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Title: High quality draft genome sequences of Pseudomonas fulva DSM 17717 T, Pseudomonas parafulva DSM 17004 T and Pseudomonas cremoricolorata DSM 17059 T type strains

Abstract

Pseudomonas has the highest number of species out of any genus of Gram-negative bacteria and is phylogenetically divided into several groups. The Pseudomonas putida phylogenetic branch includes at least 13 species of environmental and industrial interest, plant-associated bacteria, insect pathogens, and even some members that have been found in clinical specimens. In the context of the Genomic Encyclopedia of Bacteria and Archaea project, we present the permanent, high-quality draft genomes of the type strains of 3 taxonomically and ecologically closely related species in the Pseudomonas putida phylogenetic branch: Pseudomonas fulva DSM 17717 T, Pseudomonas parafulva DSM 17004 T and Pseudomonas cremoricolorata DSM 17059T. All three genomes are comparable in size (4.6-4.9Mb), with 4,119-4,459 protein-coding genes. Average nucleotide identity based on BLAST comparisons and digital genome-to-genome distance calculations are in good agreement with experimental DNA-DNA hybridization results. The genome sequences presented here will be very helpful in elucidating the taxonomy, phylogeny and evolution of the Pseudomonas putida species complex.

Authors:
 [1];  [1];  [1];  [1];  [2];  [3];  [3];  [3];  [3];  [3];  [4];  [5];  [3];  [6];  [7];  [4]
  1. Universitat de les Illes Balears, Palma de Mallorca (Spain). Dept. of Biology-Microbiology
  2. Universitat de les Illes Balears, Palma de Mallorca (Spain). Serveis Cientifico-Tecnics
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. Universitat de les Illes Balears, Palma de Mallorca (Spain). Dept. of Biology-Microbiology; Institut Mediterrani d’Estudis Avancats, Palma de Mallorca (Spain)
  5. Leibniz Inst. DSMZ - German Collection of Microorganisms and Cell Cultures (Germany)
  6. Newcastle Univ., Newcastle upon Tyne (United Kingdom). School of Biology
  7. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia). Dept. of Biological Sciences
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1377460
Grant/Contract Number:
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 11; Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Genomic Encyclopedia of Type Strains (GEBA); One Thousand Microbial Genomes Project (KMG-I); P. fulva; P. parafulva; P. cremoricolorata; Genome; Type strains

Citation Formats

Peña, Arantxa, Busquets, Antonio, Gomila, Margarita, Mulet, Magdalena, Gomila, Rosa M., Reddy, T. B. K., Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia, Markowitz, Victor, García-Valdés, Elena, Göker, Markus, Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos, and Lalucat, Jorge. High quality draft genome sequences of Pseudomonas fulva DSM 17717T, Pseudomonas parafulva DSM 17004T and Pseudomonas cremoricolorata DSM 17059T type strains. United States: N. p., 2016. Web. doi:10.1186/s40793-016-0178-2.
Peña, Arantxa, Busquets, Antonio, Gomila, Margarita, Mulet, Magdalena, Gomila, Rosa M., Reddy, T. B. K., Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia, Markowitz, Victor, García-Valdés, Elena, Göker, Markus, Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos, & Lalucat, Jorge. High quality draft genome sequences of Pseudomonas fulva DSM 17717T, Pseudomonas parafulva DSM 17004T and Pseudomonas cremoricolorata DSM 17059T type strains. United States. doi:10.1186/s40793-016-0178-2.
Peña, Arantxa, Busquets, Antonio, Gomila, Margarita, Mulet, Magdalena, Gomila, Rosa M., Reddy, T. B. K., Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia, Markowitz, Victor, García-Valdés, Elena, Göker, Markus, Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos, and Lalucat, Jorge. Thu . "High quality draft genome sequences of Pseudomonas fulva DSM 17717T, Pseudomonas parafulva DSM 17004T and Pseudomonas cremoricolorata DSM 17059T type strains". United States. doi:10.1186/s40793-016-0178-2. https://www.osti.gov/servlets/purl/1377460.
@article{osti_1377460,
title = {High quality draft genome sequences of Pseudomonas fulva DSM 17717T, Pseudomonas parafulva DSM 17004T and Pseudomonas cremoricolorata DSM 17059T type strains},
author = {Peña, Arantxa and Busquets, Antonio and Gomila, Margarita and Mulet, Magdalena and Gomila, Rosa M. and Reddy, T. B. K. and Huntemann, Marcel and Pati, Amrita and Ivanova, Natalia and Markowitz, Victor and García-Valdés, Elena and Göker, Markus and Woyke, Tanja and Klenk, Hans-Peter and Kyrpides, Nikos and Lalucat, Jorge},
abstractNote = {Pseudomonas has the highest number of species out of any genus of Gram-negative bacteria and is phylogenetically divided into several groups. The Pseudomonas putida phylogenetic branch includes at least 13 species of environmental and industrial interest, plant-associated bacteria, insect pathogens, and even some members that have been found in clinical specimens. In the context of the Genomic Encyclopedia of Bacteria and Archaea project, we present the permanent, high-quality draft genomes of the type strains of 3 taxonomically and ecologically closely related species in the Pseudomonas putida phylogenetic branch: Pseudomonas fulva DSM 17717T, Pseudomonas parafulva DSM 17004T and Pseudomonas cremoricolorata DSM 17059T. All three genomes are comparable in size (4.6-4.9Mb), with 4,119-4,459 protein-coding genes. Average nucleotide identity based on BLAST comparisons and digital genome-to-genome distance calculations are in good agreement with experimental DNA-DNA hybridization results. The genome sequences presented here will be very helpful in elucidating the taxonomy, phylogeny and evolution of the Pseudomonas putida species complex.},
doi = {10.1186/s40793-016-0178-2},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 11,
place = {United States},
year = {Thu Sep 01 00:00:00 EDT 2016},
month = {Thu Sep 01 00:00:00 EDT 2016}
}

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