Literature DB >> 21685292

De novo sequencing and assembly of the whole genome of Novosphingobium sp. strain PP1Y.

V D'Argenio1, M Petrillo, P Cantiello, B Naso, L Cozzuto, E Notomista, G Paolella, A Di Donato, F Salvatore.   

Abstract

Novosphingobium sp. strain PP1Y is a marine bacterium specifically adapted to use fuels as an energy source. We sequenced and assembled its entire genome using the Roche 454 genome sequencer system, which led to the identification of two plasmids and one megaplasmid, besides a 3.9-Mb circular chromosome.

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Year:  2011        PMID： 21685292      PMCID： PMC3147705          DOI： 10.1128/JB.05349-11

Source DB:  PubMed          Journal:  J Bacteriol        ISSN： 0021-9193            Impact factor:   3.490


  5 in total

1.  Complete genome sequence of the metabolically versatile plant growth-promoting endophyte Variovorax paradoxus S110.

Authors:  Jong-In Han; Hong-Kyu Choi; Seung-Won Lee; Paul M Orwin; Jina Kim; Sarah L Laroe; Tae-Gyu Kim; Jennifer O'Neil; Jared R Leadbetter; Sang Yup Lee; Cheol-Goo Hur; Jim C Spain; Galina Ovchinnikova; Lynne Goodwin; Cliff Han
Journal:  J Bacteriol       Date:  2010-12-23       Impact factor: 3.490

2.  Genome sequencing in microfabricated high-density picolitre reactors.

Authors:  Marcel Margulies; Michael Egholm; William E Altman; Said Attiya; Joel S Bader; Lisa A Bemben; Jan Berka; Michael S Braverman; Yi-Ju Chen; Zhoutao Chen; Scott B Dewell; Lei Du; Joseph M Fierro; Xavier V Gomes; Brian C Godwin; Wen He; Scott Helgesen; Chun Heen Ho; Chun He Ho; Gerard P Irzyk; Szilveszter C Jando; Maria L I Alenquer; Thomas P Jarvie; Kshama B Jirage; Jong-Bum Kim; James R Knight; Janna R Lanza; John H Leamon; Steven M Lefkowitz; Ming Lei; Jing Li; Kenton L Lohman; Hong Lu; Vinod B Makhijani; Keith E McDade; Michael P McKenna; Eugene W Myers; Elizabeth Nickerson; John R Nobile; Ramona Plant; Bernard P Puc; Michael T Ronan; George T Roth; Gary J Sarkis; Jan Fredrik Simons; John W Simpson; Maithreyan Srinivasan; Karrie R Tartaro; Alexander Tomasz; Kari A Vogt; Greg A Volkmer; Shally H Wang; Yong Wang; Michael P Weiner; Pengguang Yu; Richard F Begley; Jonathan M Rothberg
Journal:  Nature       Date:  2005-07-31       Impact factor: 49.962

3.  The marine isolate Novosphingobium sp. PP1Y shows specific adaptation to use the aromatic fraction of fuels as the sole carbon and energy source.

Authors:  Eugenio Notomista; Francesca Pennacchio; Valeria Cafaro; Giovanni Smaldone; Viviana Izzo; Luca Troncone; Mario Varcamonti; Alberto Di Donato
Journal:  Microb Ecol       Date:  2011-01-22       Impact factor: 4.552

4.  Helicobacter pylori genome evolution during human infection.

Authors:  Lynn Kennemann; Xavier Didelot; Toni Aebischer; Stefanie Kuhn; Bernd Drescher; Marcus Droege; Richard Reinhardt; Pelayo Correa; Thomas F Meyer; Christine Josenhans; Daniel Falush; Sebastian Suerbaum
Journal:  Proc Natl Acad Sci U S A       Date:  2011-03-07       Impact factor: 11.205

5.  Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid.

Authors:  Daniel Wibberg; Jochen Blom; Sebastian Jaenicke; Florian Kollin; Oliver Rupp; Birgit Scharf; Susanne Schneiker-Bekel; Rafael Sczcepanowski; Alexander Goesmann; Joao Carlos Setubal; Rüdiger Schmitt; Alfred Pühler; Andreas Schlüter
Journal:  J Biotechnol       Date:  2011-02-15       Impact factor: 3.307
  5 in total
  11 in total

1.  Three-Component O-Demethylase System Essential for Catabolism of a Lignin-Derived Biphenyl Compound in Sphingobium sp. Strain SYK-6.

Authors:  Taichi Yoshikata; Kazuya Suzuki; Naofumi Kamimura; Masahiro Namiki; Shojiro Hishiyama; Takuma Araki; Daisuke Kasai; Yuichiro Otsuka; Masaya Nakamura; Masao Fukuda; Yoshihiro Katayama; Eiji Masai
Journal:  Appl Environ Microbiol       Date:  2014-09-12       Impact factor: 4.792

2.  Comparison of 26 sphingomonad genomes reveals diverse environmental adaptations and biodegradative capabilities.

Authors:  Frank O Aylward; Bradon R McDonald; Sandra M Adams; Alejandra Valenzuela; Rebeccah A Schmidt; Lynne A Goodwin; Tanja Woyke; Cameron R Currie; Garret Suen; Michael Poulsen
Journal:  Appl Environ Microbiol       Date:  2013-04-05       Impact factor: 4.792

3.  Comparative genomic analysis of six bacteria belonging to the genus Novosphingobium: insights into marine adaptation, cell-cell signaling and bioremediation.

Authors:  Han Ming Gan; André O Hudson; Ahmad Yamin Abdul Rahman; Kok Gan Chan; Michael A Savka
Journal:  BMC Genomics       Date:  2013-06-28       Impact factor: 3.969

4.  A group of sequence-related sphingomonad enzymes catalyzes cleavage of β-aryl ether linkages in lignin β-guaiacyl and β-syringyl ether dimers.

Authors:  Daniel L Gall; John Ralph; Timothy J Donohue; Daniel R Noguera
Journal:  Environ Sci Technol       Date:  2014-10-01       Impact factor: 9.028

5.  Comparison of the complete genome sequences of four γ-hexachlorocyclohexane-degrading bacterial strains: insights into the evolution of bacteria able to degrade a recalcitrant man-made pesticide.

Authors:  Michiro Tabata; Satoshi Ohhata; Yuki Nikawadori; Kouhei Kishida; Takuya Sato; Toru Kawasumi; Hiromi Kato; Yoshiyuki Ohtsubo; Masataka Tsuda; Yuji Nagata
Journal:  DNA Res       Date:  2016-08-30       Impact factor: 4.458

6.  Draft Genome Sequence of Novosphingobium panipatense Strain P5:ABC, Isolated from Hydrocarbon-Contaminated Soil from Noonmati Refinery, Assam, India.

Authors:  Arvind Kumar Singh; Bobby Chettri; Arpita Ghosh; Surendra K Chikara; Timir Tripathi
Journal:  Genome Announc       Date:  2017-11-09

7.  The complete 12 Mb genome and transcriptome of Nonomuraea gerenzanensis with new insights into its duplicated "magic" RNA polymerase.

Authors:  Valeria D'Argenio; Mauro Petrillo; Daniela Pasanisi; Caterina Pagliarulo; Roberta Colicchio; Adelfia Talà; Maria Stella de Biase; Mario Zanfardino; Emanuela Scolamiero; Chiara Pagliuca; Antonio Gaballo; Annunziata Gaetana Cicatiello; Piergiuseppe Cantiello; Irene Postiglione; Barbara Naso; Angelo Boccia; Miriana Durante; Luca Cozzuto; Paola Salvatore; Giovanni Paolella; Francesco Salvatore; Pietro Alifano
Journal:  Sci Rep       Date:  2016-12-21       Impact factor: 4.379

8.  Complete sequencing of Novosphingobium sp. PP1Y reveals a biotechnologically meaningful metabolic pattern.

Authors:  Valeria D'Argenio; Eugenio Notomista; Mauro Petrillo; Piergiuseppe Cantiello; Valeria Cafaro; Viviana Izzo; Barbara Naso; Luca Cozzuto; Lorenzo Durante; Luca Troncone; Giovanni Paolella; Francesco Salvatore; Alberto Di Donato
Journal:  BMC Genomics       Date:  2014-05-19       Impact factor: 3.969

9.  Metagenomics Reveals Dysbiosis and a Potentially Pathogenic N. flavescens Strain in Duodenum of Adult Celiac Patients.

Authors:  Valeria D'Argenio; Giorgio Casaburi; Vincenza Precone; Chiara Pagliuca; Roberta Colicchio; Daniela Sarnataro; Valentina Discepolo; Sangman M Kim; Ilaria Russo; Giovanna Del Vecchio Blanco; David S Horner; Matteo Chiara; Graziano Pesole; Paola Salvatore; Giovanni Monteleone; Carolina Ciacci; Gregory J Caporaso; Bana Jabrì; Francesco Salvatore; Lucia Sacchetti
Journal:  Am J Gastroenterol       Date:  2016-04-05       Impact factor: 10.864

10.  Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium.

Authors:  Roshan Kumar; Helianthous Verma; Shazia Haider; Abhay Bajaj; Utkarsh Sood; Kalaiarasan Ponnusamy; Shekhar Nagar; Mallikarjun N Shakarad; Ram Krishan Negi; Yogendra Singh; J P Khurana; Jack A Gilbert; Rup Lal
Journal:  mSystems       Date:  2017-05-23       Impact factor: 6.496
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