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Microbiology and Biotechnology Letters

Genome Report(Note)

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Genome Report  |  Genome Report

Microbiol. Biotechnol. Lett. 2024; 52(2): 215-217

Received: November 17, 2023; Revised: April 2, 2024; Accepted: April 4, 2024

Draft Genome Sequences of Three Janthinobacterium lividum Strains Producing Violacein

Yu Jeong Lee1, Jae-Cheol Lee2, Kira Moon2, Aslan Hwanhwi Lee2, and Byung Hee Chun1,2*

1Department of Microbiology, Pukyong National University, Busan 48513, Republic of Korea
2Division of Environmental Materials, Honam National Institute of Biological Resources (HNIBR), Mokpo 58762, Republic of Korea

Correspondence to :
Byung Hee Chun,

Purple pigment producing bacterium strains AMJK, AMJM, and AMRM were isolated from sediment in sinan-gun, Korea and their draft genomes were sequenced using Illumina Hiseq 4000 platform. The lengths of AMJK, AMJM, and AMRM genomes were 6,380,747 bp, 6,381,259 bp, and 6,380,870 bp, respectively and G+C contents were 62.82%, 64.15%, and 62.82%, respectively. Comparative analysis of genomic identity showed that three strains were closely related to the group of Janthinobacterium lividum. Functional analysis of AMJK, AMJM, and AMRM genomes showed that all strains harbor genes related to producing violacein (VioABCDE).

Keywords: Janthinobacterium lividum, draft genome, violacein producing bacteria

The genus Janthinobacterium lividum is a Gramstaining negative, psychrotolerant, rod shape with flagella, and aerobic bacterium [1]. The bacterium is reported for producing violacein, a purple pigment of the bis-indol family, which has been known as its functionality for antioxidant-, anti-virus- and anti-fungal-activities [2]. Although the violacein produced by Janthinobacterium lividum is of great industrial value, research based on the optimization for production of violacein from microbes has not been conducted. Strains AMJK, AMJM, and AMRM, which exhibit purple-colored colonies, were isolated from tidal flat in Sinan-gun, Korea (34.8605 N 126.0252 E). To isolate the genomic DNAs from strains AMJK, AMJM, and AMRM, colonies of three strains were cultured on R2A broth at 30℃ for 3 days. The genomic DNAs from cultured cells were extracted using FastDNATM SPIN Kit for Soil (MP Biomedicals), following the manufacturer’s instructions. The libraries from extracted genomic DNAs were constructed using the Illumina NGS library prep kit and sequenced by Illumina HiSeq 4000 platform at Macrogen (Republic of Korea). A total of 55,545,794 (N50, 809,585 bp), 63,501,590, (N50, 809,585 bp) and 50,518,042 bp (N50, 809,585 bp) was generated after quality control of sequencing results for strains AMJK, AMJM, and AMRM, respectively, using FastQC version 0.11.5 ( Through de novo assembly using SPAdes version 3.15.0 [3] and quality analysis using CheckM v1.2.2 [4] and BUSCO v.5.7.0 [5], draft contigs with high quality for strains AMJK, AMJM, and AMRM were produced (Table 1). The genome annotation was conducted using NCBI Prokaryotic Genome Annotation Pipeline v6.6 [6] (Table 1). The genomic identities of strains AMJK, AMJM, and AMRM with their phylogenetically closely related type strains were compared using POCP ( [7], ANI (OrthoANIu, EzBioCloud) [8], and AAI (EzAAI, EzBioCloud) [9] (Table 2). The proposed POCP cut-off value for delineating genus are ≥ 50%, indicating that the strains of AMJK, AMJM, and AMRM belong to the genus of Janthinobacterium. ANI and AAI cut-off value for delineating species are both ≥ 95%. The ANI and AAI results for strains of AMJK, AMJM, and AMRM showed that these three strains belong to the Janthinobacterium lividum group. Through KEGG database [10] and BLASTP searches, genes (VioABCDE) related to producing violacein [11] were identified in the genomes of strains AMJK, AMJM, and AMRM (Fig. 1).

Table 1 . Genomic features of draft genomes in the strains AMJK, AMJM, and AMRM.

Genome featureAMJKAMJMAMRM
Genome length (bp)6,380,7476,381,2596,380,870
G + C content (%)62.8264.1562.82
Total number of genes5,7455,7465,747
Number of protein-coding genes5,6305,6315,632
Total number of RNA genes909090
rRNA genes (5S, 16S, 23S)5, 4, 15, 4, 15, 4, 1
tRNA genes767676
ncRNA genes444
Pseudo genes252525
Coverage (×)150147150
GenBank accession NO.JAVFKP000000000JAVFKR000000000JAVFKQ000000000
Completeness (%)*99.399.299.3
Contamination rate (%)*
Complete BUSCOs (%)98.899.099.0

* These analyses were conducted using CheckM [4].

Table 2 . Comparison of genomic identities of strains AMJK, AMJM, and AMRM with their phylogenetically closely related type strains using POCP, ANI, and AAI. Strains: 1, Janthinobacterium lividum NCTC9796T; 2, Janthinobacterium rivuli FT68WT; 3, Janthinobacterium violaceinigrum FT13WT; 4, Janthinobacterium agaricidamnosum NBRC 102515T

POCP (%)AMJK92.9688.4489.8468.96
ANI (%)AMJK97.7692.5991.6579.68
AAI (%)AMJK98.4694.6793.8879.27

Figure 1.A physical map of genes and their corresponding accession numbers responsible for producing violacein in the draft genomes of AMJK, AMJM, and AMRM.

The draft genome sequencing data of strains AMJK, AMJM, and AMRM derived in this study are publicly available in the GenBank database under accession numbers JAVFKP000000000, JAVFKR000000000, and JAVFKQ000000000, respectively (NCBI Bioproject number: PRJNA1007897, PRJNA1007939, and PRJNA1007934, respectively).

This work was supported by a Research Grant of Pukyong National University (2022).

The authors have no financial conflicts of interest to declare.

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