Cite this paper:
TANG Xianghai, XU Kuipeng, HAN Xiaojuan, MO Zhaolan, MAO Yunxiang. Complete genome of Cobetia marina JCM 21022T and phylogenomic analysis of the family Halomonadaceae[J]. HaiyangYuHuZhao, 2018, 36(2): 528-536

Complete genome of Cobetia marina JCM 21022T and phylogenomic analysis of the family Halomonadaceae

TANG Xianghai1, XU Kuipeng1, HAN Xiaojuan1,3, MO Zhaolan2, MAO Yunxiang1
1 Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China;
2 Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China;
3 CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
Abstract:
Cobetia marina is a model proteobacteria in researches on marine biofouling. Its taxonomic nomenclature has been revised many times over the past few decades. To better understand the role of the surface-associated lifestyle of C. marina and the phylogeny of the family Halomonadaceae, we sequenced the entire genome of C. marina JCM 21022T using single molecule real-time sequencing technology (SMRT) and performed comparative genomics and phylogenomics analyses. The circular chromosome was 4 176 300 bp with an average GC content of 62.44% and contained 3 611 predicted coding sequences, 72 tRNA genes, and 21 rRNA genes. The C. marina JCM 21022T genome contained a set of crucial genes involved in surface colonization processes. The comparative genome analysis indicated the significant differences between C. marina JCM 21022T and Cobetia amphilecti KMM 296 (formerly named C. marina KMM 296) resulted from sequence insertions or deletions and chromosomal recombination. Despite these differences, pan and core genome analysis showed similar gene functions between the two strains. The phylogenomic study of the family Halomonadaceae is reported here for the first time. We found that the relationships were well resolved among every genera tested, including Chromohalobacter, Halomonas, Cobetia, Kushneria, Zymobacter, and Halotalea.
Key words:    Cobetia marina JCM 21022T|Halomonadaceae|complete genome sequence|comparative genomics|phylogenomics|surface colonization|single molecule real-time sequencing technology (SMRT)   
Received: 2016-09-04   Revised:
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References:
Arahal D R, Castillo A M, Ludwig W et al. 2002a. Proposal of Cobetia marina gen. nov., comb. nov., within the family Halomonadaceae, to include the species Halomonas marina. Systematic and Applied Microbiology, 25(2):207-211.
Arahal D R, Ludwig W, Schleifer K H et al. 2002b. Phylogeny of the family Halomonadaceae based on 23S and 165 rDNA sequence analyses. International Journal of Systematic and Evolutionary Microbiology, 52(1):241-249.
Arpa Sancet M P. 2013. Influence of surface properties on adhesion of Cobetia marina and accumulation of marine microfoulers in the ocean. Ruperto Carola University Heidelberg, Heidelberg.
Balabanova L A, Golotin V A, Kovalchuk S N et al. 2016a. The Genome of the marine bacterium Cobetia marina KMM 296 isolated from the mussel Crenomytilus grayanus(Dunker, 1853). Russian Journal of Marine Biology, 42(1):106-109.
Balabanova L, Nedashkovskaya O, Podvolotskaya A et al. 2016b. Data supporting functional diversity of the marine bacterium Cobetia amphilecti KMM 296. Data in Brief, 8:726-732.
Barak J D, Gorski L, Naraghi-Arani P et al. 2005. Salmonella enterica virulence genes are required for bacterial attachment to plant tissue. Applied and Environmental Microbiology, 71(10):5 685-5 691.
Barnhart M M, Chapman M R. 2006. Curli biogenesis and function. Annual Review of Microbiology, 60:131-147.
Baumann L, Baumann P, Mandel M et al. 1972. Taxonomy of aerobic marine eubacteria. Journal of Bacteriology, 110(1):402-429.
Baumann L, Bowditch R D, Baumann P. 1983. Description of Deleya gen. nov. created to accommodate the marine species Alcaligenes aestus, A. pacificus, A. cupidus, A. venustus, and Pseudomonas marina. International Journal of Systematic and Evolutionary Microbiology, 33(4):793-802.
Camacho C, Coulouris G, Avagyan V et al. 2009. BLAST+:architecture and applications. BMC Bioinformatics, 10:421.
Capella-Gutiérrez S, Silla-Martínez J M, Gabaldón T. 2009. trimAl:a tool for automated alignment trimming in largescale phylogenetic analyses. Bioinformatics, 25(15):1 972-1 973.
Chin C S, Alexander D H, Marks P et al. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nature Methods, 10(6):563-569.
Cobet A B, Wirsen C Jr, Jones G E. 1970. The effect of nickel on a marine bacterium, Arthrobacter marinus sp. nov. Journal of General Microbiology, 62(2):159-169.
Copeland A, O'Connor K, Lucas S et al. 2011. Complete genome sequence of the halophilic and highly halotolerant Chromohalobacter salexigens type strain (1H11T). Standards in Genomic Sciences, 5(3):379-388.
Darriba D, Taboada G L, Doallo R et al. 2011. ProtTest 3:fast selection of best-fit models of protein evolution.Bioinformatics, 27(8):1 164-1 165.
de la Haba R R, Arahal D R, Márquez M C et al. 2010. Phylogenetic relationships within the family Halomonadaceae based on comparative 23S and 16S rRNA gene sequence analysis. International Journal of Systematic and Evolutionary Microbiology, 60(4):737-748.
Dobson S J, Franzmann P D. 1996. Unification of the genera Deleya (Baumann et al. 1983), Halomonas (Vreeland et al. 1980), and Halovibrio (Fendrich 1988) and the species Paracoccus halodenitrificans (Robinson and Gibbons 1952) into a single genus, Halomonas, and placement of the genus Zymobacter in the family Halomonadaceae. International Journal of Systematic Bacteriology, 46(2):550-558.
Eid J, Fehr A, Gray J et al. 2009. Real-time DNA sequencing from single polymerase molecules. Science, 323(5910):133-138.
Gao F, Zhang C T. 2008. Ori-Finder:a web-based system for finding oriC s in unannotated bacterial genomes. BMC Bioinformatics, 9:79.
Ista L K, Fan H Y, Baca O et al. 1996. Attachment of bacteria to model solid surfaces:oligo(ethylene glycol) surfaces inhibit bacterial attachment. FEMS Microbiology Letters, 142(1):59-63.
Ista L K, Pérez-Luna V H, López G P. 1999. Surface-grafted, environmentally sensitive polymers for biofilm release.Applied and Environmental Microbiology, 65(4):1 603-1 609.
Ivanova E P, Christen R, Sawabe T et al. 2005. Presence of ecophysiologically diverse populations within Cobetia marina strains isolated from marine invertebrate, algae and the environments. Microbes and Environments, 20(4):200-207.
Jeter C, Matthysse A G. 2005. Characterization of the binding of diarrheagenic strains of E. coli to plant surfaces and the role of curli in the interaction of the bacteria with alfalfa sprouts. Molecular Plant-Microbe Interactions, 18(11):1 235-1 242.
Katoh K, Kuma K I, Toh H et al. 2005. MAFFT version 5:improvement in accuracy of multiple sequence alignment.Nucleic Acids Research, 33(2):511-518.
Krzywinski M, Schein J, Birol I et al. 2009. Circos:an information aesthetic for comparative genomics. Genome Research, 19(9):1 639-1 645.
Kurtz S, Phillippy A, Delcher A L et al. 2004. Versatile and open software for comparing large genomes. Genome Biology, 5(2):R12.
Lagesen K, Hallin P, Rødland E A et al. 2007. RNAmmer:consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Research, 35(9):3 100-3 108.
Lowe T M, Eddy S R. 1997. tRNAscan-SE:a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research, 25(5):955-964.
Mata J A, Martínez-Cánovas J, Quesada E et al. 2002. A detailed phenotypic characterisation of the type strains of Halomonas species. Systematic and Applied Microbiology, 25(3):360-375.
Miele V, Penel S, Duret L. 2011. Ultra-fast sequence clustering from similarity networks with SiLiX. BMC Bioinformatics, 12:116.
Ntougias S, Lapidus A, Copeland A et al. 2015. High-quality permanent draft genome sequence of the extremely osmotolerant diphenol degrading bacterium Halotalea alkalilenta AW-7T, and emended description of the genus Halotalea. Standards in Genomic Sciences, 10:52.
Ntougias S, Zervakis G I, Fasseas C. 2007. Halotalea alkalilenta gen. nov., sp. nov., a novel osmotolerant and alkalitolerant bacterium from alkaline olive mill wastes, and emended description of the family Halomonadaceae Franzmann et al. 1989, emend. Dobson and Franzmann 1996. International Journal of Systematic and Evolutionary Microbiology, 57(9):1 975-1 983.
Okamoto T, Taguchi H, Nakamura K et al. 1993. Zymobacter palmae gen. nov., sp. nov., a new ethanol-fermenting peritrichous bacterium isolated from palm sap. Archives of Microbiology, 160(5):333-337.
Roberts R J, Carneiro M O, Schatz M C. 2013. The advantages of SMRT sequencing. Genome biology, 14:405.
Romanenko L A, Tanaka N, Svetashev V I et al. 2013. Description of Cobetia amphilecti sp. nov., Cobetia litoralis sp. nov. and Cobetia pacifica sp. nov., classification of Halomonas halodurans as a later heterotypic synonym of Cobetia marina and emended descriptions of the genus Cobetia and Cobetia marina. International Journal of Systematic and Evolutionary Microbiology, 63(1):288-297.
Salzberg S L, Delcher A L, Kasif S et al. 1998. Microbial gene identification using interpolated Markov models. Nucleic Acids Research, 26(2):544-548.
Sánchez-Porro C, de la Haba R R, Cruz-Hernández N et al. 2013. Draft Genome of the marine Gammaproteobacterium Halomonas titanicae. Genome Announcements, 1(2):e00083-13.
Sánchez-Porro C, de la Haba R R, Soto-Ramírez N et al. 2009. Description of Kushneria aurantia gen. nov., sp. nov., a novel member of the family Halomonadaceae, and a proposal for reclassification of Halomonas marisflavi as Kushneria marisflavi comb. nov., of Halomonas indalinina as Kushneria indalinina comb. nov. and of Halomonas avicenniae as Kushneria avicenniae comb. nov. International Journal of Systematic and Evolutionary Microbiology, 59(2):397-405.
Schwibbert K, Marin-Sanguino A, Bagyan I et al. 2011. A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581T. Environmental Microbiology, 13(8):1 973-1 994.
Sharko F S, Shapovalova A A, Tsygankova S V et al. 2016. Draft genome sequence of "Halomonaschromatireducens" Strain AGD 8-3, a Haloalkaliphilic Chromate-and Selenite-Reducing Gammaproteobacterium. Genome Announcements, 4(2):e00160-16.
Shea C, Lovelace L J, Smith-Somerville H E. 1995. Deleya marina as a model organism for studies of bacterial colonization and biofilm formation. Journal of Industrial Microbiology, 15(4):290-296.
Spangenberg C, Fislage R, Sierralta W et al. 1995. Comparison of type IV-pilin genes of Pseudomonas aeruginosa of various habitats has uncovered a novel unusual sequence. FEMS Microbiology Letters, 125(2-3):265-273.
Stamatakis A. 2006. RAxML-VI-HPC:maximum likelihoodbased phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22(21):2 688-2 690.
Thomas T, Evans F F, Schleheck D et al. 2008. Analysis of the Pseudoalteromonas tunicata genome reveals properties of a surface-associated life style in the marine environment. PLoS One, 3(9):e3252.
Vallenet D, Belda E, Calteau A et al. 2013. MicroScope-an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data. Nucleic Acids Research, 41 (D1):D636-D647.
Ventosa A, Gutierrez M C, Garcia M T et al. 1989. Classification of "Chromobacterium marismortui" in a new genus, Chromohalobacter gen. nov., as Chromohalobacter marismortui comb. nov., nom. rev. International Journal of Systematic Bacteriology, 39(4):382-386.
Vreeland R H, Litchfield C D, Martin E L et al. 1980. Halomonas elongata, a new genus and species of extremely salt-tolerant bacteria. International Journal of Systematic Bacteriology, 30(2):485-495.
Wang L, Reeves P R. 1998. Organization of Escherichia coli O157 O antigen gene cluster and identification of its specific genes. Infection and Immunity, 66(8):3 545-3 551.
Wilson K. 1997. Preparation of genomic DNA from bacteria.In:Ausubel F M, Bent R, Kingston R E et al eds. Current Protocols in Molecular Biology. John Wiley & Sons, Inc., New York. p.2.4.1-2.4.5.