Literature DB >> 23209255

Revised sequence and annotation of the Rhodobacter sphaeroides 2.4.1 genome.

Wayne S Kontur1, Wendy S Schackwitz, Natalia Ivanova, Joel Martin, Kurt Labutti, Shweta Deshpande, Hope N Tice, Christa Pennacchio, Erica Sodergren, George M Weinstock, Daniel R Noguera, Timothy J Donohue.   

Abstract

The DNA sequences of chromosomes I and II of Rhodobacter sphaeroides strain 2.4.1 have been revised, and the annotation of the entire genomic sequence, including both chromosomes and the five plasmids, has been updated. Errors in the originally published sequence have been corrected, and ~11% of the coding regions in the original sequence have been affected by the revised annotation.

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Year:  2012        PMID： 23209255      PMCID： PMC3510577          DOI： 10.1128/JB.01214-12

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


  7 in total

1.  GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes.

Authors:  Amrita Pati; Natalia N Ivanova; Natalia Mikhailova; Galina Ovchinnikova; Sean D Hooper; Athanasios Lykidis; Nikos C Kyrpides
Journal:  Nat Methods       Date:  2010-05-02       Impact factor: 28.547

2.  The home stretch, a first analysis of the nearly completed genome of Rhodobacter sphaeroides 2.4.1.

Authors:  C Mackenzie; M Choudhary; F W Larimer; P F Predki; S Stilwagen; J P Armitage; R D Barber; T J Donohue; J P Hosler; J E Newman; J P Shapleigh; R E Sockett; J Zeilstra-Ryalls; S Kaplan
Journal:  Photosynth Res       Date:  2001       Impact factor: 3.573

3.  Mapping short DNA sequencing reads and calling variants using mapping quality scores.

Authors:  Heng Li; Jue Ruan; Richard Durbin
Journal:  Genome Res       Date:  2008-08-19       Impact factor: 9.043

4.  IMG ER: a system for microbial genome annotation expert review and curation.

Authors:  Victor M Markowitz; Konstantinos Mavromatis; Natalia N Ivanova; I-Min A Chen; Ken Chu; Nikos C Kyrpides
Journal:  Bioinformatics       Date:  2009-06-27       Impact factor: 6.937

5.  Genome sequence of Rhodobacter sphaeroides Strain WS8N.

Authors:  Steven L Porter; David A Wilkinson; Elaine D Byles; George H Wadhams; Stephen Taylor; Nigel J Saunders; Judith P Armitage
Journal:  J Bacteriol       Date:  2011-05-27       Impact factor: 3.490

6.  Complete genome sequence of Rhodobacter sphaeroides KD131.

Authors:  Si-Kyu Lim; Sang Jun Kim; Sun Ho Cha; You-Kwan Oh; Hae-Jin Rhee; Mi-Sun Kim; Jeong K Lee
Journal:  J Bacteriol       Date:  2008-11-21       Impact factor: 3.490

7.  The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes.

Authors:  Konstantinos Mavromatis; Natalia N Ivanova; I-Min A Chen; Ernest Szeto; Victor M Markowitz; Nikos C Kyrpides
Journal:  Stand Genomic Sci       Date:  2009-07-20
  7 in total
  20 in total

1.  Role of small subunit in mediating assembly of red-type form I Rubisco.

Authors:  Jidnyasa Joshi; Oliver Mueller-Cajar; Yi-Chin C Tsai; F Ulrich Hartl; Manajit Hayer-Hartl
Journal:  J Biol Chem       Date:  2014-11-04       Impact factor: 5.157

Review 2.  The Divided Bacterial Genome: Structure, Function, and Evolution.

Authors:  George C diCenzo; Turlough M Finan
Journal:  Microbiol Mol Biol Rev       Date:  2017-08-09       Impact factor: 11.056

3.  Metabolism of Multiple Aromatic Compounds in Corn Stover Hydrolysate by Rhodopseudomonas palustris.

Authors:  Samantha Austin; Wayne S Kontur; Arne Ulbrich; J Zachary Oshlag; Weiping Zhang; Alan Higbee; Yaoping Zhang; Joshua J Coon; David B Hodge; Timothy J Donohue; Daniel R Noguera
Journal:  Environ Sci Technol       Date:  2015-07-09       Impact factor: 9.028

4.  Oxygen-dependent regulation of bacterial lipid production.

Authors:  Kimberly C Lemmer; Alice C Dohnalkova; Daniel R Noguera; Timothy J Donohue
Journal:  J Bacteriol       Date:  2015-03-02       Impact factor: 3.490

5.  Quantifying the effects of light intensity on bioproduction and maintenance energy during photosynthetic growth of Rhodobacter sphaeroides.

Authors:  Saheed Imam; Colin M Fitzgerald; Emily M Cook; Timothy J Donohue; Daniel R Noguera
Journal:  Photosynth Res       Date:  2014-11-27       Impact factor: 3.573

6.  Bacterial PerO Permeases Transport Sulfate and Related Oxyanions.

Authors:  Marie-Christine Hoffmann; Yvonne Pfänder; Marc Tintel; Bernd Masepohl
Journal:  J Bacteriol       Date:  2017-06-27       Impact factor: 3.490

7.  Synthesis and scavenging role of furan fatty acids.

Authors:  Rachelle A S Lemke; Amelia C Peterson; Eva C Ziegelhoffer; Michael S Westphall; Henrik Tjellström; Joshua J Coon; Timothy J Donohue
Journal:  Proc Natl Acad Sci U S A       Date:  2014-08-04       Impact factor: 11.205

8.  Characterization of a Rhodobacter sphaeroides primary fatty acid kinase.

Authors:  Maxwell J Bachochin; Michelle Van Allen; Robert D Barber
Journal:  Arch Microbiol       Date:  2020-10-10       Impact factor: 2.552

9.  An integrated approach to reconstructing genome-scale transcriptional regulatory networks.

Authors:  Saheed Imam; Daniel R Noguera; Timothy J Donohue
Journal:  PLoS Comput Biol       Date:  2015-02-27       Impact factor: 4.475

10.  Metaproteomics reveals major microbial players and their biodegradation functions in a large-scale aerobic composting plant.

Authors:  Dongming Liu; Mingxiao Li; Beidou Xi; Yue Zhao; Zimin Wei; Caihong Song; Chaowei Zhu
Journal:  Microb Biotechnol       Date:  2015-05-19       Impact factor: 5.813
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