling
#17
Y Jourdy, N Chatron, M Fretigny, M L Carage, H Chambost, S Claeyssens-Donadel, V Roussel-Robert, C Negrier, D Sanlaville, C Vinciguerra
BACKGROUND: Genomic inversions are usually balanced, but unusual patterns have been described in haemophilia A (HA) patients for intron 22 (Inv22) and intron 1 (Inv1) inversions leading to the hypothesis of more complex rearrangements involving deletions or duplications. AIM: To characterize five abnormal patterns either in Southern blot and long-range PCR for Inv22 or in PCR for Inv1. MATERIALS AND METHODS: All patients were studied using cytogenetic microarray analysis (CMA)...
May 5, 2017: Haemophilia: the Official Journal of the World Federation of Hemophilia
https://www.readbyqxmd.com/read/28403535/assembly-and-comparison-of-two-closely-related-brassica-napus-genomes
#18
Philipp E Bayer, Bhavna Hurgobin, Agnieszka A Golicz, Chon-Kit Kenneth Chan, Yuxuan Yuan, HueyTyng Lee, Michael Renton, Jinling Meng, Ruiyuan Li, Yan Long, Jun Zou, Ian Bancroft, Boulos Chalhoub, Graham J King, Jacqueline Batley, David Edwards
As an increasing number of plant genome sequences become available, it is clear that gene content varies between individuals, and the challenge arises to predict the gene content of a species. However, genome comparison is often confounded by variation in assembly and annotation. Differentiating between true gene absence and variation in assembly or annotation is essential for the accurate identification of conserved and variable genes in a species. Here we present the de novo assembly of the B. napus cultivar Tapidor and comparison with an improved assembly of the B...
April 12, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28369330/comparative-genomics-of-rhodococcus-equi-virulence-plasmids-indicates-host-driven-evolution-of-the-vap-pathogenicity-island
#19
Iain MacArthur, Elisa Anastasi, Sonsiray Alvarez, Mariela Scortti, José A Vázquez-Boland
The conjugative virulence plasmid is a key component of the Rhodococcus equi accessory genome essential for pathogenesis. Three host-associated virulence plasmid types have been identified the equine pVAPA and porcine pVAPB circular variants, and the linear pVAPN found in bovine (ruminant) isolates. We recently characterized the R. equi pangenome (Anastasi E, et al. 2016. Pangenome and phylogenomic analysis of the pathogenic actinobacterium Rhodococcus equi. Genome Biol Evol. 8:3140-3148.) and we report here the comparative analysis of the virulence plasmid genomes...
May 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28350002/why-prokaryotes-have-pangenomes
#20
James O McInerney, Alan McNally, Mary J O'Connell
No abstract text is available yet for this article.
March 28, 2017: Nature Microbiology
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