Abstract
Oceaniovalibus guishaninsula, as a representative of a new genus within the family Rhodobacteraceae, was isolated from surface seawater that was sulfidic. Here, we present the draft genome sequence of the type strain, JLT2003T.
GENOME ANNOUNCEMENT
Oceaniovalibus guishaninsula JLT2003T was isolated from surface seawater off Kueishantao islet, northeast Taiwan (4), where the shallow-sea hydrothermal vents discharge elemental sulfur and hydrogen sulfide (1). It was proposed that this isolate represented one species in a new genus within the family Rhodobacteraceae in the class Alphaproteobacteria, belonging to the Roseobacter clade (4). Given the importance of marine roseobacters in biogeochemical cycles of the ocean and global abundance, roseobacters are ideal for elucidating bacterial diversification and adaptation to ocean environments (5, 8). Here we report the whole-genome sequence of O. guishaninsula JLT2003T.
The nucleotide sequence of the O. guishaninsula genome was obtained via a massively parallel pyrosequencing technology (Roche 454 GS FLX). In total, 68 contigs (>500 bp) with a total size of 2,897,133 bp were assembled from 145,387 reads (average length of 497 bp), providing 25-fold coverage. The average contig length was 42,604 bp, and the maximum contig length was 374,197 bp, with the overall G+C content of the O. guishaninsula genome assemblies being 67.37%.
A total of 2,840 protein-coding sequences with an average length of 936 bp were determined by combining the prediction results of Glimmer3.02 (2) and ZCURVE (3), occupying 91.7% of the genome. Among all the predicted genes, 1,787 proteins (62.9%) were assigned to the functional COG categories (7), and another 500 proteins (17.6%) were assigned with general function prediction only. The genome contained 42 tRNA genes and 3 rRNA operons. O. guishaninsula was predicted to have complete pentose phosphate and Entner-Doudoroff pathways. However, it possessed an incomplete Embden-Meyerhoff-Parnas pathway in that the genome lacked the enzyme 6-phosphofructokinase. O. guishaninsula also had genes responsible for N-acetylglucosamine (GlcNAc) assimilation as a carbon source, including those for a GlcNAc ABC transporter system, GlcNAc deaminase, and GlcNAc deacetylase. O. guishaninsula contained the genes (phaABCZP) necessary to synthesize and metabolize polyhydroxyalkanoate/polyhydroxybutyrate. Genes encoding enzymes potentially involved in the oxidation of sulfur compound were predicted, including sulfide-quinone reductase and thiosulfate sulfurtransferase. Two genes for predicted sulfate permease and genes for sulfate assimilation were present in the genome. Genes encoding nitrite reductases, nitric oxide reductases, and nitrous oxide reductases were present in the genome, but the gene encoding nitrate reductase, necessary for a complete denitrification pathway, was not. Genes encoding aa3-type and cbb3-type cytochrome c oxidase were identified in the genome, enabling bacteria to cope with fluctuating oxygen concentrations.
Similar to other Roseobacter strains (6), O. guishaninsula had abundant predicted ABC transporters (156 genes) and tripartite ATP-independent periplasmic protein transporters (54 genes) encoded in the genome. O. guishaninsula contained genes encoding anaerobic dimethyl sulfoxide reductase and carbon monoxide dehydrogenase but lacked genes for dimethylsulfoniopropionate (DMSP) utilization. Further comparative analysis of Roseobacter genomes will help us better understand their diverse physiological features and evolutionary characteristics.
Nucleotide sequence accession numbers.
The Oceaniovalibus guishaninsula JLT2003T shotgun genome sequence has been deposited at DDBJ/EMBL/GenBank under the accession no. AMGO00000000. The version described in this paper is the first version, AMGO01000000.
ACKNOWLEDGMENTS
This work was supported by NSFC 41276131 and 40906079, the SOA project 201105021, and the Scientific Research Foundation for the Returned Overseas Chinese Scholars, Ministry of Education of China.
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