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Title: Genome Data Provides High Support for Generic Boundaries in Burkholderia Sensu Lato

Although the taxonomy of Burkholderia has been extensively scrutinized, significant uncertainty remains regarding the generic boundaries and composition of this large and heterogeneous taxon. Here we used the amino acid and nucleotide sequences of 106 conserved proteins from 92 species to infer robust maximum likelihood phylogenies with which to investigate the generic structure of Burkholderia sensu lato. These data unambiguously supported five distinct lineages, of which four correspond to Burkholderia sensu stricto and the newly introduced genera Paraburkholderia, Caballeronia, and Robbsia. The fifth lineage was represented by P. rhizoxinica. Based on these findings, we propose 13 new combinations for those species previously described as members of Burkholderia but that form part of Caballeronia. These findings also suggest revision of the taxonomic status of P. rhizoxinica as it is does not form part of any of the genera currently recognized in Burkholderia sensu lato. From a phylogenetic point of view, Burkholderia sensu stricto has a sister relationship with the Caballeronia+Paraburkholderia clade. Also, the lineages represented by P. rhizoxinica and R. andropogonis, respectively, emerged prior to the radiation of the Burkholderia sensu stricto+Caballeronia+Paraburkholderia clade. Our findings therefore constitute a solid framework, not only for supporting current and future taxonomic decisions, but alsomore » for studying the evolution of this assemblage of medically, industrially and agriculturally important species.« less
Authors:
 [1] ;  [1] ;  [1] ;  [1] ;  [1] ;  [1] ;  [2] ;  [2] ;  [2] ;  [2] ;  [2] ;  [2] ;  [2] ;  [2] ;  [2] ;  [2] ;  [2] ;  [2] ;  [2] ;  [2] more »;  [3] ;  [4] ;  [1] ;  [1] « less
  1. Univ. of Pretoria (South Africa). Dept. of Microbiology and Plant Pathology. Forestry and Agricultural Biotechnology Inst.
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  3. Justus Liebig Univ. Giessen (Germany). Bioinformatics and Systems Biology
  4. Univ. of Georgia, Athens, GA (United States). Dept. of Microbiology
Publication Date:
Grant/Contract Number:
AC02-05CH11231
Type:
Published Article
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 8; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Research Org:
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of Pretoria (South Africa)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); National Research Foundation (NRF) (South Africa); Dept. of Science and Technology (South Africa)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Burkholderia; Paraburkholderia; Caballeronia; phylogenomics; Robbsia andropogonis; Burkholderia rhizoxinica
OSTI Identifier:
1423489
Alternate Identifier(s):
OSTI ID: 1460296

Beukes, Chrizelle W., Palmer, Marike, Manyaka, Puseletso, Chan, Wai Y., Avontuur, Juanita R., van Zyl, Elritha, Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Stamatis, Dimitrios, Reddy, T. B. K., Daum, Chris, Shapiro, Nicole, Markowitz, Victor, Ivanova, Natalia, Kyrpides, Nikos, Woyke, Tanja, Blom, Jochen, Whitman, William B., Venter, Stephanus N., and Steenkamp, Emma T.. Genome Data Provides High Support for Generic Boundaries in Burkholderia Sensu Lato. United States: N. p., Web. doi:10.3389/fmicb.2017.01154.
Beukes, Chrizelle W., Palmer, Marike, Manyaka, Puseletso, Chan, Wai Y., Avontuur, Juanita R., van Zyl, Elritha, Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Stamatis, Dimitrios, Reddy, T. B. K., Daum, Chris, Shapiro, Nicole, Markowitz, Victor, Ivanova, Natalia, Kyrpides, Nikos, Woyke, Tanja, Blom, Jochen, Whitman, William B., Venter, Stephanus N., & Steenkamp, Emma T.. Genome Data Provides High Support for Generic Boundaries in Burkholderia Sensu Lato. United States. doi:10.3389/fmicb.2017.01154.
Beukes, Chrizelle W., Palmer, Marike, Manyaka, Puseletso, Chan, Wai Y., Avontuur, Juanita R., van Zyl, Elritha, Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Stamatis, Dimitrios, Reddy, T. B. K., Daum, Chris, Shapiro, Nicole, Markowitz, Victor, Ivanova, Natalia, Kyrpides, Nikos, Woyke, Tanja, Blom, Jochen, Whitman, William B., Venter, Stephanus N., and Steenkamp, Emma T.. 2017. "Genome Data Provides High Support for Generic Boundaries in Burkholderia Sensu Lato". United States. doi:10.3389/fmicb.2017.01154.
@article{osti_1423489,
title = {Genome Data Provides High Support for Generic Boundaries in Burkholderia Sensu Lato},
author = {Beukes, Chrizelle W. and Palmer, Marike and Manyaka, Puseletso and Chan, Wai Y. and Avontuur, Juanita R. and van Zyl, Elritha and Huntemann, Marcel and Clum, Alicia and Pillay, Manoj and Palaniappan, Krishnaveni and Varghese, Neha and Mikhailova, Natalia and Stamatis, Dimitrios and Reddy, T. B. K. and Daum, Chris and Shapiro, Nicole and Markowitz, Victor and Ivanova, Natalia and Kyrpides, Nikos and Woyke, Tanja and Blom, Jochen and Whitman, William B. and Venter, Stephanus N. and Steenkamp, Emma T.},
abstractNote = {Although the taxonomy of Burkholderia has been extensively scrutinized, significant uncertainty remains regarding the generic boundaries and composition of this large and heterogeneous taxon. Here we used the amino acid and nucleotide sequences of 106 conserved proteins from 92 species to infer robust maximum likelihood phylogenies with which to investigate the generic structure of Burkholderia sensu lato. These data unambiguously supported five distinct lineages, of which four correspond to Burkholderia sensu stricto and the newly introduced genera Paraburkholderia, Caballeronia, and Robbsia. The fifth lineage was represented by P. rhizoxinica. Based on these findings, we propose 13 new combinations for those species previously described as members of Burkholderia but that form part of Caballeronia. These findings also suggest revision of the taxonomic status of P. rhizoxinica as it is does not form part of any of the genera currently recognized in Burkholderia sensu lato. From a phylogenetic point of view, Burkholderia sensu stricto has a sister relationship with the Caballeronia+Paraburkholderia clade. Also, the lineages represented by P. rhizoxinica and R. andropogonis, respectively, emerged prior to the radiation of the Burkholderia sensu stricto+Caballeronia+Paraburkholderia clade. Our findings therefore constitute a solid framework, not only for supporting current and future taxonomic decisions, but also for studying the evolution of this assemblage of medically, industrially and agriculturally important species.},
doi = {10.3389/fmicb.2017.01154},
journal = {Frontiers in Microbiology},
number = ,
volume = 8,
place = {United States},
year = {2017},
month = {6}
}

Works referenced in this record:

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