GENOME ANNOUNCEMENT
Draft Genome Sequence of the Xylan-Degrading Marine Bacterium Strain S124, Representing a Novel Species of the Genus Oceanicola Young-Kyung Kwon,a,b Jennifer Jooyoun Kim,a Ji Hyung Kim,a,c Seon-Mi Jeon,a Bo-Ram Ye,a,b Jiyi Jang,a Soo-Jin Heo,a Se Chang Park,c Do-Hyung Kang,a and Chulhong Oha Korea Institute of Ocean Science & Technology, Ansan, Republic of Koreaa; Department of Environmental Marine Sciences, Hanyang University, Ansan, Gyonggi-do, Republic of Koreab; and Laboratory of Aquatic Animal Medicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Republic of Koreac
We isolated a xylan-degrading bacterium from seawater of Micronesia and identified it as Oceanicola sp. strain S124. We sequenced the Oceanicola sp. S124 genome using GSFLX 454 pyrosequencing and predicted 4,433 open reading frames (ORFs) including putative saccharification and phage-related genes.
B
acterial samples were collected from seawater of Chuuk State in Micronesia. Then, the collected samples were cultured on XYS agar plates (0.2% xylan, 0.2% yeast extract, and 1.5% agar in natural seawater) at 30°C. The xylanase activities of cultured strains were tested by using the dinitrosalicyclic acid method (5). We selected a highly active xylan-degrading strain and identified it by its 16S rRNA gene sequence. The strain showed 97.0% identity to Oceanicola marinus strain AZO-C (GenBank accession number, DQ822569). Hence it was named Oceanicola sp. strain S124 (GenBank accession number, JN654451). The genus Oceanicola is a member of the Alphaproteobacteria that was first described by Cho and Giovannoni (1). Most Oceanicola spp. are isolated from seawater in different marine environments (1, 2, 3, 7, 8). In a recent study, genome sequences of Oceanicola batsensis and Oceanicola granulosus were analyzed (6). The Oceanicola sp. S124 genome was sequenced by Roche GSFLX 454 technology (Macrogen, Republic of Korea). The genome sequence had a total of 48,577,968 bases and 119,314 reads, with an average read length of 885 bp. The genome contained 116,246 assembled reads and 1,133 partial assembled reads. The reads were assembled into 339 large contigs (length, ⬎500 bp) and 346 small contigs (length, ⬎100 bp) using the genome sequencer FLX system De Novo software v. 2.3. The average contig size was 13,715, and the genome contained 4,433 predicted coding sequences (CDS). The results showed that the genome consists of 226 singletons. The complete genome of Oceanicola sp. S124 was 4,649,474 bp, with an average G⫹C content of 67.29%. Additionally, the Oceanicola sp. S124 genome contained 20 rRNA operons. Gene ontology (GO) searches were performed using all complete coding sequences, and the results revealed that 35, 37, and 9% of genes were related to biological process, molecular function, and cellular components, respectively. Within the GO category of biological process, metabolic process was the most dominant term, representing 38% of genes. In the cellular component category, 48% of the genes were unknown. Based on their molecular function, 45% of the genes were identified to have catalytic activities. More importantly, the strain S124 genome includes promising candidate genes for saccharification enzymes such as cellulase and alpha-amylase. These enzymes are important for bioethanol production from biomasses like cellulose and starch
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(4). However, xylan degradation-related genes were not detected in published sequences. Furthermore, 20 putative bacteriophagerelated genes were also found in the S124 genome sequence with different sites. This finding can be useful for understanding the phage-host mechanism. Nucleotide sequence accession number. The genome sequence of Oceanicola sp. S124 has been deposited in GenBank under the accession number AFPM00000000. ACKNOWLEDGMENTS This research was financially supported by research grants (PE98751, PE98705, and PE9881B) from the Korea Institute of Ocean Science and Technology (KIOST) and the National Agenda Program (NAP) through the Korea Research Council of Fundamental Science and Technology (KRCF).
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Received 29 August 2012 Accepted 31 August 2012 Address correspondence to Do-Hyung Kang,
[email protected], or Chulhong Oh,
[email protected]. Copyright © 2012, American Society for Microbiology. All Rights Reserved. doi:10.1128/JB.01614-12
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