Genome sequence of a high agarase-producing strain Flammeovirga sp. SJP92
© The Author(s). 2017
Received: 18 March 2016
Accepted: 7 December 2016
Published: 26 January 2017
Flammeovirga sp. SJP92 is a Gram-negative, aerobic, rod-shaped, non-motile and non-flagellated strain that belongs to the family Flammeovirgaceae of the class Cytophagia. The strain was isolated from the intestine of abalone, which produces many extracellular agarases and exhibits efficient degradation activities on various polysaccharides, especially agarose. Here we present the high-quality draft genome of Flammeovirga sp. SJP92, together with its phenotypic characteristics. The genome sequence is 8, 534, 834 bp, which comprised with one chromosome and no plasmid. It contained 6, 291 protein-coding and 99 RNA genes, including 93 tRNA, 5 rRNA and 1 ncRNA genes.
KeywordsFlammeovirga Genome High agarase-producing
Flammeovirga is one of genera belonging to the family Flammeovirgaceae of the class Cytophagia . There are five species have been reported in this genus, including F. aprica , F. arenaria , F. yaeyamensis , F. kamogawensis  and F. pacifica . They are all marine bacterium and have a potent ability to degrade marine complex polysaccharides, such as agar, carrageenan [3, 5–8]. Among them, only two draft genome sequences have been published , namely Flammeovirga sp. OC4 (NZ_JTAM01000001.1)  and F. pacifica WPAGA1T (=CCTCC AB 2010364T=LMG 26175T=DSM 24597T=MCCC 1A06425T) .
Flammeovirga sp. SJP92 with high-producing agarase was isolated and identified from the intestine of abalone in Xiamen, China. It is closely related with Flammeovirga sp. NBRC 100896 (AB681288.1) and shared 99% similarities of 16S rRNA. In order to provide more genome information of Flammeovirga species and realize the function of Flammeovirga sp. SJP92 when degradingmarine complex polysaccharides, the genome of Flammeovirga sp. SJP92 was sequenced. In this study, we summarized its genomic characteristics, as well as general phenotypic properties. Other species of Flammeovirga genus were also compared with Flammeovirga sp. SJP92 in both phenotypic and genomic aspects.
Classification and features
Classification and general features of Flammeovirga sp.SJP92
Species Flammeovirga sp.
15 ~ 40 °C
25 ~ 30 °C
pH range; Optimum
5 ~ 9, 8
Agar, Starch, Carrageenan, D-galactose, L-fructose, Tween40&80
0.5–8% NaCl (w/v)
Xamen city, China
Differential phenotypic characteristics between Flammeovirga sp. SJP92 and other Flammeovirga species
Cell diameter (um)
11 ~ 13 × 0.75
3.0 ~ 8.0 × 0.5 ~ 0.8
1.7 ~ 96 × 0.5 ~ 0.9
0.5 ~ 8%/2 ~ 4%
Temperature range (°C)
15 ~ 40
Number of polar flagella
157 °249′ 310″ E 19° 309′ 300″ N
Seaweeds/coastal sands/dead leaves
Genome sequencing information
Genome project history
Genome sequencing project information for Flammeovirga sp. SJP92
500 bp pair-end&5 kb mate-end libraries
Gene calling method
NCBI PGAP pipeline
GenBank Date of Release
March 9th, 2016
Source Material identifier
Growth conditions and genomic DNA preparation
Flammeovirga sp. SJP92 was incubated aerobically in the modified 2216E medium (2.2% NaCl, 0.365% MgCl2·6H2O, 0.729% MgSO4 · 7H2O, 0.03% CaCl2 · 2H2O, 0.05% KCl, 0.042% KH2PO4, 0.005% NaBr, 0.002% SrCl · 6H2O, 0.002% Fe (NH4) Citrate, 1.326% tryptone) supplied with 0.2% agar. After incubation at 32 °C, 200 rpm for 24 h, the bacteria was collected at 13000 rpm for 30–60 min at 4 °C. The CTAB/NaCl method  was used for the extraction of chromosomal DNA of Flammeovirga sp. SJP92.
Genome sequencing and assembly
The genome of Flammeovirga sp. SJP92 was sequenced with MPS (massively parallel sequencing) Illumina technology. Three DNA libraries were constructed: a paired-end library with an insert size of 500 bp and two mate-pair libraries with an insert size of 5 kb. The 500 bp library and the 5 kb libraries were sequenced using an Illumina HiSeq2500 by PE125 strategy. Library construction and sequencing was performed at the Beijing Novogene Bioinformatics Technology Co., Ltd. Quality control of both paired-end and mate-pair reads were performed using in-house program. The final coverage reached 215-folds of the genome. SOAPdenovo [11, 12] was used for sequence assembly, and the final assembly yielded 123 contigs which generated a genome of 8.53 Mb.
The genes of Flammeovirga sp. SJP92 was identified by NCBI Prokaryotic Genome Annotation Pipeline server online . Functional predicted was performed by comparing them with sequences in RPS-BLAST against Clusters of Orthologous Groups database and pfam database [14–16]. SignalP was used to predict signal peptide , and transmembrane helice was analyzed by TMHMM program . CRISPRFinder was used for CRISPR identification .
Genome Statistics for Flammeovirga sp. SJP92
% of Totala
Genome size (bp)
DNA coding (bp)
DNA G + C (bp)
Genes in internal clusters
Genes with function prediction
Genes assigned to COGs
Genes assigned Pfam domains
Genes with signal peptides
Genes with transmembrane helices
Number of protein coding gene of Flammeovirga sp. SJP92 associated with COG functional categories
Translation, ribosomal structure and biogenesis
RNA processing and modification
Replication, recombination and repair
Chromatin structure and dynamics
Cell cycle control, cell division, chromosome partitioning
Signal transduction mechanisms
Cell wall/membrane/envelope biogenesis
Intracellular trafficking, secretion, and vesicular transport
Posttranslational modification, protein turnover, chaperones
Energy production and conversion
Carbohydrate transport and metabolism
Amino acid transport and metabolism
Nucleotide transport and metabolism
Coenzyme transport and metabolism
Lipid transport and metabolism
Inorganic ion transport and metabolism
Secondary metabolites biosynthesis, transport and catabolism
General function prediction only
Not in COGs
Insights from the genome sequence
Comparison of genomes with Flammeovirga sp. SJP92, F. pacifica WPAGA1T and Flammeovirga sp. OC4
F. pacifica WPAGA1T
Genome size (bp)
8, 534, 834
6, 507, 364
8, 065, 497
Protein with function
Genes of agarase
Annotation of the genome indicated that this strain possessed many agarase (14 agarases at least), which was coincident with its high agar-degrading ability. Many sulfatases were also predicted and sequence alignment of proteins indicated that these sulfatases were novel. It is an aerobic strain and the existence of genes encoding superoxide dismutase and catalase were consistent with this phenotype. Flammeovirga sp. SJP92 contained many genes related to the metabolism and transport of amino acids. Also, metabolic pathway analysis and Biolog GN2 experiments illustrated that this strain could utilize many amino acids. These evidences may reflect its ability to grow by using proteinaceous media as the carbon and energy source.
Flammeovirga sp. SJP92 is another strain with the genome sequence of the genus Flammeovirga together with F. pacifica WPAGA1T and Flammeovirga sp. OC4. It is an agar-degrading bacterium with efficient agarose liquefying ability and had an extracellular agarase system containing 14 agarases at least. These genomic data will provide insights into the mechanisms of how these agarases cooperation to degrade agar or other polysaccharide.
This work was supported by the Marine Scientific Research Foundation for Public Sector Program (No. 201105027).
LR conceived and supervised the study. QD performed the laboratory work and performed all the bioinformatics analysis with the help of HS. QD and HS drafted the manuscript and Lingwei Ruan revised the manuscript. All authors read and approved the final manuscript.
The authors declare that they have no competing interests.
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- Nakagawa Y, Hamana K, Sakane T, Yamasato K. Reclassification of Cytophaga aprica (Lewin 1969) Reichenbach 1989 in Flammeovirga gen. nov. as Flammeovirga aprica comb. nov. and of Cytophaga diffluens (ex Stanier 1940; emend. Lewin 1969) Reichenbach 1989 in Persicobacter gen. nov. as Persicobacter diffluens comb. nov. Int J Syst Bacteriol. 1997;47:220–3.View ArticleGoogle Scholar
- Takahashi M, Suzuki K-i, Nakagawa Y. Emendation of the genus Flammeovirga and Flammeovirga aprica with the proposal of Flammeovirga arenaria nom. rev., comb. nov. and Flammeovirga yaeyamensis sp. nov. Int J Syst Evol Microbiol. 2006;56:2095–100.View ArticlePubMedGoogle Scholar
- Hosoya S, Yokota A. Flammeovirga kamogawensis sp. nov., isolated from coastal seawater in Japa. Int J Syst Evol Microbiol. 2007;57:1327–30.View ArticlePubMedGoogle Scholar
- Han W, Gu J, Yan Q, Li J, Wu Z, Gu Q, et al. A polysaccharide-degrading marine bacterium Flammeovirga sp. MY04 and its extracellular agarase system. J Ocean Univ China. 2012;11:375–82.View ArticleGoogle Scholar
- Liu Y, Yi Z, Cai Y, Zeng R. Draft genome sequence of algal polysaccharides degradation bacterium, Flammeovirga sp. OC4. Mar Genomics. 2015;21:21–2.View ArticlePubMedGoogle Scholar
- Han W, Gu J, Cheng Y, Liu H, Li Y, Li F. A Novel Alginate Lyase (Aly5) from a Polysaccharide-Degrading Marine Bacterium Flammeovirga sp. MY04: Effects of Module Truncation to the Biochemical Characteristics, Alginate-Degradation Patterns, and Oligosaccharide-Yielding Properties. Appl Environ Microbiol. 2015;82(1):364–74.View ArticlePubMedPubMed CentralGoogle Scholar
- Chan Z, Wang R, Liu S, Zhao C, Yang S, Zeng R. Draft genome sequence of an agar-degrading marine bacterium Flammeovirga pacifica WPAGA1. Mar Genomics. 2015;20:23–4.View ArticlePubMedGoogle Scholar
- Xu H, Fu Y, Yang N, Ding Z, Lai Q, Zeng R. Flammeovirga pacifica sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol. 2012;62:937–41.View ArticlePubMedGoogle Scholar
- Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008;26:541–7.View ArticlePubMedPubMed CentralGoogle Scholar
- Wilson K. Preparation of genomic DNA from bacteria. Curr Protoc Mol Biol. 2001 Nov;Chapter 2:Unit 2.4. doi: 10.1002/0471142727.mb0204s56.
- Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics. 2008;24:713–4.View ArticlePubMedGoogle Scholar
- Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 2010;20:265–72.View ArticlePubMedPubMed CentralGoogle Scholar
- Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D, Garrity GM, et al. Toward an online repository of Standard Operating Procedures (SOPs) for (meta) genomic annotation. OMICS. 2008;12:137–41.View ArticlePubMedPubMed CentralGoogle Scholar
- Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997;25:4876–82.View ArticlePubMedPubMed CentralGoogle Scholar
- Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics. 2003;4:41.View ArticlePubMedPubMed CentralGoogle Scholar
- Finn RD, Miller BL, Clements J, Bateman A. iPfam: a database of protein family and domain interactions found in the Protein Data Bank. Nucleic Acids Res. 2014;42:D364–D73.View ArticlePubMedGoogle Scholar
- Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: SignalP 3. J Mol Biol. 2004;340:783–95.View ArticlePubMedGoogle Scholar
- Krogh A, Larsson B, Von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001;305:567–80.View ArticlePubMedGoogle Scholar
- Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 2007;35:W52–W7.View ArticlePubMedPubMed CentralGoogle Scholar
- Tamura K, Dudley J, Nei M, Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol. 2007;24:1596–9.View ArticlePubMedGoogle Scholar
- Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A. 1990;87:4576–9.View ArticlePubMedPubMed CentralGoogle Scholar
- Krieg NR, Ludwig W, Euzéby J, Whitman WB. Bergey’s Manual of Systematic Bacteriology. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB, editors. Phylum XIV: Bacteroidetes phyl. nov, vol. 4. 2nd ed. New York: Springer; 2011. p. 25.Google Scholar
- Nakagawa Y, Class IV. Cytophagia class. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB, editors. Bergey’s Manual of Systematic Bacteriology, vol. 4. 2nd ed. The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes. New York: Springer; 2010. p. 370.
- List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol. 2012;62:1–4.
- Leadbetter ER, Order II. Cytophagales nomen novum. In: Buchanan RE, Gibbons NE, editors. Bergey’s Manual of Determinative Bacteriology. 8th ed. Baltimore: The Williams and Wilkins Co.; 1974. p. 99.Google Scholar
- Skerman VBD, McGowan V, Sneath PHA, Moore WEC, Moore LVH. Approved Lists. Int J Syst Bacteriol. 1980; 30:225–420.
- Yoon J, Adachi K, Park S, Kasai H, Yokota A. Aureibacter tunicatorum gen. nov., sp. nov., a marine bacterium isolated from a coral reef sea squirt, and description of Flammeovirgaceae fam. nov. Int J Syst Evol Microbiol. 2011;61:2342–7.View ArticlePubMedGoogle Scholar
- Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene Ontology: tool for the unification of biology. Nat Genet. 2000;25:25–9.View ArticlePubMedPubMed CentralGoogle Scholar