Genome characterization of a novel Burkholderia cepacia complex genomovar isolated from dieback affected mango orchards

Asifullah Khan; Huma Asif; David J. Studholme; Ishtiaq A. Khan; M. Kamran Azim

doi:10.1007/s11274-013-1366-5

Genome characterization of a novel Burkholderia cepacia complex genomovar isolated from dieback affected mango orchards

Asifullah Khan, Huma Asif, David J. Studholme, Ishtiaq A. Khan, M. Kamran Azim

Obstetrics and Gynecology

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5 Scopus citations

Abstract

We characterized the genome of the antibiotic resistant, caseinolytic and non-hemolytic Burkholderia sp. strain TJI49, isolated from mango trees (Mangifera indica L.) with dieback disease. This isolate produced severe disease symptoms on the indicator plants. Next generation DNA sequencing and short-read assembly generated the 60X deep 7,631,934 nucleotide draft genome of Burkholderia sp. TJI49 which comprised three chromosomes and at least one mega plasmid. Genome annotation studies revealed a total 8,992 genes, out of which 8,940 were protein coding genes. Comparative genomics and phylogenetics identified Burkholderia sp. TJI49 as a distinct species of Burkholderia cepacia complex (BCC), closely related to B. multivorans ATCC17616. Genome-wide sequence alignment of this isolate with replicons of BCC members showed conservation of core function genes but considerable variations in accessory genes. Subsystem-based gene annotation identified the active presence of wide spread colonization island and type VI secretion system in Burkholderia sp. TJI49. Sequence comparisons revealed (a) 28 novel ORFs that have no database matches and (b) 23 ORFs with orthologues in species other than Burkholderia, indicating horizontal gene transfer events. Fold recognition of novel ORFs identified genes encoding pertactin autotransporter-like proteins (a constituent of type V secretion system) and Hap adhesion-like proteins (involved in cell-cell adhesion) in the genome of Burkholderia sp. TJI49. The genomic characterization of this isolate provided additional information related to the 'pan-genome' of Burkholderia species.

Original language	English (US)
Pages (from-to)	2033-2044
Number of pages	12
Journal	World Journal of Microbiology and Biotechnology
Volume	29
Issue number	11
DOIs	https://doi.org/10.1007/s11274-013-1366-5
State	Published - Nov 2013

Funding

Acknowledgments Huma Asif and Ishtiaq A. Khan acknowledge the financial support from Higher Education Commission, Islamabad, Pakistan under Indigenous PhD Scholarship program. Authors are thankful to Prof. Dr. Hans-Peter Muehlbach, Hamburg University for helpful discussion. We are grateful to Muhammad Aurongzeb, Ni-zakat Ali and Junaid Ahmed Kori for assistance in bacteriological characterization and Hypersensitive response test.

Keywords

Comparative bacterial genomics
Mangifera indica
Next generation sequencing
Plant-associated bacteria

ASJC Scopus subject areas

Biotechnology
Physiology
Applied Microbiology and Biotechnology

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title = "Genome characterization of a novel Burkholderia cepacia complex genomovar isolated from dieback affected mango orchards",

abstract = "We characterized the genome of the antibiotic resistant, caseinolytic and non-hemolytic Burkholderia sp. strain TJI49, isolated from mango trees (Mangifera indica L.) with dieback disease. This isolate produced severe disease symptoms on the indicator plants. Next generation DNA sequencing and short-read assembly generated the 60X deep 7,631,934 nucleotide draft genome of Burkholderia sp. TJI49 which comprised three chromosomes and at least one mega plasmid. Genome annotation studies revealed a total 8,992 genes, out of which 8,940 were protein coding genes. Comparative genomics and phylogenetics identified Burkholderia sp. TJI49 as a distinct species of Burkholderia cepacia complex (BCC), closely related to B. multivorans ATCC17616. Genome-wide sequence alignment of this isolate with replicons of BCC members showed conservation of core function genes but considerable variations in accessory genes. Subsystem-based gene annotation identified the active presence of wide spread colonization island and type VI secretion system in Burkholderia sp. TJI49. Sequence comparisons revealed (a) 28 novel ORFs that have no database matches and (b) 23 ORFs with orthologues in species other than Burkholderia, indicating horizontal gene transfer events. Fold recognition of novel ORFs identified genes encoding pertactin autotransporter-like proteins (a constituent of type V secretion system) and Hap adhesion-like proteins (involved in cell-cell adhesion) in the genome of Burkholderia sp. TJI49. The genomic characterization of this isolate provided additional information related to the 'pan-genome' of Burkholderia species.",

keywords = "Comparative bacterial genomics, Mangifera indica, Next generation sequencing, Plant-associated bacteria",

author = "Asifullah Khan and Huma Asif and Studholme, {David J.} and Khan, {Ishtiaq A.} and Azim, {M. Kamran}",

note = "Funding Information: Acknowledgments Huma Asif and Ishtiaq A. Khan acknowledge the financial support from Higher Education Commission, Islamabad, Pakistan under Indigenous PhD Scholarship program. Authors are thankful to Prof. Dr. Hans-Peter Muehlbach, Hamburg University for helpful discussion. We are grateful to Muhammad Aurongzeb, Ni-zakat Ali and Junaid Ahmed Kori for assistance in bacteriological characterization and Hypersensitive response test.",

year = "2013",

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doi = "10.1007/s11274-013-1366-5",

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AU - Khan, Ishtiaq A.

AU - Azim, M. Kamran

N1 - Funding Information: Acknowledgments Huma Asif and Ishtiaq A. Khan acknowledge the financial support from Higher Education Commission, Islamabad, Pakistan under Indigenous PhD Scholarship program. Authors are thankful to Prof. Dr. Hans-Peter Muehlbach, Hamburg University for helpful discussion. We are grateful to Muhammad Aurongzeb, Ni-zakat Ali and Junaid Ahmed Kori for assistance in bacteriological characterization and Hypersensitive response test.

PY - 2013/11

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N2 - We characterized the genome of the antibiotic resistant, caseinolytic and non-hemolytic Burkholderia sp. strain TJI49, isolated from mango trees (Mangifera indica L.) with dieback disease. This isolate produced severe disease symptoms on the indicator plants. Next generation DNA sequencing and short-read assembly generated the 60X deep 7,631,934 nucleotide draft genome of Burkholderia sp. TJI49 which comprised three chromosomes and at least one mega plasmid. Genome annotation studies revealed a total 8,992 genes, out of which 8,940 were protein coding genes. Comparative genomics and phylogenetics identified Burkholderia sp. TJI49 as a distinct species of Burkholderia cepacia complex (BCC), closely related to B. multivorans ATCC17616. Genome-wide sequence alignment of this isolate with replicons of BCC members showed conservation of core function genes but considerable variations in accessory genes. Subsystem-based gene annotation identified the active presence of wide spread colonization island and type VI secretion system in Burkholderia sp. TJI49. Sequence comparisons revealed (a) 28 novel ORFs that have no database matches and (b) 23 ORFs with orthologues in species other than Burkholderia, indicating horizontal gene transfer events. Fold recognition of novel ORFs identified genes encoding pertactin autotransporter-like proteins (a constituent of type V secretion system) and Hap adhesion-like proteins (involved in cell-cell adhesion) in the genome of Burkholderia sp. TJI49. The genomic characterization of this isolate provided additional information related to the 'pan-genome' of Burkholderia species.

AB - We characterized the genome of the antibiotic resistant, caseinolytic and non-hemolytic Burkholderia sp. strain TJI49, isolated from mango trees (Mangifera indica L.) with dieback disease. This isolate produced severe disease symptoms on the indicator plants. Next generation DNA sequencing and short-read assembly generated the 60X deep 7,631,934 nucleotide draft genome of Burkholderia sp. TJI49 which comprised three chromosomes and at least one mega plasmid. Genome annotation studies revealed a total 8,992 genes, out of which 8,940 were protein coding genes. Comparative genomics and phylogenetics identified Burkholderia sp. TJI49 as a distinct species of Burkholderia cepacia complex (BCC), closely related to B. multivorans ATCC17616. Genome-wide sequence alignment of this isolate with replicons of BCC members showed conservation of core function genes but considerable variations in accessory genes. Subsystem-based gene annotation identified the active presence of wide spread colonization island and type VI secretion system in Burkholderia sp. TJI49. Sequence comparisons revealed (a) 28 novel ORFs that have no database matches and (b) 23 ORFs with orthologues in species other than Burkholderia, indicating horizontal gene transfer events. Fold recognition of novel ORFs identified genes encoding pertactin autotransporter-like proteins (a constituent of type V secretion system) and Hap adhesion-like proteins (involved in cell-cell adhesion) in the genome of Burkholderia sp. TJI49. The genomic characterization of this isolate provided additional information related to the 'pan-genome' of Burkholderia species.

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KW - Next generation sequencing

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Genome characterization of a novel Burkholderia cepacia complex genomovar isolated from dieback affected mango orchards

Abstract

Funding

Keywords

ASJC Scopus subject areas

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