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Archive

September 2019; Volume 8,Issue 38

Genome Sequences

  • <span class="named-content genus-species" id="named-content-1">Bacillus velezensis</span> UTB96 Is an Antifungal Soil Isolate with a Reduced Genome Size Compared to That of <span class="named-content genus-species" id="named-content-2">Bacillus velezensis</span> FZB42
    Genome Sequences
    Bacillus velezensis UTB96 Is an Antifungal Soil Isolate with a Reduced Genome Size Compared to That of Bacillus velezensis FZB42

    Bacillus velezensis UTB96 was isolated from soil based on its antifungal activity. Whole-genome sequencing of strain UTB96 provided further information about its secondary metabolite gene clusters. Compared to the well-known strain FZB42, UTB96 lacks an IS3 element and a type I restriction endonuclease.

    Maliheh Vahidinasab, Masoud Ahmadzadeh, Marius Henkel, Rudolf Hausmann, Kambiz Morabbi Heravi
    19 Sep 2019
  • Revealing the Draft Genome Sequence of <em>Bradyrhizobium</em> sp. Strain USDA 3458, an Effective Symbiotic Diazotroph Isolated from Cowpea (<em>Vigna unguiculata</em>) Genotype IT82E-16
    Genome Sequences
    Revealing the Draft Genome Sequence of Bradyrhizobium sp. Strain USDA 3458, an Effective Symbiotic Diazotroph Isolated from Cowpea (Vigna unguiculata) Genotype IT82E-16

    Pairing plants with plant growth-promoting bacteria is critical to the future of agriculture. Bradyrhizobium sp. strain USDA 3458 isolated from Vigna unguiculata (cowpea) paired with cowpea genotype IT82E-16 represents a novel combination in arid regions. Here, we report the draft genome sequence of...

    Richard Allen White, III, Jeffrey S. Norman, Emily E. Mclachlan, Joseph P. Dunham, Aaron Garoutte, Maren L. Friesen
    19 Sep 2019
  • Complete Genome Sequence of Bacteriocin-Producing <span class="named-content genus-species" id="named-content-1">Enterococcus faecium</span> HY07
    Genome Sequences
    Complete Genome Sequence of Bacteriocin-Producing Enterococcus faecium HY07

    Here, we report the draft genome sequence of the bacteriocin-producing Enterococcus faecium strain HY07, isolated from traditional Chinese fermented sausages. The genome comprises 2,585,631 bp with 2,624 coding sequences, as assigned by NCBI, which may provide fundamental molecular information on elucidating the adaption mechanism of...

    Xiyu Duan, Hui Yang, Yun Tian, Rongrong Wang, Chengguo Liu, Hui Zhou
    19 Sep 2019
  • Draft Genome Sequences of <span class="named-content genus-species" id="named-content-1">Mycoplasma mycoides</span> subsp. <em>mycoides</em> Strains APF9 and AP108, Isolated in Nigeria in 2014 to 2016
    Genome Sequences
    Draft Genome Sequences of Mycoplasma mycoides subsp. mycoides Strains APF9 and AP108, Isolated in Nigeria in 2014 to 2016

    Mycoplasma mycoides subsp. mycoides is the etiological agent of contagious bovine pleuropneumonia (CBPP). While several findings on CBPP prevalence in Nigeria were documented, no data were reported about the genomic characterization of Nigerian M. mycoides subsp. mycoides strains....

    M. Di Federico, M. Orsini, M. Ancora, M. Marcacci, M. Di Domenico, I. Krasteva, K. Zilli, J. A. Musa, M. I. Francis, F. Sacchini, M. Scacchia, C. Cammà
    19 Sep 2019
  • Identification of the Coding-Complete Genome of <em>Cycas Necrotic Stunt Virus</em> in Transcriptomic Data Sets of Alfalfa (<em>Medicago sativa</em>)
    Genome Sequences
    Identification of the Coding-Complete Genome of Cycas Necrotic Stunt Virus in Transcriptomic Data Sets of Alfalfa (Medicago sativa)

    We present evidence here that alfalfa (Medicago sativa L.) can be a natural host species for a new strain of Cycas necrotic stunt virus (CNSV), for which the name CNSV-A (alfalfa) is proposed. Prior to this report, the virus has not been identified in alfalfa.

    Peng Jiang, Jonathan Shao, Lev G. Nemchinov
    19 Sep 2019
  • Complete Genome Sequence of <em>Lysinibacillus</em> sp. Strain SGAir0095, Isolated from Tropical Air Samples Collected in Singapore
    Genome Sequences
    Complete Genome Sequence of Lysinibacillus sp. Strain SGAir0095, Isolated from Tropical Air Samples Collected in Singapore

    Lysinibacillus sp. strain SGAir0095 was isolated from tropical air samples collected in Singapore, and its complete genome was sequenced with a hybrid strategy using single-molecule real-time sequencing and short reads. The genome consists of one chromosome of 4.14 Mbp and encompasses 3,885 protein-coding genes, 39 rRNAs, and 101 tRNAs.

    Anthony Wong, Ana Carolina M. Junqueira, Akira Uchida, Rikky W. Purbojati, James N. I. Houghton, Caroline Chénard, Megan E. Clare, Kavita K. Kushwaha, Alexander Putra, Nicolas E. Gaultier, Balakrishnan N. V. Premkrishnan, Vineeth Kodengil Vettath, Cassie E. Heinle, Daniela I. Drautz-Moses, Stephan C. Schuster
    19 Sep 2019
  • Complete Genome Sequences of <span class="named-content genus-species" id="named-content-1">Mycobacterium smegmatis</span> Phages NihilNomen and Carlyle, Isolated in Las Vegas, Nevada
    Genome Sequences
    Complete Genome Sequences of Mycobacterium smegmatis Phages NihilNomen and Carlyle, Isolated in Las Vegas, Nevada

    We present the complete genomes of the Mycobacterium smegmatis phages Carlyle and NihilNomen, isolated from soil in Las Vegas, Nevada. The phages were isolated and annotated by undergraduate students enrolled in the Phage Discovery course offered by the School of Life Sciences at the University of Nevada Las Vegas.

    Alicia Salisbury, Ryan Doss, Astha Mehta, Khadija Bhatti, Ciera Dapra, Audrey Huntsinger, Stephanie Rodriguez, Scott Yacek, Rylee Sandberg, Alexis Gildore, Jacinda Knudtson, Frances Tibayan, Tiannah Ohta, Neha Zafar, Guadalupe Mercado, Alan Le, Natalie Mekhaeel, Justin Willer, Edith Rodrich-Zuniga, Merissa McFarland, Kurt Regner, Christy Strong, Philippos K. Tsourkas
    19 Sep 2019
  • Draft Genome Sequence of the Griseofulvin-Producing Fungus <span class="named-content genus-species" id="named-content-1">Xylaria flabelliformis</span> Strain G536
    Genome Sequences
    Draft Genome Sequence of the Griseofulvin-Producing Fungus Xylaria flabelliformis Strain G536

    The draft genome of the ascomycete fungus Xylaria flabelliformis (previously known as Xylaria cubensis) was sequenced using Illumina paired-end technology. The assembled genome is 41.2 Mb long and contains 11,404 genes. This genome will contribute to our understanding of X. flabelliformis...

    Matthew E. Mead, Huzefa A. Raja, Jacob L. Steenwyk, Sonja L. Knowles, Nicholas H. Oberlies, Antonis Rokas
    19 Sep 2019
  • Draft Genome Sequence of <span class="named-content genus-species" id="named-content-1">Lactobacillus crispatus</span> Strain V4, Isolated from a Vaginal Swab from a Young Healthy Nonmenopausal Woman
    Genome Sequences
    Draft Genome Sequence of Lactobacillus crispatus Strain V4, Isolated from a Vaginal Swab from a Young Healthy Nonmenopausal Woman

    Lactobacillus crispatus strain V4 was isolated from a vaginal swab from a healthy nonmenopausal 35-year-old French woman. We report here its draft genome sequence of 2,091,889 bp, with an average G+C content of 37.02%.

    Maximilien Clabaut, Amine M. Boukerb, Pierre-Jean Racine, Chantal Pichon, Coralie Kremser, Aïna Queiroz, Madina Karsybayeva, Gérard Redziniak, Sylvie Chevalier, Marc G. J. Feuilloley
    19 Sep 2019
  • Draft Genome Sequence of Multidrug-Resistant <span class="named-content genus-species" id="named-content-1">Proteus mirabilis</span> CKTH01, Isolated from Raw Chicken Meat
    Genome Sequences
    Draft Genome Sequence of Multidrug-Resistant Proteus mirabilis CKTH01, Isolated from Raw Chicken Meat

    Proteus mirabilis CKTH01 is a pathogenic bacterium isolated from raw chicken meat. The genome sequence of P. mirabilis CKTH01 contains genes encoding multidrug efflux pumps, which are the virulence factors of the antibiotic-resistant bacterium. This 3.98-Mb draft genome sequence of...

    Supatra Areekit, Nuttida Thongpramul, Wariya Yamprayoonswat, Watthanachai Jumpathong, Satapanawat Sittihan, Suwanan Wanthongchareon, Pattarawan Ruangsuj, Sirirat Wachiralurpan, Kosum Chansiri, Montri Yasawong
    19 Sep 2019
  • Draft Genome Sequence of <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> DSM 12242, a Highly Efficient Host Strain for the Isolation of Somatic Coliphages
    Genome Sequences
    Draft Genome Sequence of Escherichia coli DSM 12242, a Highly Efficient Host Strain for the Isolation of Somatic Coliphages

    Here, we report the draft genome sequence and characterization of the commercial strain Escherichia coli DSM 12242 (=ATCC 13706/60 =NZRM 3262) derived from strain C (ATCC 13706), which is suitable for the isolation of coliphages from environmental and clinical samples.

    Cátia Pacífico, Dmitrij Sofka, João André Carriço, Friederike Hilbert
    19 Sep 2019
  • Foot-and-Mouth Disease Virus Serotype A Genome Sequence from Kenya in 2016
    Genome Sequences
    Foot-and-Mouth Disease Virus Serotype A Genome Sequence from Kenya in 2016

    We report the genome sequence of a foot-and-mouth disease virus (FMDV) serotype A topotype Africa isolate collected from bovine vesicular epithelium from Kenya in 2016. This novel sequence updates the knowledge of FMDV diversity in eastern Africa and has important implications for FMDV epidemiology and molecular analyses.

    Rachel M. Palinski, Abraham Sangula, Francis Gakuya, Miranda R. Bertram, Steven J. Pauszek, Ethan J. Hartwig, George R. Smoliga, Vincent Obanda, George Omondi, Kimberly VanderWaal, Jonathan Arzt
    19 Sep 2019
  • Genome Sequences of 11 Conspecific <em>Streptomyces</em> sp. Strains
    Genome Sequences
    Genome Sequences of 11 Conspecific Streptomyces sp. Strains

    The genomes of 11 conspecific Streptomyces strains, i.e., from the same species and inhabiting the same ecological niche, were sequenced and assembled. This data set offers an ideal framework to assess the genome evolution of Streptomyces species in their ecological context.

    Abdoul-Razak Tidjani, Jean-Noël Lorenzi, Maxime Toussaint, Erwin van Dijk, Delphine Naquin, Olivier Lespinet, Cyril Bontemps, Pierre Leblond
    19 Sep 2019
  • Complete Genome Sequence of <span class="named-content genus-species" id="named-content-1">Salmonella enterica</span> Myophage Matapan
    Genome Sequences
    Complete Genome Sequence of Salmonella enterica Myophage Matapan

    Here, we describe the Salmonella enterica serovar Heidelberg phage Matapan. A myophage with a 157,408-kb genome, Matapan is most closely related to Vi01-like phages.

    Jasmine Juliette, Yicheng Xie, Heather Newkirk, Mei Liu, Jason J. Gill, Jolene Ramsey
    19 Sep 2019
  • Complete Genome Sequence of <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> Myophage Mansfield
    Genome Sequences
    Complete Genome Sequence of Escherichia coli Myophage Mansfield

    Mansfield is a PB1-like Escherichia bacteriophage with a 68,120-bp genome and a predicted 3,673-bp direct terminal repeat. This myophage encodes 105 proteins, for which 32 functions were predicted.

    Genevieve M. D’Souza, Kathryn Klotz, Russell Moreland, Mei Liu, Jolene Ramsey
    19 Sep 2019
  • First Draft Genome Sequence of Wheat Spot Blotch Pathogen <em>Bipolaris sorokiniana</em> BS_112 from India, Obtained Using Hybrid Assembly
    Genome Sequences
    First Draft Genome Sequence of Wheat Spot Blotch Pathogen Bipolaris sorokiniana BS_112 from India, Obtained Using Hybrid Assembly

    Bipolaris sorokiniana is a devastating fungal pathogen causing spot blotch of wheat. We report here the first draft genome of Bipolaris sorokiniana strain BS_112 from India using sequence reads from the Ion Torrent, Illumina HiSeq, and Nanopore platforms. The genome size was estimated at 35.64 Mb with an average G+C content of 50.20%.

    Rashmi Aggarwal, Sapna Sharma, Kartar Singh, Malkhan Singh Gurjar, Mahender Singh Saharan, Sangeeta Gupta, Bishnu Maya Bashyal, Kishor Gaikwad
    19 Sep 2019
  • Whole-Genome Sequencing of <em>Streptomyces</em> sp. Strain UYFA156, a Cultivar-Specific Plant Growth-Promoting Endophyte of <em>Festuca arundinacea</em>
    Genome Sequences
    Whole-Genome Sequencing of Streptomyces sp. Strain UYFA156, a Cultivar-Specific Plant Growth-Promoting Endophyte of Festuca arundinacea

    Streptomyces spp. produce many and diverse bioactive metabolites. Plant growth-promoting (PGP) activity by Streptomyces spp. has been reported repeatedly; however, the mechanisms are largely unknown. We report the sequencing of the genome of a PGP endophytic Streptomyces sp. strain, which will contribute to the understanding of the underlying mechanisms for growth promotion.

    Patricia Vaz Jauri, Martín Beracochea, Belén Fernández, Federico Battistoni
    19 Sep 2019
  • Complete Genome Sequences of Four <span class="named-content genus-species" id="named-content-1">Salmonella enterica</span> Strains Associated with Pistachios Assembled Using a Combination of Short- and Long-Read Sequencing
    Genome Sequences
    Complete Genome Sequences of Four Salmonella enterica Strains Associated with Pistachios Assembled Using a Combination of Short- and Long-Read Sequencing

    Here, we report the genomes of two Salmonella enterica subsp. enterica serovar Montevideo strains (CFSAN005645 and FCC0123) and two Salmonella enterica subsp. enterica serovar Senftenberg strains (FSW0104 and CFSAN087304...

    Julie Haendiges, Narjol Gonzalez-Escalona, Jesse D. Miller, Maria Hoffmann
    19 Sep 2019
  • Complete Genome Sequence of <em>Pantoea</em> sp. Strain CCBC3-3-1, an Antagonistic Endophytic Bacterium Isolated from a <em>Cotinus coggygria</em> Branch
    Genome Sequences
    Complete Genome Sequence of Pantoea sp. Strain CCBC3-3-1, an Antagonistic Endophytic Bacterium Isolated from a Cotinus coggygria Branch

    Pantoea sp. strain CCBC3-3-1, having antagonistic activity against Verticillium dahlia, was isolated from Cotinus coggygria. We report the complete genome sequence of this strain determined by PacBio single-molecule real-time (...

    Jianghong Zhou, Fei Xia, Shaochen Che, Li Zhong, Guofeng Zhang
    19 Sep 2019
  • Complete Genome Sequence of Shelby, a Siphophage Infecting Carbapenemase-Producing <span class="named-content genus-species" id="named-content-1">Klebsiella pneumoniae</span>
    Genome Sequences
    Complete Genome Sequence of Shelby, a Siphophage Infecting Carbapenemase-Producing Klebsiella pneumoniae

    Carbapenem-resistant Klebsiella pneumoniae, a bacterium of the family Enterobacteriaceae, is a high-priority antibiotic-resistant pathogen that causes nosocomial infections. Here, we describe the isolation and annotation of the K....

    Robert Saldana, Heather Newkirk, Mei Liu, Jason J. Gill, Jolene Ramsey
    19 Sep 2019
  • Complete Genome Sequence of <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> Myophage Mangalitsa
    Genome Sequences
    Complete Genome Sequence of Escherichia coli Myophage Mangalitsa

    Enteropathogenic Escherichia coli is a prevalent Gram-negative bacterium that can lead to fatal complications from infection in humans. Here, we present the isolation and complete annotation of the 52,329-bp genome of enteropathogenic E. coli ATCC 23545 myophage Mangalitsa. Predicted terminal...

    Cameron L. Atkison, Justin Boeckman, Heather Newkirk, Mei Liu, Jason J. Gill, Jesse Cahill, Jolene Ramsey
    19 Sep 2019
  • Complete Genome Sequence of <span class="named-content genus-species" id="named-content-1">Serratia marcescens</span> Myophage MyoSmar
    Genome Sequences
    Complete Genome Sequence of Serratia marcescens Myophage MyoSmar

    Serratia marcescens is an opportunistic pathogen that causes respiratory, urinary, and digestive tract infections in humans. Here, we describe the annotation of Serratia marcescens myophage MyoSmar. The 68,745-bp genome encodes 105 predicted proteins and is most similar to the genomes of...

    Savannah Cooper, Quang Nguyen, Heather Newkirk, Mei Liu, Jesse Cahill, Jolene Ramsey
    19 Sep 2019
  • Complete Genome Sequence of <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> Siphophage Sciku
    Genome Sequences
    Complete Genome Sequence of Escherichia coli Siphophage Sciku

    Escherichia coli is a Gram-negative bacterium that is found in humans and animals as both a commensal organism and a pathogen. This report describes the isolation of Sciku, a siphophage infecting E. coli 4s, with 73 protein-coding genes. Genome comparisons suggest that Sciku is related to phages...

    Isla Hernandez, Micah Castillo, Russell Moreland, Mei Liu, Jolene Ramsey
    19 Sep 2019
  • Whole-Genome Sequence of <span class="named-content genus-species" id="named-content-1">Salmonella enterica</span> subsp. <span class="named-content genus-species" id="named-content-2">diarizonae</span> Serovar 61:k:1,5,(7) Strain 1569 (14PM0011), Isolated from German Sheep
    Genome Sequences
    Whole-Genome Sequence of Salmonella enterica subsp. diarizonae Serovar 61:k:1,5,(7) Strain 1569 (14PM0011), Isolated from German Sheep

    Here, we report the draft genome sequence of Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) strain 1569, alternatively named 14PM0011, which is a common serovar in German sheep that is unrepresented in the databases and considered and described as being host adapted with low virulence....

    Anne Busch, Herbert Tomaso, Ulrich Methner
    19 Sep 2019
  • Complete Genome Sequence of a <span class="named-content genus-species" id="named-content-1">Pseudomonas aeruginosa</span> Isolate from a Kidney Stone
    Genome Sequences
    Complete Genome Sequence of a Pseudomonas aeruginosa Isolate from a Kidney Stone

    Recently, we isolated a temperate bacteriophage, Pseudomonas phage Dobby, from a calcium oxalate kidney stone. Here, we present the complete genome of the bacterial host harboring this phage, Pseudomonas aeruginosa UMB2738. From the analysis of the genome sequence, five additional prophage sequences were identified.

    Genevieve Johnson, Nicole Stark, Alan J. Wolfe, Catherine Putonti
    19 Sep 2019
  • Draft Genome Sequences of Two <span class="named-content genus-species" id="named-content-1">Veillonella tobetsuensis</span> Clinical Isolates from Intraoperative Bronchial Fluids of Elderly Patients with Pulmonary Carcinoma
    Genome Sequences
    Draft Genome Sequences of Two Veillonella tobetsuensis Clinical Isolates from Intraoperative Bronchial Fluids of Elderly Patients with Pulmonary Carcinoma

    To date, Veillonella tobetsuensis has been known as an oral anaerobe and a facilitator of early-stage oral biofilm development with streptococci. Here, we report the draft genome sequences of 2 strains of V. tobetsuensis first isolated from intraoperative bronchial fluids of elderly patients with...

    Izumi Mashima, Tohru Miyoshi-Akiyama, Junko Tomida, Ryo Kutsuna, Jumpei Washio, Nobuhiro Takahashi, Futoshi Nakazawa, Takuichi Sato, Yoshiaki Kawamura
    19 Sep 2019
  • Complete Genome Sequences of Two <span class="named-content genus-species" id="named-content-1">Klebsiella pneumoniae</span> Phages Isolated as Part of an International Effort
    Genome Sequences
    Complete Genome Sequences of Two Klebsiella pneumoniae Phages Isolated as Part of an International Effort

    We report the genomic sequences of phages KpCHEMY26 and KpGranit, isolated in Israel during a worldwide effort against a multidrug- and phage-resistant strain of Klebsiella pneumoniae from a patient in Finland. These results demonstrate the importance of an efficient worldwide network for collaborating in personalized therapy for infectious diseases.

    ...
    Ortal Yerushalmy, Shunit Coppenhagen-Glazer, Ran Nir-Paz, Henni Tuomala, Mikael Skurnik, Saija Kiljunen, Ronen Hazan
    19 Sep 2019
  • Draft Genome Sequence of <em>Streptomyces</em> sp. Strain AM-2504, Identified by 16S rRNA Comparative Analysis as a <span class="named-content genus-species" id="named-content-1">Streptomyces kasugaensis</span> Strain
    Genome Sequences
    Draft Genome Sequence of Streptomyces sp. Strain AM-2504, Identified by 16S rRNA Comparative Analysis as a Streptomyces kasugaensis Strain

    We report here the draft genome sequence of Streptomyces sp. strain AM-2504, a microorganism producing a broad range of biotechnologically relevant molecules. The comparative analysis of its 16S rRNA sequence allowed the assignment of this strain to the Streptomyces kasugaensis species, thus fostering functional characterization of the secondary metabolites...

    Valerio Napolioni, Lucia Cimarelli, Antonino Miano, Anna La Teana, Retina Çapuni, Anna Maria Giuliodori, Attilio Fabbretti, Roberto Spurio
    19 Sep 2019
  • Complete Genome Sequence of <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> Podophage Penshu1
    Genome Sequences
    Complete Genome Sequence of Escherichia coli Podophage Penshu1

    Escherichia coli 4s is a Gram-negative bacterium found in the equine intestinal ecosystem alongside diverse other coliform bacteria and bacteriophages. This announcement describes the complete genome of the T7-like E. coli 4s podophage Penshu1. From its 39,263-bp genome, 54 protein-encoding genes...

    Douglas Pechacek, Myung Hwangbo, Russell Moreland, Mei Liu, Jolene Ramsey
    19 Sep 2019
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