Draft Genome Sequence of Larkinella sp. Strain BK230, Isolated from Populus deltoides Roots

Pelletier, Dale A.; Burdick, Leah H.; Podar, Mircea; Schadt, Christopher W.; Kalluri, Udaya C.; Stewart, ed., Frank J.

doi:10.1128/MRA.00159-20

Title: Draft Genome Sequence of Larkinella sp. Strain BK230, Isolated from Populus deltoides Roots

Abstract

Larkinella sp. strain BK230, a heterotrophic bacterium of the phylum Bacteroidetes, was isolated from the roots of a field-grown eastern cottonwood tree (Populus deltoides) located in Georgia. The draft 7.27-Mb genome has a G+C content of 53.4% and contains 6,026 coding sequences, including 41 tRNA genes.

Authors:: Pelletier, Dale A.; Burdick, Leah H.; Podar, Mircea; Schadt, Christopher W.; Kalluri, Udaya C.; Stewart, ed., Frank J.

Publication Date:: Thu Mar 19 00:00:00 EDT 2020

Research Org.:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). BioEnergy Science Center (BESC); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI Identifier:: 1605295

Alternate Identifier(s):: OSTI ID: 1606641

Grant/Contract Number:: AC05-00OR22725; AC02-05CH11231

Resource Type:: Published Article

Journal Name:: Microbiology Resource Announcements

Additional Journal Information:: Journal Name: Microbiology Resource Announcements Journal Volume: 9 Journal Issue: 12; Journal ID: ISSN 2576-098X

Publisher:: SSPA - American Society for Microbiology

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES

Citation Formats


                    Pelletier, Dale A., Burdick, Leah H., Podar, Mircea, Schadt, Christopher W., Kalluri, Udaya C., and Stewart, ed., Frank J. Draft Genome Sequence of Larkinella sp. Strain BK230, Isolated from Populus deltoides Roots.  United States: N. p., 2020. 
Web.  doi:10.1128/MRA.00159-20.

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                    Pelletier, Dale A., Burdick, Leah H., Podar, Mircea, Schadt, Christopher W., Kalluri, Udaya C., & Stewart, ed., Frank J. Draft Genome Sequence of Larkinella sp. Strain BK230, Isolated from Populus deltoides Roots.  United States.  https://doi.org/10.1128/MRA.00159-20

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                    Pelletier, Dale A., Burdick, Leah H., Podar, Mircea, Schadt, Christopher W., Kalluri, Udaya C., and Stewart, ed., Frank J. Thu .  
"Draft Genome Sequence of Larkinella sp. Strain BK230, Isolated from Populus deltoides Roots".  United States.  https://doi.org/10.1128/MRA.00159-20.

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@article{osti_1605295,

  title        = {Draft Genome Sequence of Larkinella sp. Strain BK230, Isolated from Populus deltoides Roots},

  author       = {Pelletier, Dale A. and Burdick, Leah H. and Podar, Mircea and Schadt, Christopher W. and Kalluri, Udaya C. and Stewart, ed., Frank J.},

  abstractNote = {Larkinella sp. strain BK230, a heterotrophic bacterium of the phylum Bacteroidetes, was isolated from the roots of a field-grown eastern cottonwood tree (Populus deltoides) located in Georgia. The draft 7.27-Mb genome has a G+C content of 53.4% and contains 6,026 coding sequences, including 41 tRNA genes.},

  doi          = {10.1128/MRA.00159-20},

  journal      = {Microbiology Resource Announcements},

  number       = 12,

  volume       = 9,

  place        = {United States},

  year         = {Thu Mar 19 00:00:00 EDT 2020},

  month        = {Thu Mar 19 00:00:00 EDT 2020}

}

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Works referenced in this record:

KBase: The United States Department of Energy Systems Biology Knowledgebase
journal, July 2018

Arkin, Adam P.; Cottingham, Robert W.; Henry, Christopher S.
Nature Biotechnology, Vol. 36, Issue 7
DOI: 10.1038/nbt.4163

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data
journal, April 2012

Kearse, M.; Moir, R.; Wilson, A.
Bioinformatics, Vol. 28, Issue 12
DOI: 10.1093/bioinformatics/bts199

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
journal, May 2012

Bankevich, Anton; Nurk, Sergey; Antipov, Dmitry
Journal of Computational Biology, Vol. 19, Issue 5
DOI: 10.1089/cmb.2012.0021

Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis
journal, July 2016

Utturkar, Sagar M.; Cude, W. Nathan; Robeson, Michael S.
Applied and Environmental Microbiology, Vol. 82, Issue 18
DOI: 10.1128/AEM.01285-16

Solexa Ltd
journal, June 2004

Bennett, Simon
Pharmacogenomics, Vol. 5, Issue 4
DOI: 10.1517/14622416.5.4.433

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Title: Draft Genome Sequence of Larkinella sp. Strain BK230, Isolated from Populus deltoides Roots

Abstract

Citation Formats

KBase: The United States Department of Energy Systems Biology Knowledgebase journal, July 2018

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data journal, April 2012

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing journal, May 2012

Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis journal, July 2016

Solexa Ltd journal, June 2004

KBase: The United States Department of Energy Systems Biology Knowledgebase
journal, July 2018

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data
journal, April 2012

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
journal, May 2012

Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis
journal, July 2016

Solexa Ltd
journal, June 2004