skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305 T), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae

Abstract

Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall consisting of a proteinaceous layer rather than a peptidoglycan layer. The first strains of P. brasiliensis, including the type strain IFAM 1448 T, were isolated from a water sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the second completed genome sequence of a type strain of the genus Planctomyces to be published and the sixth type strain genome sequence from the family Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and 54 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. We study phylogenomic analyses that indicate that the classification within the Planctomycetaceae is partially in conflict with its evolutionary history, as the positioning of Schlesneria renders the genus Planctomyces paraphyletic. A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera. A quantitative comparison of phylogenetic and phenotypic aspects indicates that the three Planctomyces species with type strains availablemore » in public culture collections should be placed in separate genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to accommodate P. maris, P. limnophilus and P. brasiliensis, respectively. Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions. Lastly, in addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the order should be emended.« less

Authors:
 [1];  [1];  [2];  [3];  [3];  [3];  [4];  [3];  [3];  [3];  [3];  [3];  [3];  [3];  [5];  [5];  [6];  [7];  [8];  [9] more »;  [10];  [1];  [2];  [3];  [11];  [5];  [12];  [1];  [13];  [1] « less
  1. DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig (Germany)
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States) ; Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  5. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  6. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States) ; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  7. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States) ; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  8. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  9. Jomo Kenyatta University of Agriculture and Technology, Nairobi (Kenya)
  10. Helmholtz Centre for Infection Research (HZI), Braunschweig (Germany)
  11. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Davis, CA (United States)
  12. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of Queensland, Brisbane (Australia)
  13. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
Work for Others (WFO); USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1286834
Alternate Identifier(s):
OSTI ID: 1511412
Grant/Contract Number:  
AC05-00OR22725; AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 9; Journal Issue: 10; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Non-peptidoglycan bacteria; Stalked bacteria; Halotolerant; Gram-negative; Taxonomic descriptions; Planctomycetales; Planctomycetes; GEBA

Citation Formats

Scheuner, Carmen, Tindall, Brian J., Lu, Megan, Nolan, Matt, Lapidus, Alla L., Cheng, Jan-Fang, Goodwin, Lynne A., Pitluck, Sam, Huntemann, Marcel, Liolios, Konstantinos, Pagani, Ioanna, Mavromatis, Konstantinos, Ivanova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Jeffries, Cynthia D., Hauser, Loren John, Land, Miriam L., Mwirichia, Romano, Rohde, Manfred, Abt, Birte, Detter, John Chris, Woyke, Tanja, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Goker, Markus, Kyrpides, Nikos C., and Klenk, Hans-Peter. Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305T), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae. United States: N. p., 2014. Web. doi:10.1186/1944-3277-9-10.
Scheuner, Carmen, Tindall, Brian J., Lu, Megan, Nolan, Matt, Lapidus, Alla L., Cheng, Jan-Fang, Goodwin, Lynne A., Pitluck, Sam, Huntemann, Marcel, Liolios, Konstantinos, Pagani, Ioanna, Mavromatis, Konstantinos, Ivanova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Jeffries, Cynthia D., Hauser, Loren John, Land, Miriam L., Mwirichia, Romano, Rohde, Manfred, Abt, Birte, Detter, John Chris, Woyke, Tanja, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Goker, Markus, Kyrpides, Nikos C., & Klenk, Hans-Peter. Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305T), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae. United States. doi:10.1186/1944-3277-9-10.
Scheuner, Carmen, Tindall, Brian J., Lu, Megan, Nolan, Matt, Lapidus, Alla L., Cheng, Jan-Fang, Goodwin, Lynne A., Pitluck, Sam, Huntemann, Marcel, Liolios, Konstantinos, Pagani, Ioanna, Mavromatis, Konstantinos, Ivanova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Jeffries, Cynthia D., Hauser, Loren John, Land, Miriam L., Mwirichia, Romano, Rohde, Manfred, Abt, Birte, Detter, John Chris, Woyke, Tanja, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Goker, Markus, Kyrpides, Nikos C., and Klenk, Hans-Peter. Mon . "Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305T), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae". United States. doi:10.1186/1944-3277-9-10. https://www.osti.gov/servlets/purl/1286834.
@article{osti_1286834,
title = {Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305T), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae},
author = {Scheuner, Carmen and Tindall, Brian J. and Lu, Megan and Nolan, Matt and Lapidus, Alla L. and Cheng, Jan-Fang and Goodwin, Lynne A. and Pitluck, Sam and Huntemann, Marcel and Liolios, Konstantinos and Pagani, Ioanna and Mavromatis, Konstantinos and Ivanova, Natalia and Pati, Amrita and Chen, Amy and Palaniappan, Krishna and Jeffries, Cynthia D. and Hauser, Loren John and Land, Miriam L. and Mwirichia, Romano and Rohde, Manfred and Abt, Birte and Detter, John Chris and Woyke, Tanja and Eisen, Jonathan A. and Markowitz, Victor and Hugenholtz, Philip and Goker, Markus and Kyrpides, Nikos C. and Klenk, Hans-Peter},
abstractNote = {Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall consisting of a proteinaceous layer rather than a peptidoglycan layer. The first strains of P. brasiliensis, including the type strain IFAM 1448 T, were isolated from a water sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the second completed genome sequence of a type strain of the genus Planctomyces to be published and the sixth type strain genome sequence from the family Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and 54 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. We study phylogenomic analyses that indicate that the classification within the Planctomycetaceae is partially in conflict with its evolutionary history, as the positioning of Schlesneria renders the genus Planctomyces paraphyletic. A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera. A quantitative comparison of phylogenetic and phenotypic aspects indicates that the three Planctomyces species with type strains available in public culture collections should be placed in separate genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to accommodate P. maris, P. limnophilus and P. brasiliensis, respectively. Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions. Lastly, in addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the order should be emended.},
doi = {10.1186/1944-3277-9-10},
journal = {Standards in Genomic Sciences},
issn = {1944-3277},
number = 10,
volume = 9,
place = {United States},
year = {2014},
month = {12}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 18 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
journal, September 1997

  • Altschul, Stephen F.; Madden, Thomas L.; Sch�ffer, Alejandro A.
  • Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402
  • DOI: 10.1093/nar/25.17.3389

MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004

  • Edgar, R. C.
  • Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797
  • DOI: 10.1093/nar/gkh340