Abstract
This report describes the draft genome sequence of Alcanivorax sp. strain KX64203, isolated from deep-sea sediment samples. The reads generated by an Ion Torrent PGM were assembled into contigs, with a total size of 4.76 Mb. The data will improve our understanding of the strain’s function in alkane degradation.
GENOME ANNOUNCEMENT
Bacteria of the genus Alcanivorax belong to a group of slow-growing marine hydrocarbonoclastic bacteria that can use oil hydrocarbons as its exclusive source of carbon and energy (1). By now, the genome sequences of six species in this genus isolated from various marine environments have been reported, including A. borkumensis (1), A. pacificus W11-5T (2), A. hongdengensis A-11-3T (3), A. dieselolei B5T (4), and A. jadensis. The Alcanivorax sp. strain KX64203 was isolated from sediment samples which were collected by using an electrohydraulic grab with an underwater television camera during the cruise conducted by the scientific research vessel KEXUE in Okinawa Trough (126°54.32′ E, 27°48.47′ N, ~1190-m depth, around a hydrothermal vent). Analysis of the 16S rRNA gene sequence (GenBank accession number KU954765) showed that it shared 99% identity (100% coverage) with that of A. dieselolei strain PTG4-3, and almost 99% identity with this gene in other Alcanivorax strains.
The sequencing reads were generated by an Ion Torrent PGM using 314 Chip version 2 and a 400-bp sequencing kit, assembled by the Torrent SPAdes plugin (version 2.3) de novo assembler, and then merged using a CISA contig integrator (5). Protein-coding sequences were predicted by Glimmer software (version 3.02) (6) Ribosomal RNA genes were detected using RNAmmer software version 1.2 (7) and tRNA genes were detected using tRNAscan-SE (8).
The genome of KX64203 consisted of 4,757,396 bases in 79 contigs (N50 159,927 bp and N90 36,849 bp), and had a G+C content of 61.4%. Both the genome size and G+C content were similar to published data for A. dieselolei type strain B5 (total length of 4.86 Mb and G+C% of 61.5%). Forty-three tRNA genes for all 20 amino acids and six rRNA genes were identified in the draft genome sequence. There were a total of 4,464 putative open reading frames (with an average size of 932 bp), giving a coding intensity of 87.43%. A total of 2,988 proteins were assigned to cluster of orthologous group (COG) families. The genes encoding three integral-membrane alkane monooxygenases (AlkB) and only one cytochrome P450 enzyme were found in the genome. Moreover, there were also some other proteins involved in the alkane degradation pathway, including three AlkKs, one AlkL, and one AlkN. Two genes, rubA and rubB encoding a rubredoxin and a rubredoxin reductase, respectively, were likely to be involved in alkane catabolism. The genome sequence and its gene annotation shed new light on the functional genomics of this species.
Accession number(s).
This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession no. LVIC00000000. The version described in this study is the first version LVIC01000000.
ACKNOWLEDGMENTS
We thank the research vessel KEXUE of the Chinese Academy of Sciences for collecting samples and the WPOS sample center for providing samples. We also thank Ping Zhang and Zengfang Zhao from the High Performance Computing Center of the Institute of Oceanology, CAS, for the computing resources and service they kindly provided.
This work was supported by grants from the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA11030202) and High Technology Project (863 Project, 2014AA093501) from the Chinese Ministry of Science and Technology.
Footnotes
Citation Zhang H, Liu R, Wang M, Wang H, Gao Q, Hou Z, Gao D, Wang L. 2016. Draft genome sequence of Alcanivorax sp. strain KX64203 isolated from deep-sea sediments of Iheya North, Okinawa Trough. Genome Announc 4(4):e00872-16. doi:10.1128/genomeA.00872-16.
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