Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome

Bryndan P. Durham; Jana Grote; Kerry A. Whittaker; Sara J. Bender; Haiwei Luo; Sharon L. Grim; Julia M. Brown; John R. Casey; Antony Dron; Lennin Florez-Leiva; Andreas Krupke; Catherine M. Luria; Aric H. Mine; Olivia D. Nigro; Santhiska Pather; Agathe Talarmin; Emma K. Wear; Thomas S. Weber; Jesse M. Wilson; Matthew J. Church; Edward F. DeLong; David M. Karl; Grieg F. Steward; John M. Eppley; Nikos C. Kyrpides; Stephan Schuster; Michael S. Rappé

doi:10.4056/sigs.4998989

Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome

Bryndan P. Durham
, Jana Grote
, Kerry A. Whittaker
, Sara J. Bender
, Haiwei Luo
, Sharon L. Grim
, Julia M. Brown
, John R. Casey
, Antony Dron
, Lennin Florez-Leiva
, Andreas Krupke
, Catherine M. Luria
, Aric H. Mine
, Olivia D. Nigro
, Santhiska Pather
, Agathe Talarmin
, Emma K. Wear
, Thomas S. Weber
, Jesse M. Wilson
, Matthew J. Church

Edward F. DeLong, David M. Karl, Grieg F. Steward, John M. Eppley, Nikos C. Kyrpides, Stephan Schuster, Michael S. Rappé

University of Hawaii
University of Georgia
University of Rhode Island Narragansett Bay Campus
University of Washington School of Oceanography
Marine Biological Laboratory
Cornell University
Observatoire Océanologique de Villefranche Sur Mer
Universidad del Magdalena
University of Bremen Max Planck Institute for Marine Microbiology
Brown University
University of Chicago
University of Massachusetts Dartmouth
University of California, Santa Barbara
UCLA
University of California
Massachusetts Institute of Technology
Department of Energy Joint Genome Institute

Research output: Contribution to journal › Article › peer-review

52 Scopus citations

Abstract

Strain HIMB11 is a planktonic marine bacterium isolated from coastal seawater in Kaneohe Bay, Oahu, Hawaii belonging to the ubiquitous and versatile Roseobacter clade of the alphaproteobacterial family Rhodobacteraceae. Here we describe the preliminary characteristics of strain HIMB11, including annotation of the draft genome sequence and comparative genomic analysis with other members of the Roseobacter lineage. The 3,098,747 bp draft genome is arranged in 34 contigs and contains 3,183 protein-coding genes and 54 RNA genes. Phylogenomic and 16S rRNA gene analyses indicate that HIMB11 represents a unique sublineage within the Roseobacter clade. Comparison with other publicly available genome sequences from members of the Roseobacter lineage reveals that strain HIMB11 has the genomic potential to utilize a wide variety of energy sources (e.g. organic matter, reduced inorganic sulfur, light, carbon monoxide), while possessing a reduced number of substrate transporters.

Original language	British English
Pages (from-to)	632-645
Number of pages	14
Journal	Standards in Genomic Sciences
Volume	9
Issue number	3
DOIs	https://doi.org/10.4056/sigs.4998989
State	Published - 30 Oct 2015

Keywords

Aerobic anoxygenic phototroph
Dimethylsulfoniopropionate
Marine bacterioplankton
Roseobacter

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10.4056/sigs.4998989

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Durham, B. P., Grote, J., Whittaker, K. A., Bender, S. J., Luo, H., Grim, S. L., Brown, J. M., Casey, J. R., Dron, A., Florez-Leiva, L., Krupke, A., Luria, C. M., Mine, A. H., Nigro, O. D., Pather, S., Talarmin, A., Wear, E. K., Weber, T. S., Wilson, J. M., ... Rappé, M. S. (2015). Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome. Standards in Genomic Sciences, 9(3), 632-645. https://doi.org/10.4056/sigs.4998989

@article{ffaade3ac9f644448604d3197da8728a,

title = "Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome",

abstract = "Strain HIMB11 is a planktonic marine bacterium isolated from coastal seawater in Kaneohe Bay, Oahu, Hawaii belonging to the ubiquitous and versatile Roseobacter clade of the alphaproteobacterial family Rhodobacteraceae. Here we describe the preliminary characteristics of strain HIMB11, including annotation of the draft genome sequence and comparative genomic analysis with other members of the Roseobacter lineage. The 3,098,747 bp draft genome is arranged in 34 contigs and contains 3,183 protein-coding genes and 54 RNA genes. Phylogenomic and 16S rRNA gene analyses indicate that HIMB11 represents a unique sublineage within the Roseobacter clade. Comparison with other publicly available genome sequences from members of the Roseobacter lineage reveals that strain HIMB11 has the genomic potential to utilize a wide variety of energy sources (e.g. organic matter, reduced inorganic sulfur, light, carbon monoxide), while possessing a reduced number of substrate transporters.",

keywords = "Aerobic anoxygenic phototroph, Dimethylsulfoniopropionate, Marine bacterioplankton, Roseobacter",

author = "Durham, \{Bryndan P.\} and Jana Grote and Whittaker, \{Kerry A.\} and Bender, \{Sara J.\} and Haiwei Luo and Grim, \{Sharon L.\} and Brown, \{Julia M.\} and Casey, \{John R.\} and Antony Dron and Lennin Florez-Leiva and Andreas Krupke and Luria, \{Catherine M.\} and Mine, \{Aric H.\} and Nigro, \{Olivia D.\} and Santhiska Pather and Agathe Talarmin and Wear, \{Emma K.\} and Weber, \{Thomas S.\} and Wilson, \{Jesse M.\} and Church, \{Matthew J.\} and DeLong, \{Edward F.\} and Karl, \{David M.\} and Steward, \{Grieg F.\} and Eppley, \{John M.\} and Kyrpides, \{Nikos C.\} and Stephan Schuster and Rapp{\'e}, \{Michael S.\}",

note = "Funding Information: We thank the entire C-MORE staff and visiting scientists for support and instruction during the 2011 Summer Course in Microbial Oceanography. Dr. Mary Ann Moran at the University of Georgia provided invaluable instruction on Roseobacter genomics and bioinformatic analyses. We gratefully acknowledge the support of the Gordon and Betty Moore Foundation, which funded the sequencing of this genome. Annotation was performed as part of the 2011 C-MORE",

year = "2015",

month = oct,

day = "30",

doi = "10.4056/sigs.4998989",

language = "British English",

volume = "9",

pages = "632--645",

journal = "Standards in Genomic Sciences",

issn = "1944-3277",

publisher = "BioMed Central Ltd.",

number = "3",

}

Durham, BP, Grote, J, Whittaker, KA, Bender, SJ, Luo, H, Grim, SL, Brown, JM, Casey, JR, Dron, A, Florez-Leiva, L, Krupke, A, Luria, CM, Mine, AH, Nigro, OD, Pather, S, Talarmin, A, Wear, EK, Weber, TS, Wilson, JM, Church, MJ, DeLong, EF, Karl, DM, Steward, GF, Eppley, JM, Kyrpides, NC, Schuster, S & Rappé, MS 2015, 'Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome', Standards in Genomic Sciences, vol. 9, no. 3, pp. 632-645. https://doi.org/10.4056/sigs.4998989

Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome. / Durham, Bryndan P.; Grote, Jana; Whittaker, Kerry A. et al.
In: Standards in Genomic Sciences, Vol. 9, No. 3, 30.10.2015, p. 632-645.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome

AU - Durham, Bryndan P.

AU - Grote, Jana

AU - Whittaker, Kerry A.

AU - Bender, Sara J.

AU - Luo, Haiwei

AU - Grim, Sharon L.

AU - Brown, Julia M.

AU - Casey, John R.

AU - Dron, Antony

AU - Florez-Leiva, Lennin

AU - Krupke, Andreas

AU - Luria, Catherine M.

AU - Mine, Aric H.

AU - Nigro, Olivia D.

AU - Pather, Santhiska

AU - Talarmin, Agathe

AU - Wear, Emma K.

AU - Weber, Thomas S.

AU - Wilson, Jesse M.

AU - Church, Matthew J.

AU - DeLong, Edward F.

AU - Karl, David M.

AU - Steward, Grieg F.

AU - Eppley, John M.

AU - Kyrpides, Nikos C.

AU - Schuster, Stephan

AU - Rappé, Michael S.

N1 - Funding Information: We thank the entire C-MORE staff and visiting scientists for support and instruction during the 2011 Summer Course in Microbial Oceanography. Dr. Mary Ann Moran at the University of Georgia provided invaluable instruction on Roseobacter genomics and bioinformatic analyses. We gratefully acknowledge the support of the Gordon and Betty Moore Foundation, which funded the sequencing of this genome. Annotation was performed as part of the 2011 C-MORE

PY - 2015/10/30

Y1 - 2015/10/30

N2 - Strain HIMB11 is a planktonic marine bacterium isolated from coastal seawater in Kaneohe Bay, Oahu, Hawaii belonging to the ubiquitous and versatile Roseobacter clade of the alphaproteobacterial family Rhodobacteraceae. Here we describe the preliminary characteristics of strain HIMB11, including annotation of the draft genome sequence and comparative genomic analysis with other members of the Roseobacter lineage. The 3,098,747 bp draft genome is arranged in 34 contigs and contains 3,183 protein-coding genes and 54 RNA genes. Phylogenomic and 16S rRNA gene analyses indicate that HIMB11 represents a unique sublineage within the Roseobacter clade. Comparison with other publicly available genome sequences from members of the Roseobacter lineage reveals that strain HIMB11 has the genomic potential to utilize a wide variety of energy sources (e.g. organic matter, reduced inorganic sulfur, light, carbon monoxide), while possessing a reduced number of substrate transporters.

AB - Strain HIMB11 is a planktonic marine bacterium isolated from coastal seawater in Kaneohe Bay, Oahu, Hawaii belonging to the ubiquitous and versatile Roseobacter clade of the alphaproteobacterial family Rhodobacteraceae. Here we describe the preliminary characteristics of strain HIMB11, including annotation of the draft genome sequence and comparative genomic analysis with other members of the Roseobacter lineage. The 3,098,747 bp draft genome is arranged in 34 contigs and contains 3,183 protein-coding genes and 54 RNA genes. Phylogenomic and 16S rRNA gene analyses indicate that HIMB11 represents a unique sublineage within the Roseobacter clade. Comparison with other publicly available genome sequences from members of the Roseobacter lineage reveals that strain HIMB11 has the genomic potential to utilize a wide variety of energy sources (e.g. organic matter, reduced inorganic sulfur, light, carbon monoxide), while possessing a reduced number of substrate transporters.

KW - Aerobic anoxygenic phototroph

KW - Dimethylsulfoniopropionate

KW - Marine bacterioplankton

KW - Roseobacter

UR - https://www.scopus.com/pages/publications/84954096031

U2 - 10.4056/sigs.4998989

DO - 10.4056/sigs.4998989

M3 - Article

AN - SCOPUS:84954096031

SN - 1944-3277

VL - 9

SP - 632

EP - 645

JO - Standards in Genomic Sciences

JF - Standards in Genomic Sciences

IS - 3

ER -

Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome

Abstract

Keywords

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