Vampirovibrio chlorellavorus draft genome sequence, annotation, and preliminary characterization of pathogenicity determinants

Hovde, Blake T.; Steichen, Seth A.; Starkenburg, Shawn R.; Brown, Judith K.

doi:10.1111/pre.12392

Title: Vampirovibrio chlorellavorus draft genome sequence, annotation, and preliminary characterization of pathogenicity determinants

Abstract

Vampirovibrio chlorellavorus is recognized as a pathogen of commercially-relevant Chlorella species. Algal infection and total loss of productivity (biomass) often occurs when susceptible algal hosts are cultivated in outdoor open pond systems. The pathogenic life cycle of this bacterium has been inferred from laboratory and field observations, and corroborated in part by the genomic analyses for two Arizona isolates recovered from an open algal reactor. V. chlorellavorus predation has been reported to occur in geographically-and environmentally-diverse conditions. Genomic analyses of these and additional field isolates is expected to reveal new information about the extent of ecological diversity and genes involved in host-pathogen interactions. The draft genome sequences for two isolates of the predatory V. chlorellavorus (Cyanobacteria; Ca. Melainabacteria) from an outdoor cultivation system located in the Arizona Sonoran Desert were assembled and annotated. The genomes were sequenced and analyzed to identify genes (proteins) with predicted involvement in predation, infection, and cell death of Chlorella host species prioritized for biofuel production at sites identified as highly suitable for algal production in the southwestern USA. Genomic analyses identified several predicted genes encoding secreted proteins that are potentially involved in pathogenicity, and at least three apparently complete sets of virulence (Vir) genes, characteristicmore »« less

Authors:

^[1]; Steichen, Seth A. ^[2]; Starkenburg, Shawn R. ^[1]; Brown, Judith K. ^[2]

Bioscience Division, Los Alamos National Laboratory Los Alamos New Mexico USA
School of Plant SciencesThe University of Arizona Tucson Arizona USA

Publication Date:: Wed Jul 17 00:00:00 EDT 2019

Research Org.:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States); Univ. of Arizona, Tucson, AZ (United States)

Sponsoring Org.:: USDOE Office of Energy Efficiency and Renewable Energy (EERE)

OSTI Identifier:: 1592174

Alternate Identifier(s):: OSTI ID: 1557759; OSTI ID: 1592175; OSTI ID: 1592757

Report Number(s):: LA-UR-19-20027
Journal ID: ISSN 1322-0829

Grant/Contract Number:: 89233218CNA000001; EE0006269; NL0029949

Resource Type:: Published Article

Journal Name:: Phycological Research

Additional Journal Information:: Journal Name: Phycological Research Journal Volume: 68 Journal Issue: 1; Journal ID: ISSN 1322-0829

Publisher:: Wiley

Country of Publication:: Australia

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; Biological Science; Algae pathogens; algal pathogen; chlorella; melainabacteria; VirB

Citation Formats


                    Hovde, Blake T., Steichen, Seth A., Starkenburg, Shawn R., and Brown, Judith K. Vampirovibrio chlorellavorus draft genome sequence, annotation, and preliminary characterization of pathogenicity determinants.  Australia: N. p., 2019. 
Web.  doi:10.1111/pre.12392.

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                    Hovde, Blake T., Steichen, Seth A., Starkenburg, Shawn R., & Brown, Judith K. Vampirovibrio chlorellavorus draft genome sequence, annotation, and preliminary characterization of pathogenicity determinants.  Australia.  https://doi.org/10.1111/pre.12392

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                    Hovde, Blake T., Steichen, Seth A., Starkenburg, Shawn R., and Brown, Judith K. Wed .  
"Vampirovibrio chlorellavorus draft genome sequence, annotation, and preliminary characterization of pathogenicity determinants".  Australia.  https://doi.org/10.1111/pre.12392.

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@article{osti_1592174,

  title        = {Vampirovibrio chlorellavorus draft genome sequence, annotation, and preliminary characterization of pathogenicity determinants},

  author       = {Hovde, Blake T. and Steichen, Seth A. and Starkenburg, Shawn R. and Brown, Judith K.},

  abstractNote = {Vampirovibrio chlorellavorus is recognized as a pathogen of commercially-relevant Chlorella species. Algal infection and total loss of productivity (biomass) often occurs when susceptible algal hosts are cultivated in outdoor open pond systems. The pathogenic life cycle of this bacterium has been inferred from laboratory and field observations, and corroborated in part by the genomic analyses for two Arizona isolates recovered from an open algal reactor. V. chlorellavorus predation has been reported to occur in geographically-and environmentally-diverse conditions. Genomic analyses of these and additional field isolates is expected to reveal new information about the extent of ecological diversity and genes involved in host-pathogen interactions. The draft genome sequences for two isolates of the predatory V. chlorellavorus (Cyanobacteria; Ca. Melainabacteria) from an outdoor cultivation system located in the Arizona Sonoran Desert were assembled and annotated. The genomes were sequenced and analyzed to identify genes (proteins) with predicted involvement in predation, infection, and cell death of Chlorella host species prioritized for biofuel production at sites identified as highly suitable for algal production in the southwestern USA. Genomic analyses identified several predicted genes encoding secreted proteins that are potentially involved in pathogenicity, and at least three apparently complete sets of virulence (Vir) genes, characteristic of the VirB-VirD type system encoding the canonical VirB1-11 and VirD4 proteins, respectively. Additional protein functions were predicted suggesting their involvement in quorum sensing and motility. The genomes of two previously uncharacterized V. chlorellavorus isolates reveal nucleotide and protein level divergence between each other, and a previously sequenced V. chlorellavorus genome. This new knowledge will enhance the fundamental understanding of trans-kingdom interactions between a unique cosmopolitan cyanobacterial pathogen and its green microalgal host, of broad interest as a source of harvestable biomass for biofuels or bioproducts.},

  doi          = {10.1111/pre.12392},

  journal      = {Phycological Research},

  number       = 1,

  volume       = 68,

  place        = {Australia},

  year         = {Wed Jul 17 00:00:00 EDT 2019},

  month        = {Wed Jul 17 00:00:00 EDT 2019}

}

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Title: Vampirovibrio chlorellavorus draft genome sequence, annotation, and preliminary characterization of pathogenicity determinants

Abstract

Citation Formats

The host Range of the Chlorellavorous Bacterium ("Vampirovibrio Chlorellvorus") journal, December 1986

Association of Vampirovibrio chlorellavorus with decline and death of Chlorella sorokiniana in outdoor reactors journal, October 2018

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth journal, April 2012

Prokka: rapid prokaryotic genome annotation journal, March 2014

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs journal, June 2015

UniProt: the universal protein knowledgebase journal, November 2016

A Greedy Algorithm for Aligning DNA Sequences journal, February 2000

QGB: Combined Use of Sequence Similarity and Codon Bias for Coding Region Identification journal, January 1994

VirB1* Promotes T-Pilus Formation in the vir-Type IV Secretion System of Agrobacterium tumefaciens journal, July 2007

ABC transporter-mediated uptake of iron, siderophores, heme and vitamin B12 journal, April 2001

Real-time quantitative detection of Vampirovibrio chlorellavorus, an obligate bacterial pathogen of Chlorella sorokiniana journal, October 2018

Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus journal, January 2015

A large-scale evaluation of algorithms to calculate average nucleotide identity journal, February 2017

Antagonistic association of the chlorellavorus bacterium (“Bdellovibrio” chlorellavorus) withChlorella vulgaris journal, January 1978

ATP-Binding Cassette Transporters in Bacteria journal, June 2004

The Mosaic Type IV Secretion Systems journal, January 2016

A novel predatory bacterium infecting the eukaryotic alga Nannochloropsis journal, June 2018

A validated model to predict microalgae growth in outdoor pond cultures subjected to fluctuating light intensities and water temperatures journal, January 2016

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper journal, April 2017

Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements journal, June 2004

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform journal, November 2016

The ABC of ABCs: a phylogenetic and functional classification of ABC systems in living organisms journal, April 2001

CDD/SPARCLE: functional classification of proteins via subfamily domain architectures journal, November 2016

The host Range of the Chlorellavorous Bacterium ("Vampirovibrio Chlorellvorus")
journal, December 1986

Association of Vampirovibrio chlorellavorus with decline and death of Chlorella sorokiniana in outdoor reactors
journal, October 2018

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
journal, April 2012

Prokka: rapid prokaryotic genome annotation
journal, March 2014

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
journal, June 2015

UniProt: the universal protein knowledgebase
journal, November 2016

A Greedy Algorithm for Aligning DNA Sequences
journal, February 2000

QGB: Combined Use of Sequence Similarity and Codon Bias for Coding Region Identification
journal, January 1994

VirB1* Promotes T-Pilus Formation in the vir-Type IV Secretion System of Agrobacterium tumefaciens
journal, July 2007

ABC transporter-mediated uptake of iron, siderophores, heme and vitamin B12
journal, April 2001

Real-time quantitative detection of Vampirovibrio chlorellavorus, an obligate bacterial pathogen of Chlorella sorokiniana
journal, October 2018

Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus
journal, January 2015

A large-scale evaluation of algorithms to calculate average nucleotide identity
journal, February 2017

Antagonistic association of the chlorellavorus bacterium (“Bdellovibrio” chlorellavorus) withChlorella vulgaris
journal, January 1978

ATP-Binding Cassette Transporters in Bacteria
journal, June 2004

The Mosaic Type IV Secretion Systems
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A novel predatory bacterium infecting the eukaryotic alga Nannochloropsis
journal, June 2018

A validated model to predict microalgae growth in outdoor pond cultures subjected to fluctuating light intensities and water temperatures
journal, January 2016

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper
journal, April 2017

Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements
journal, June 2004

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform
journal, November 2016

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journal, April 2001

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journal, November 2016