- Open Access
Genome sequence of the marine bacterium Corynebacterium maris type strain Coryn-1T (= DSM 45190T)
© The Author(s) 2013
- Published: 30 July 2013
Corynebacterium maris Coryn-1T Ben-Dov et al. 2009 is a member of the genus Corynebacterium which contains Gram-positive, non-spore forming bacteria with a high G+C content. C. maris was isolated from the mucus of the Scleractinian coral Fungia granulosa and belongs to the aerobic and non-haemolytic corynebacteria. It displays tolerance to salts (up to 10%) and is related to the soil bacterium Corynebacterium halotolerans. As this is a type strain in a subgroup of Corynebacterium without complete genome sequences, this project, describing the 2.78 Mbp long chromosome and the 45.97 kbp plasmid pCmaris1, with their 2,584 protein-coding and 67 RNA genes, will aid the Genomic Encyclopedia of Bacteria and Archaea project.
- non-spore forming
Strain Coryn-1T (= DSM 45190T) is the type strain of the species Corynebacterium maris originally isolated from the mucus of the coral Fungia granulosa from the Gulf of Eilat (Red Sea, Israel) . The genus Corynebacterium is comprised of Gram-positive bacteria with a high G+C content. It currently contains over 80 members  isolated from diverse backgrounds like human clinical samples  and animals , but also from soil  and ripening cheese .
Within this diverse genus, C. maris has been proposed to form a distinct lineage with C. halotolerans YIM 70093T demonstrating 94% similarity related to the 16S rRNA gene sequences . Similar to the closest phylogenetic relative C. halotolerans, which displays the highest resistance to salt described for the genus Corynebacterium to date, C. maris Coryn-1T is able to live under conditions with high salinity. This species grows on LB agar plates with salinity ranging between 0 and 10%. Optimal growth was detected between 0.5 and 4.0% . Aside from this Coryn-1T is an alkaline-tolerant bacterium, which grows well at pH 7.2–9.0 (optimum pH 7.2) .
Here we present a summary classification and a set of features for C. maris DSM 45190T, together with the description of the genomic sequencing and annotation.
A representative genomic 16S rRNA sequence of C. maris DSM 45190T was compared to the Ribosomal Database Project database  confirming the initial taxonomic classification. C. maris shows highest similarity to C. halotolerans (94%). Because sequence similarity greater than 97% was not obtained with any member of the genus Corynebacteria, it was suggested that C. maris forms an new novel species, a hypothesis that is backed by other taxonomic classifiers .
Classification and general features of C. maris Coryn-1T according to the MIGS recommendations .
Species Corynebacterium maris
Type-strain Coryne-1T (=DSM 45190T)
0–10% (w/v) NaCl or sea-salt mixture (instant ocean)
maltose, lactulose, β-hydroxybutyric acid, α-ketovaleric acid, Tween 40, phenylethylamine, N-acetyl-d-galactosamine, malonic acid, l-threonine, l-glutamic acid, l-fucose, l-alanyl glycine, inosine, raffinose, d-arabitol, l-asparigine and citric acid
Terminal electron acceptor
mucus of the Scleractinian coral Fungia granulosa
agarsphere culturing technique
Gulf of Eilat, Red Sea, Israel
Sample collection time
E 34° 94′
It is described as non-motile , which coincides with a complete lack of genes associated with ‘cell motility’ (functional category N in COGs table).
Optimal growth of Coryn-1T was shown between 0.5 and 4.0% (w/v) salinity (NaCl or sea-salt mixture); however, ranges between 0 and 10% salinity are accepted . C. maris grows at temperatures between 26–37 °C (optimum at 35 °C). Carbon sources utilized by strain Coryn-1T include maltose, lactulose, β-hydroxybutyric acid, α-ketovaleric acid, Tween 40, phenylethylamine, N-acetyl-d-galactosamine, malonic acid, l-threonine, l-glutamic acid, l-fucose, l-alanyl glycine, inosine, raffinose, d-arabitol, l-asparigine and citric acid were used weakly .
Coryn-1T is susceptible to sulfamethoxazole/trimethoprim, tetracycline, chloramphenicol, erythromycin, ampicillin and meticillin. The strain is resistant to nalidixic acid .
In C. maris cellular fatty acids are composed of 58% oleic acid (C18:1ω9c), 30% palmitic acid (C16:0) and 12% tuberculostearic acid 10-methyl (C18:0). The mycolic acids of C. maris are short-chained, like many but not all corynemycol acids (6% C30, 27% C32, 47% C34 and 20% C36).
The biochemical characterization by Ben-Dov et al.  revealed positive signals for the following enzymes/reactions: alkaline phosphatase, esterase (C4), esterase lipase (C8), lipase (C14), leucine arylamidase, α-glucosidase, pyrazinamidase, pyrrolidonyl arylamidase, and gelatin hydrolysis activities.
Genome project history
Genome sequencing project information
Nextera DNA Sample Prep Kit
Newbler version 2.6
Gene calling method
GenBank Date of Release
July 30, 2013
NCBI project ID
Source material identifier
Growth conditions and DNA isolation
C. maris strain Coryn-1T, DSM 45190, was grown aerobically in LB broth (Carl Roth GmbH, Karlsruhe, Germany) at 37 °C. DNA was isolated from ∼ 108 cells using the protocol described by Tauch et al. 1995 .
Genome sequencing and assembly
A WGS library was prepared using the Illumina-Compatible Nextera DNA Sample Prep Kit (Epicentre, WI, U.S.A) according to the manufacturer’s protocol. The library was sequenced in a 2 × 150 bp paired read run on the MiSeq platform, yielding 1,238,702 total reads, providing 56.45× coverage of the genome. Reads were assembled using the Newbler assembler v2.6 (Roche). The initial Newbler assembly consisted of 26 contigs in seven scaffolds. Analysis of the seven scaffolds revealed one to be an extrachromosomal element (plasmid pCmaris1), five to make up the chromosome with the remaining one containing the four copies of the RRN operon which caused the scaffold breaks. The scaffolds were ordered based on alignments to the complete genome of C. halotolerans  and subsequent verification by restriction digestion, Southern blotting and hybridization with a 16S rDNA specific probe.
The Phred/Phrap/Consed software package [27–30] was used for sequence assembly and quality assessment in the subsequent finishing process. After the shotgun stage, gaps between contigs were closed by editing in Consed (for repetitive elements) and by PCR with subsequent Sanger sequencing (IIT Biotech GmbH, Bielefeld, Germany). A total of 67 additional reactions were necessary to close gaps not caused by repetitive elements.
Gene prediction and annotation were done using the PGAAP pipeline . Genes were identified using GeneMark , GLIMMER , and Prodigal . For annotation, BLAST searches against the NCBI Protein Clusters Database  are performed and the annotation is enriched by searches against the Conserved Domain Database  and subsequent assignment of coding sequences to COGs. Non-coding genes and miscellaneous features were predicted using tRNAscan-SE , Infernal , RNAMMer , Rfam , TMHMM , and SignalP .
% of totala
Genome size (bp)
DNA Coding region (bp)
DNA G+C content (bp)
Genes with function prediction (protein)
Genes assigned to COGs
Genes in paralog clusters
Genes with signal peptides
Genes with transmembrane helices
Number of genes associated with the general 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 biogenesis
Intracellular trafficking and 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
Christian Rückert acknowledges funding through a grant by the Federal Ministry for Eduction and Research (0316017A) within the BioIndustry2021 initiative.
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