Abstract
Alcanivorax sp. strain 97CO-5 was isolated from a crude-oil-degrading consortium, enriched from Yellow Sea sediment of China. Here, we present the draft genome of strain 97CO-5, which comprises 3,251,558 bp with a G+C content of 54.54% and contains 2,962 protein-coding genes and 42 tRNAs.
GENOME ANNOUNCEMENT
The bacteria of genus Alcanivorax are recognized as typical representatives of obligate hydrocarbonoclastic bacteria (OHCB), which play a pivotal role in the biological removal of petroleum hydrocarbons from polluted marine environments (1–3). Alcanivorax sp. strain 97CO-5 (CGMCC no. 3735) was isolated from Yellow Sea sediment of China (lat 36.67; long 121.99; depth 17.8 m) for its ability to use n-alkanes as a sole carbon and energy source (4). Many genome sequences of the Alcanivorax species have been published since the report of the first sequenced genome of Alcanivorax borkumensis SK2 (GenBank accession number AM286690), which is a ubiquitous hydrocarbon-degrading marine bacterium (3). Nevertheless, a genome sequence of an alkane-degrading species Alcanivorax sp. 97CO-5 from Yellow Sea sediment of China could further aid in understanding the Alcanivorax species’ biodiversity and capacity for petroleum hydrocarbon biodegradation in marine environments.
The genome sequence of Alcanivorax sp. 97CO-5 was determined by Shanghai Majorbio Bio-pharm Technology Co., Ltd. (Shanghai, China) using Solexa paired-end sequencing technology. A total of 16,700,406 paired-end reads (180-bp and 800-bp libraries) were generated with the Illumina HiSeq 2000 platform (Illumina Inc., SanDiego, CA, USA) to reach a 513-fold coverage. The reads were assembled using SOAPdenovo version 1.05 (5, 6). The resulting genome sequence of Alcanivorax sp. 97CO-5 consists of 37 contigs (N90 = 79,842) of 3,251,558 bp with an average G+C content of 54.54%. Gene annotation was carried out using the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html), which was followed by manual editing. The genome contains 2,962 candidate protein-encoding genes (with an average size of 959 bp), giving a coding intensity of 87.40%. A total of 2,192 proteins were assigned to cluster of orthologous groups (COG) families, and 42 tRNA genes for all 20 amino acids and one 16S-23S-5S rRNA operon were identified by tRNAscan version 1.23 (7) and rRNAmmer version 1.2 (8).
In particular, we analyzed the genes possibly responsible for alkane degradation. Two genes encoding alkane 1-monooxygenase and two genes encoding cytochrome P450 enzymes were found in the genome of Alcanivorax sp. 97CO-5. Moreover, one gene encoding the haloalkane dehalogenase was also found in the genome sequence. The 97CO-5 genome sequence and its curated annotation are important assets for better understanding the physiology and metabolic potential of Alcanivorax spp. in the Yellow Sea and will open up new opportunities in the functional genomics of this species.
Nucleotide sequence accession number.
The nucleotide sequence comprising the Alcanivorax sp. 97CO-5 genome was deposited at DDBJ/EMBL/GenBank under the accession number AZYR00000000 (chromosome). The version described in this paper is the first version.
ACKNOWLEDGMENTS
This work was supported by Ministry of Science and Technology of China (2012FY130300), the National Natural Science Foundation of China (41306074), and the Basic Scientific Fund for National Public Research Institutes of China (2014G12).
Footnotes
Citation Luan X, Cui Z, Gao W, Li Q, Yin X, Zheng L. 2014. Genome sequence of the petroleum hydrocarbon-degrading bacterium Alcanivorax sp. strain 97CO-5. Genome Announc. 2(6):e01277-14. doi:10.1128/genomeA.01277-14.
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