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https://www.readbyqxmd.com/read/28935727/complete-genome-sequences-of-lactobacillus-curvatus-kg6-l-curvatus-mrs6-and-lactobacillus-sakei-fam18311-isolated-from-fermented-meat-products
#1
Christoph Jans, Sandra Lagler, Christophe Lacroix, Leo Meile, Marc J A Stevens
The genomes of Lactobacillus curvatus KG6, L. curvatus MRS6, and Lactobacillus sakei FAM18311 were sequenced and assembled using PacBio single-molecule real-time (SMRT) technology. The strains were isolated from Swiss fermented meat products. Circular chromosomes were of 1.98 Mbp (KG6), 2.11 Mbp (MRS6), and 1.95 Mbp (FAM18311), with a G+C content of 41.3 to 42.0%.
September 21, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28935722/genome-and-plasmid-sequences-of-escherichia-coli-kv7-an-extended-spectrum-%C3%AE-lactamase-isolate-derived-from-feces-of-a-healthy-pig
#2
Michael D Bateman, Stefan P W de Vries, Srishti Gupta, Luca Guardabassi, Lina M Cavaco, Andrew J Grant, Mark A Holmes
We present single-contig assemblies for Escherichia coli strain KV7 (serotype O27, phylogenetic group D) and its six plasmids, isolated from a healthy pig, as determined by PacBio RS II and Illumina MiSeq sequencing. The chromosome of 4,997,475 bp and G+C content of 50.75% harbored 4,540 protein-encoding genes.
September 21, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28932209/the-mobilome-a-major-contributor-to-escherichia-coli-stx2-positive-o26-h11-strains-intra-serotype-diversity
#3
Sabine Delannoy, Patricia Mariani-Kurkdjian, Hattie E Webb, Stephane Bonacorsi, Patrick Fach
Shiga toxin-producing Escherichia coli of serotype O26:H11/H- constitute a diverse group of strains and several clones with distinct genetic characteristics have been identified and characterized. Whole genome sequencing was performed using Illumina and PacBio technologies on eight stx2-positive O26:H11 strains circulating in France. Comparative analyses of the whole genome of the stx2-positive O26:H11 strains indicate that several clones of EHEC O26:H11 are co-circulating in France. Phylogenetic analysis of the French strains together with stx2-positive and stx-negative E...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28924494/genomic-and-functional-analysis-of-romboutsia-ilealis-crib-t-reveals-adaptation-to-the-small-intestine
#4
Jacoline Gerritsen, Bastian Hornung, Bernadette Renckens, Sacha A F T van Hijum, Vitor A P Martins Dos Santos, Ger T Rijkers, Peter J Schaap, Willem M de Vos, Hauke Smidt
BACKGROUND: The microbiota in the small intestine relies on their capacity to rapidly import and ferment available carbohydrates to survive in a complex and highly competitive ecosystem. Understanding how these communities function requires elucidating the role of its key players, the interactions among them and with their environment/host. METHODS: The genome of the gut bacterium Romboutsia ilealis CRIB(T) was sequenced with multiple technologies (Illumina paired-end, mate-pair and PacBio)...
2017: PeerJ
https://www.readbyqxmd.com/read/28916321/analysis-of-resistance-genes-in-pan-resistant-myroides-odoratimimus-clinical-strain-pr63039-using-whole-genome-sequencing
#5
Desong Ming, Qing-Qing Chen, Xiao-Tin Chen
To clarify the antibiotic resistance mechanisms of Myroides odoratimimus, pan-resistant M. odoratimimus strain PR63039 was isolated and its genome sequenced and analyzed. Antimicrobial susceptibility testing was conducted using the Kirby-Bauer disk diffusion method, and the Phoenix-100 Automated Microbiology System with a NMIC/ID-4 panel including aminoglycosides, β-lactams, polypeptides, quinolones, sulfonamides, chloramphenicols, and tetracyclines. Single-molecule real-time whole genome sequencing was conducted using the PacBio RSII system, and genome annotation was performed using RAST and IMG ER...
September 12, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28914759/isoform-sequencing-provides-a-more-comprehensive-view-of-the-panax-ginseng-transcriptome
#6
Ick-Hyun Jo, Jinsu Lee, Chi Eun Hong, Dong Jin Lee, Wonsil Bae, Sin-Gi Park, Yong Ju Ahn, Young Chang Kim, Jang Uk Kim, Jung Woo Lee, Dong Yun Hyun, Sung-Keun Rhee, Chang Pyo Hong, Kyong Hwan Bang, Hojin Ryu
Korean ginseng (Panax ginseng C.A. Meyer) has been widely used for medicinal purposes and contains potent plant secondary metabolites, including ginsenosides. To obtain transcriptomic data that offers a more comprehensive view of functional genomics in P. ginseng, we generated genome-wide transcriptome data from four different P. ginseng tissues using PacBio isoform sequencing (Iso-Seq) technology. A total of 135,317 assembled transcripts were generated with an average length of 3.2 kb and high assembly completeness...
September 15, 2017: Genes
https://www.readbyqxmd.com/read/28912315/complete-genome-sequence-of-ralstonia-solanacearum-fjat-91-a-high-virulence-pathogen-of-tomato-wilt
#7
Deju Chen, Bo Liu, Yujing Zhu, Haifeng Zhang, Zheng Chen, Xuefang Zheng, Rongfeng Xiao, Yanping Chen
Ralstonia solanacearum FJAT-91, which displays higher virulence toward plants belonging to the family Solanaceae, was isolated from a wilted tomato plant vessel in Fujian province, southeast China. Here, we report the complete genome sequence of R. solanacearum FJAT-91 using long-read single-molecule PacBio sequencing technology. The genome comprises a 3,873,214-bp circular chromosome and a 2,000,873-bp circular megaplasmid with an overall G+C content of 66.85%.
September 14, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28912314/complete-genome-sequence-of-dehalobacterium-formicoaceticum-strain-dmc-a-strictly-anaerobic-dichloromethane-degrading-bacterium
#8
Gao Chen, Robert W Murdoch, E Erin Mack, Edward S Seger, Frank E Löffler
Dehalobacterium formicoaceticum utilizes dichloromethane as the sole energy source in defined anoxic bicarbonate-buffered mineral salt medium. The products are formate, acetate, inorganic chloride, and biomass. The bacterium's genome was sequenced using PacBio, assembled, and annotated. The complete genome consists of one 3.77-Mb circular chromosome harboring 3,935 predicted protein-encoding genes.
September 14, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28906012/pacbio-metabarcoding-of-fungi-and-other-eukaryotes-errors-biases-and-perspectives
#9
Leho Tedersoo, Ave Tooming-Klunderud, Sten Anslan
Second-generation, high-throughput sequencing methods have greatly improved our understanding of the ecology of soil microorganisms, yet the short barcodes (< 500 bp) provide limited taxonomic and phylogenetic information for species discrimination and taxonomic assignment. Here, we utilized the third-generation Pacific Biosciences (PacBio) RSII and Sequel instruments to evaluate the suitability of full-length internal transcribed spacer (ITS) barcodes and longer rRNA gene amplicons for metabarcoding Fungi, Oomycetes and other eukaryotes in soil samples...
September 14, 2017: New Phytologist
https://www.readbyqxmd.com/read/28893775/a-nosocomial-outbreak-of-extensively-drug-resistant-xdr-acinetobacter-baumannii-isolates-containing-blaoxa-237-encoded-on-a-plasmid
#10
Andrea M Hujer, Paul G Higgins, Susan D Rudin, Genevieve L Buser, Steven H Marshall, Kyriaki Xanthopoulou, Harald Seifert, Laura J Rojas, T Nicholas Domitrovic, P Maureen Cassidy, Margaret C Cunningham, Robert Vega, Jon P Furuno, Christopher D Pfeiffer, Zintars G Beldavs, Meredith S Wright, Michael R Jacobs, Mark D Adams, Robert A Bonomo
Carbapenem antibiotics are among the mainstay for treating infections caused by Acinetobacter baumannii, especially in the Northwest United States where carbapenem resistant A. baumannii remain relatively rare. However, between June 2012 and October 2014, an outbreak of carbapenem-resistant A. baumannii occurred in 16 patients from 5 healthcare facilities in the state of Oregon. All isolates were defined as extensively-drug resistant (XDR). MLST revealed that the isolates belonged to sequence type 2 (international clone 2, IC2), and were greater than 95% similar by rep-PCR analysis...
September 11, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28893646/whole-genome-sequence-of-a-carbapenem-resistant-hypermucoviscous-klebsiella-pneumoniae-isolate-swu01-with-capsular-serotype-k47-that-belongs-to-st11-from-a-patient-in-china
#11
Luhua Zhang, Ying Li, Wei Shen, Guangxi Wang, Yingshun Zhou
OBJECTIVES: In recent years, Klebsiella pneumoniae is emerging as a leading cause of nosocomial infection due to the rapid prevalence of multidrug resistant strains, particularly the carbapenem resistant isolates. In this study, we completed the genome sequence of a carbapenem-resistant K. pneumoniae SWU01. METHODS: Antimicrobial susceptibilities and hypermucoviscous phenotype were determined by the disk diffusion method and a positive string test, respectively...
September 8, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/28888816/the-repeat-structure-of-two-paralogous-genes-yersinia-ruckeri-invasin-yrinv-and-a-y-ruckeri-invasin-like-molecule-yrilm-sheds-light-on-the-evolution-of-adhesive-capacities-of-a-fish-pathogen
#12
Agnieszka Wrobel, Claudio Ottoni, Jack C Leo, Snorre Gulla, Dirk Linke
Inverse autotransporters comprise the recently identified type Ve secretion system and are exemplified by intimin from enterohaemorrhagic Escherichia coli and invasin from enteropathogenic Yersiniae. These proteins share a common domain architecture and promote bacterial adhesion to host cells. Here, we identified and characterized two putative inverse autotransporter genes in the fish pathogen Yersinia ruckeri NVH_3758, namely yrInv (for Y. ruckeri invasin) and yrIlm (for Y. ruckeri invasin-like molecule)...
September 6, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28883139/complete-genome-sequences-of-four-extensively-drug-resistant-pseudomonas-aeruginosa-strains-isolated-from-adults-with-ventilator-associated-pneumonia-at-a-tertiary-referral-hospital-in-mexico-city
#13
Luis F Espinosa-Camacho, Gabriela Delgado, Gloria Soberón-Chávez, Luis D Alcaraz, Jorge Castañon, Rosario Morales-Espinosa
Four extensively drug-resistant Pseudomonas aeruginosa strains, isolated from patients with pneumonia, were sequenced using PacBio RS-II single-molecule real-time (SMRT) technology. Genome sequence analysis identified great variability among mobile genetic elements, as well as some previously undescribed genomic islands and new variants of class 1 integrons (In1402, In1403, In1404, and In1408).
September 7, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28883134/first-complete-genome-sequences-of-xanthomonas-citri-pv-vignicola-strains-cfbp7111-cfbp7112-and-cfbp7113-obtained-using-long-read-technology
#14
Mylène Ruh, Martial Briand, Sophie Bonneau, Marie-Agnès Jacques, Nicolas W G Chen
Xanthomonas citri pv. vignicola strains cause bacterial blight of the legume crop cowpea. We report whole-genome sequences of three X. citri pv. vignicola strains obtained using PacBio single-molecule real-time sequencing. Such genomic data provide new information on pathogenicity factors, such as transcription activator-like effectors.
September 7, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28881995/debgr-an-efficient-and-near-exact-representation-of-the-weighted-de-bruijn-graph
#15
Prashant Pandey, Michael A Bender, Rob Johnson, Rob Patro
Motivation: Almost all de novo short-read genome and transcriptome assemblers start by building a representation of the de Bruijn Graph of the reads they are given as input. Even when other approaches are used for subsequent assembly (e.g. when one is using 'long read' technologies like those offered by PacBio or Oxford Nanopore), efficient k -mer processing is still crucial for accurate assembly, and state-of-the-art long-read error-correction methods use de Bruijn Graphs. Because of the centrality of de Bruijn Graphs, researchers have proposed numerous methods for representing de Bruijn Graphs compactly...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28878043/the-rapid-in-vivo-evolution-of-pseudomonas-aeruginosa-in-ventilator-associated-pneumonia-patients-leads-to-attenuated-virulence
#16
Ke Wang, Yi-Qiang Chen, May M Salido, Gurjeet S Kohli, Jin-Liang Kong, Hong-Jie Liang, Zi-Ting Yao, Yan-Tong Xie, Hua-Yu Wu, Shuang-Qi Cai, Daniela I Drautz-Moses, Aaron E Darling, Stephan C Schuster, Liang Yang, Yichen Ding
Pseudomonas aeruginosa is an opportunistic pathogen that causes severe airway infections in humans. These infections are usually difficult to treat and associated with high mortality rates. While colonizing the human airways, P. aeruginosa could accumulate genetic mutations that often lead to its better adaptability to the host environment. Understanding these evolutionary traits may provide important clues for the development of effective therapies to treat P. aeruginosa infections. In this study, 25 P. aeruginosa isolates were longitudinally sampled from the airways of four ventilator-associated pneumonia (VAP) patients...
September 2017: Open Biology
https://www.readbyqxmd.com/read/28871634/assembly-and-analysis-of-a-qingke-reference-genome-demonstrates-its-close-genetic-relation-to-modern-cultivated-barley
#17
Fei Dai, Xiaolei Wang, Xiao-Qi Zhang, Zhonghua Chen, Eviatar Nevo, Gulei Jin, Dezhi Wu, Chengdao Li, Guoping Zhang
Qingke, the local name of hulless barley in the Tibetan Plateau, is a staple food for Tibetans. The availability of its reference genome sequences could be useful for studies on breeding and molecular evolution. Taking advantage of the third-generation sequencer (PacBio), we de novo assembled a 4.84 Gb genome sequence of qingke, cv. Zangqing320 and anchored a 4.59 Gb sequence to seven chromosomes. Of the 46,787 annotated 'high-confidence' genes, 31,564 were validated by RNA-sequencing data of 39 wild and cultivated barley genotypes with wide genetic diversity, and the results were also confirmed by non-redundant protein database from NCBI...
September 4, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28868132/comprehensive-comparison-of-pacific-biosciences-and-oxford-nanopore-technologies-and-their-applications-to-transcriptome-analysis
#18
Jason L Weirather, Mariateresa de Cesare, Yunhao Wang, Paolo Piazza, Vittorio Sebastiano, Xiu-Jie Wang, David Buck, Kin Fai Au
Background: Given the demonstrated utility of Third Generation Sequencing [Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT)] long reads in many studies, a comprehensive analysis and comparison of their data quality and applications is in high demand. Methods: Based on the transcriptome sequencing data from human embryonic stem cells, we analyzed multiple data features of PacBio and ONT, including error pattern, length, mappability and technical improvements over previous platforms. We also evaluated their application to transcriptome analyses, such as isoform identification and quantification and characterization of transcriptome complexity, by comparing the performance of PacBio, ONT and their corresponding Hybrid-Seq strategies (PacBio+Illumina and ONT+Illumina)...
2017: F1000Research
https://www.readbyqxmd.com/read/28867496/draft-genome-sequence-of-multidrug-resistant-staphylococcus-haemolyticus-ipk_tsa25-harbouring-a-staphylococcus-aureus-plasmid-ps0385-1
#19
Hyung Jun Kim, Soojin Jang
OBJECTIVES: Staphylococcus haemolyticus is the second most frequently isolated coagulase-negative staphylococci from blood cultures. Moreover, multidrug resistance associated with the genome flexibility of S. haemolyticus has been increasingly reported worldwide. Here we report the draft genome sequence of multidrug-resistant S. haemolyticus IPK_TSA25 isolated from a building surface in South Korea. METHODS: Genomic DNA of S. haemolyticus IPK_TSA25 was sequenced using the PacBio RS II sequencing platform...
September 1, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/28861277/long-read-reference-genome-free-reconstruction-of-a-full-length-transcriptome-from-astragalus-membranaceus-reveals-transcript-variants-involved-in-bioactive-compound-biosynthesis
#20
Jun Li, Yuka Harata-Lee, Matthew D Denton, Qianjin Feng, Judith R Rathjen, Zhipeng Qu, David L Adelson
Astragalus membranaceus, also known as Huangqi in China, is one of the most widely used medicinal herbs in Traditional Chinese Medicine. Traditional Chinese Medicine formulations from Astragalus membranaceus have been used to treat a wide range of illnesses, such as cardiovascular disease, type 2 diabetes, nephritis and cancers. Pharmacological studies have shown that immunomodulating, anti-hyperglycemic, anti-inflammatory, antioxidant and antiviral activities exist in the extract of Astragalus membranaceus...
2017: Cell Discovery
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