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Stand Genomic Sci. 2014 Mar 15;9(3):632-45. doi: 10.4056/sigs.4998989. eCollection 2014 Jun 15.

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.

Author information

1
Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Department of Microbiology, University of Georgia, Athens, Georgia, USA.
2
Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Department of Oceanography, University of Hawaii, Honolulu, Hawaii, USA.
3
Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA.
4
Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; School of Oceanography, University of Washington, Seattle, Washington, USA.
5
Department of Marine Sciences, University of Georgia, Athens, Georgia, USA.
6
Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Marine Biological Laboratory, Woods Hole, Massachusetts, USA.
7
Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Department of Microbiology, Cornell University, Ithaca, New York, USA.
8
Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Observatoire Océanologique de Villefranche, Villefranche-sur-mer, France.
9
Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Universidad Del Magdalena, Santa Marta, Colombia.
10
Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Max Plank Institute for Marine Microbiology, Bremen, Germany.
11
Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, USA.
12
Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Department of Geophysical Sciences, University of Chicago, Chicago, Illinois, USA.
13
Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; School for Marine Science and Technology, University of Massachusetts Dartmouth, Dartmouth, Massachusetts, USA.
14
Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Department of Earth System Science, University of California Irvine, Irvine, CA, USA.
15
Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Marine Science Institute, University of California Santa Barbara, Santa Barbara, California, USA.
16
Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Department of Atmospheric and Ocean Sciences, University of California Los Angeles, Los Angeles, California, USA.
17
Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; School of Natural Sciences, University of California Merced, Merced, California, USA.
18
Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
19
Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Department of Energy Joint Genome Institute, Walnut Creek, California, USA.
20
Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Singapore Centre on Environmental Life Sciences Engineering, Singapore.
21
Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, Hawaii, USA.

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:

Roseobacter; aerobic anoxygenic phototroph; dimethylsulfoniopropionate; marine bacterioplankton

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