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Genome sequence of Lysobacter dokdonensis DS-58T, a gliding bacterium isolated from soil in Dokdo, Korea


Lysobacter dokdonensis DS-58, belonging to the family Xanthomonadaceae, was isolated from a soil sample in Dokdo, Korea in 2011. Strain DS-58 is the type strain of L. dokdonensis. In this study, we determined the genome sequence to describe the genomic features including annotation information and COG functional categorization. The draft genome sequence consists of 25 contigs totaling 3,274,406 bp (67.24 % G + C) and contains 3,155 protein coding genes, 2 copies of ribosomal RNA operons, and 48 transfer RNA genes. Among the protein coding genes, 75.91 % of the genes were annotated with a putative function and 87.39 % of the genes were assigned to the COG category. In the genome of L. dokdonensis, a large number of genes associated with protein degradation and antibiotic resistance were detected.


The genus Lysobacter was firstly described by Christensen and Cook in 1979 as high G + C Gram-negative bacterium with gliding motility [1]. In the past, Lysobacter species were classified as “unidentified myxobacters” due to their high G + C ratio and gliding motility. However, the genus Lysobacter has features distinctive from myxobacteria and had been proposed as a new genus of Gammaproteobacteria . Lysobacter species are ubiquitous and have been found in a variety of environments such as soil, water, and the rhizosphere. Currently, more than 30 Lysobacter species were registered in the GenBank taxonomy database and among them, 28 species have been validly published [2]. Some of the Lysobacter species were known to produce several kinds of lytic enzymes and antibiotics [3] and have an antimicrobial activity against plant pathogens [4]. Moreover, several Lysobacter species are known to produce bioactive natural products such as cyclodepsipeptide, cyclic lipodepsipeptide, cephem-type β-lactam, and polycyclic tetramate macrolactam [5]. Despite their ubiquitous distribution, many identified species, and possible usefulness as a biocontrol agent, deciphered Lysobacter genomes are relatively limited. Here, we present the genome sequence and the genomic information of Lysobacter dokdonensis DS-58T (KCTC 12822 T = DSM1 7958 T), which is the type strain of the species.

Organism information

Classification and features

L. dokdonensis DS-58T is a Gram-staining-negative, non-motile, and rod-shaped bacterium and was isolated from the soil sample in Dokdo, an island in the East Sea, Korea, in 2011 [6]. L. dokdonensis DS-58 grows at the temperature range of 4 to 38 °C, the pH range of 6.0 to 8.0, and the NaCl concentration of 0 to 0.5 % (w/v) [6]. Colony size of L. dokdonensis DS-58 is about 1.0 – 2.0 mm on nutrient agar medium and the cell size is 1.0–5.0 μm long and 0.4–0.8 μm wide [6] (Fig. 1). L. dokdonensis DS-58 can assimilate dextrin, Tween 40, maltose, α-ketobutyric acid, alaninamide, l-alanine, l-alanyl glycine, and l-glutamic acid as a carbon source [6]. Minimum information about a genome sequence (MIGS) for L. dokdonensis DS-58 is described in Table 1. Phylogenetically, L. dokdonensis DS-58 belongs to the family Xanthomonadaceae of the class Gammaproteobacteria , and the 16S rRNA gene showed the highest sequence similarity (96.93 %) with L. niastensis GH41-7. However, a phylogenetic tree based on the 16S rRNA gene showed that the strain DS-58 is located in the deep branch of the genus Lysobacter (Fig. 2).

Fig. 1
figure 1

Transmission electron microscopic image of Lysobacter dokdonensis DS-58

Table 1 Classification and general features of Lysobacter dokdonensis DS-58T according to the MIGS recommendations [24]
Fig. 2
figure 2

Neighbour-joining tree of the type species of the genus Lysobacter. Neighbor-joining tree based on the 16S rRNA gene sequence was constructed using MEGA 5. The evolutionary distances were calculated using Jukes-Cantor model and phylogenetic tree was generated based on the comparison of 1,379 nucleotides. Bootstrap values (percentages of 1,000 replications) greater than 50 % are shown at each node and Xanthomonas campestris ATCC 33913 (AE008922) were used as an out-group. The scale bar represents 0.005 nucleotide substitutions per site. Accession numbers of the 16S rRNA gene are presented in the parentheses. *species whose genome has been sequenced

Genome sequencing information

Genome project history

The genome sequencing and analysis of L. dokdonensis DS-58 were performed by the Laboratory of Microbial Genomics and Systems/Synthetic Biology at Yonsei University using the next generation sequencing. The genomic information was deposited in the GenBank (Accession number is JRKJ00000000). Summary of the genome project is provided in Table 2.

Table 2 Genome sequencing project information

Growth conditions and genomic DNA preparation

L. dokdonensis DS-58 (accession numbers of culture collection: KCTC 12822 = DSM1 7958) was routinely cultured on nutrient medium at 30 °C. Strain DS-58 forms light yellow colored colonies with average 1.0–2.0 mm of diameter in 5 days (Table 1) [6]. For the genome sequencing, single colony of L. dokdonensis DS-58 was inoculated in nutrient medium and incubated in the shacking incubator at 30 °C. Genomic DNA was extracted using chemical and enzymatic method as described in Molecular Cloning, A Laboratory Manual [7]. Cell lysis was conducted using sodium dodecyl sulfate and proteinase K. From the cell lysate, genomic DNA was purified using phenol:chloroform, precipitated using isopropanol, and finally eluted into Tris-EDTA buffer.

Genome sequencing and assembly

For the whole genome shotgun sequencing, a library with 500-bp insert size was prepared and paired-end genome sequencing was performed with HiSeq2000 of the Illumina/Solexa platform (Macrogen, Inc., South Korea). Sequence trimming was conducted using CLC Genomics Workbench 5.1 (CLC bio, Qiagen, Netherlands) with parameters of 0.01 quality score and none of the ambiguous nucleotide. Sequence reads below 60 bp in length were discarded. After trimming, a total of 28,810,330 reads with an average read length of 95.8 bp were generated. De novo assembly was performed with CLC Genomics Workbench with parameters of automatic word and bubble size, deletion and insertion cost of 3, mismatch cost of 2, similarity fraction of 1.0, length fraction of 0.5, and minimum contig length of 500 bp. After the de novo assembly, scaffolding was performed using SSPACE [8] and automatic gap filling was carried out with IMAGE [9]. Following the automatic gap filling, manual gap filling was conducted using CLC Genomics Workbench with the function of Find Broken Pair Mates in the end of the contigs. Basic information of the genome sequencing project is described in Table 2.

Genome annotation

Structural gene prediction was conducted using Glimmer 3 [10] in RAST server [11] with automatic fixation of errors and frame shifts. Functional assignment of the predicted protein coding sequences (CDSs) was performed using AutoFact [12] with the results of BLASTP or RPS-BLAST with Uniref100, NR, COG, and Pfam databases. For the accurate annotation, the functional assignment results from the RAST server and BLAST were compared each other. When assignment of the gene function was not the same between the results from RAST and BLAST, an additional BLASTP search was performed with NR database at NCBI and the top-hit result was selected for the annotation.

Genome properties

The draft genome sequence of the strain DS-58 consists of 25 contigs and the sum of the contigs is 3,274,406 bp (G + C content 67.24 %) (Table 3 and Fig. 3). From the genome of the strain DS-58, 3,155 CDSs, 2 copies of ribosomal RNA operons, and 48 transfer RNAs were detected. Among the predicted CDSs, 2,436 CDSs were annotated with a putative function and 2,757 CDSs were assigned to a COG category. The numbers and percentages of COG assigned genes are shown in Table 4.

Table 3 Genome Statistics
Fig. 3
figure 3

Circular representation of the draft genome of Lysobacter dokdonensis DS-58. The first circle from inside shows the 25 contigs sorted by size. The second and the third circles indicate COG- assigned genes in color codes. Yellow circle represents the G + C content and red-blue circle is for the G + C skew. Innermost, blue-scattered spots indicate the tRNA genes and red-scattered spots indicate the rRNA genes. Red lines are to indicate connections of paired-end reads at the end of each contig

Table 4 Number of protein coding genes of Lysobacter dokdonensis DS-58 associated with the general COG functional categories

Insights from the genome sequence

Some Lysobacter species are known to produce the secondary metabolite with antimicrobial activities [13, 14]. In the genome of L. dokdonensis DS-58, biosynthetic gene clusters for a bacteriocin and an arylpolyene were detected. The structure of bacteriocin-biosynthetic gene cluster of DS-58 was similar to the one in L. arseniciresistens ZS79 and the structure of arylpolyene-biosynthetic gene cluster was similar to the one in Xanthomonas campestris NCPPB 4392 (Fig. 4).

Fig. 4
figure 4

Biosynthetic gene clusters for bacteriocin and arylpolyene. Gene clusters for biosynthesis of secondary metabolites were detected using the AntiSMASH webserver [23]. a Bacteriocin-biosynthetic gene cluster. b Arylpolyene biosynthetic gene cluster. Same colors in different strains indicate the same genes. White-colored genes are genes unrelated to the secondary metabolite gene clusters. 1, hypothetical protein (LF41_2288); 2, non-heme chloroperoxidase (LF41_2289); 3, alkylhydroperoxidase (LF41_2290); 4, membrane protein-like protein (LF41_2291); 5, 23S rRNA (guanosine-2′-O-)-methyltransferase (LF41_2292); 6, permease (LF41_2293); 7, ribonuclease T (LF41_2294); 8, hypothetical protein (LF41_2295); 9, DUF692 domain containing protein (LF41_2296); 10, hypothetical protein (LF41_2297); 11, phosphate transport system regulatory protein (LF41_2298); 12, phosphate transport ATP-binding protein (LF41_2299); 13, phosphate transport system permease protein (LF41_2300); 14, phosphate transport system permease protein (LF41_2301); 15, phosphate ABC transporter, periplasmic phosphate-binding protein (LF41_2302); 16, coproporphyrinogen-III oxidase (LF41_3101); 17, DNA polymerase I (LF41_3103); 18, DUF2785 domain containing protein (LF41_3104); 19, putative exporter (LF41_3121); 20, fatty acyl-CoA synthetase (LF41_3122); 21, acyltransferase (LF41_3123); 22, dehydratase (LF41_3124); 23, acyl carrier protein (LF41_3126); 24, monooxygenase (LF41_3127); 25, pteridine-dependent deoxygenase (LF41_3128). Strains are: Lysobacter dokdonensis DS-58, Lysobacter arseniciresistens ZS79, Arenimonas composti DSM 18010, Lysobacter daejeonensis GH1-9, Xanthomonas albilineans GPE PC73, Pseudoxanthomonas suwonensis 11–1, Xanthomonas campestris NCPPB 4392, Xanthomonas vasicola NCPPB 206, Xanthomonas gardneri ATCC 19865

In the genome of L. dokdonensis DS-58, a number of genes associated with proteolysis were detected that include 63 genes encoding peptidases and 33 genes encoding proteases. Microbial proteases are among the most important industrial enzymes due to their diverse activities and the genus Bacillus is major source of protease in the market [15, 16]. Results from the text mining of annotated gene products indicated that L. dokdonensis DS-58 has more genes encoding proteases and peptidases than other genome-sequenced Lysobacter species except for L. antibioticus ASM73109v1 and L. capsici AZ78. Moreover, in the genome of the strain DS-58, genes encoding 17 β-lactamases for degrading chemicals such as β-lactam antibiotics, biotin-biosynthetic proteins, and type IV fimbrial biogenesis proteins that could be involved in gliding motility were detected.

Distinct from other genera in the Xanthomonadaceae , Lysobacter spp. exhibit gliding motility [1]. Type IV pili-associated bacterial motility is widespread in members of diverse taxa such as Proteobacteria , Bacteroidetes , and Fibrobacteres [17] and known to be responsible for S-motility in Myxococcus and twitching motility in Lysobacter [18] as well as Pseudomonas and Neisseria [19]. Thus, there is a possibility that the gliding motility of Lysobacter is associated with type IV fimbriae. On the other hand, GltA, which is involved in A-motility of Myxococcus xanthus that best fits the definition of gliding motility [20], was detected in the genome of DS-58 (56 % identity with 88 % coverage).

Lysobacter species typically have been isolated from soil and water, but several studies indicated that Lysobacter species may survive in more diverse habitats of anaerobic or extreme-cold [21, 22]. A great diversity of secreted degrading enzymes such as proteases and ß-lactamases may contribute to the adaptation of Lysobacter species to such diverse environments. Abundant genes encoding proteases and peptidases in the genome of DS-58 may contribute to the discovery of effective and commercially useful proteolytic enzymes. Moreover, in the genome of DS-58, dozens of genes involved in the biosynthesis of type IV fimbriae were detected. The mechanism of gliding motility has not yet been clearly revealed, and we expect that the genome information of DS-58 may contribute to the genetic analysis of bacterial gliding motility.


L. dokdonensis DS-58, the type strain of the species, is a soil bacterium isolated from Dokdo in Korea. Through a phylogenetic analysis of the 16S rRNA gene, L. dokdonensis is located in a deep branch of the genus Lysobacter . The genome sequence of L. dokdonensis DS-58 is comprised of 25 contigs of 3,274,406 bp with G + C content of 67.24 %. In the genome of DS-58, a total of 3,155 CDSs were predicted and 87.39 % of the CDSs were functionally assigned to COG categories. Dozens of genes associated with protein degradation and resistance to antibiotics were detected. Through the genome analysis of L. dokdonensis DS-58, we report that this soil bacterium harbors a large number of peptidases and proteases, which may represent a rich source of protein-degrading enzymes.



Clusters of Orthologous Groups




UniProt Reference Clusters


Protein families


SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension


Iterative Mapping and Assembly for Gap Elimination


Rapid Annotation using Subsystem Technology


Automatic Functional Annotation and Classification Tool


Basic Local Alignment Search Tool


Reversed Position Specific-BLAST


Molecular Evolutionary Genetics Analysis


Minimum Information about a Genome Sequence


Clustered Regularly Interspaced Short Palindromic Repeat.


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This work was financially supported by the National Research Foundation (NRF-2011-0017670) of the Ministry of Science, ICT and Future Planning, Republic of Korea.

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Correspondence to Jihyun F. Kim.

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The authors declare that they have no competing interests.

Authors’ contributions

JFK conceived, organized and supervised the project, interpreted the results, and edited the manuscript. SKK prepared the high-quality genomic DNA and arranged the acquisition of sequence data. MJK performed the sequence assembly, gene prediction, gene annotation, analyzed the genome information, and drafted the manuscript. JHY provided the bacterium and its microscopic image. All of the authors read and approved the final version of the manuscript before submission.

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Kwak, MJ., Kwon, SK., Yoon, JH. et al. Genome sequence of Lysobacter dokdonensis DS-58T, a gliding bacterium isolated from soil in Dokdo, Korea. Stand in Genomic Sci 10, 123 (2015).

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