Contact us
닫기
Article Search
닫기

Microbiology and Biotechnology Letters

Genome Report(Note)

View PDF

Genome Report  |  Genome Report

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

https://doi.org/10.48022/mbl.2311.11011

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,          bhchun@pknu.ac.kr

Abstract

Go to

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

Body

Go to

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 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). 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 (https://github.com/hoelzer/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 (%)*7.27.27.2
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

ProgramStrains1234
POCP (%)AMJK92.9688.4489.8468.96
AMJM92.9688.4589.8568.97
AMRM92.9888.4289.8568.93
ANI (%)AMJK97.7692.5991.6579.68
AMJM97.8392.6491.6879.68
AMRM97.7992.6591.6079.78
AAI (%)AMJK98.4694.6793.8879.27
AMJM98.4694.6893.8979.28
AMRM98.4694.6793.8979.27


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.

Nucleotide Sequence Accession Number

Go to

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).

Acknowledgments

Go to

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

Conflicts of Interest

Go to

The authors have no financial conflicts of interest to declare.

References

Go to
  1. Gillis M, Logan NA. 2015, pp. 1-12. Janthinobacterium. Bergey's Manual of Systematics of Archaea and Bacteria.
    Pubmed CrossRef
  2. Jung WJ, Kim SW, Giri SS, Kim HJ, Kim SG, Kang JW, et al. 2021. Janthinobacterium tructae sp. nov., isolated from kidney of rainbow trout (Oncorhynchus mykiss). Pathogen 10: 229.
    Pubmed KoreaMed CrossRef
  3. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19: 455-477.
    Pubmed KoreaMed CrossRef
  4. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25: 1043-1055.
    Pubmed KoreaMed CrossRef
  5. Manni M, Berkeley MR, Seppey M, Zdobnov EM. 2021. BUSCO: assessing genomic data quality and beyond. Curr. Protoc. 1: e323.
    Pubmed CrossRef
  6. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, et al. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 44: 6614-6624.
    Pubmed KoreaMed CrossRef
  7. Qin QL, Xie BB, Zhang XY, Chen XL, Zhou BC, Zhou J, et al. 2014. A proposed genus boundary for the prokaryotes based on genomic insights. J. Bacteriol. 196: 2210-2215.
    Pubmed KoreaMed CrossRef
  8. Lee I, Kim YO, Park S, Chun J. 2016. OrthoANI. An improved algorithm and software for calculating average nucleotide identity. Int. J. Syst. Evol. Microbiol. 66: 1100-1103.
    Pubmed CrossRef
  9. Kim D, Park S, Chun J. 2021. Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity. J. Microbiol. 59: 476-480.
    Pubmed CrossRef
  10. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, et al. 2007. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 36: D480-D484.
    Pubmed KoreaMed CrossRef
  11. Hui C, Guo Y, Liu L, Zhang N, Gao C, Yang X, et al. 2020. Genetic control of violacein biosynthesis to enable a pigment-based whole-cell lead biosensor. RSC Adv. 10: 28106-28113.
    Pubmed KoreaMed CrossRef

Article Tools

Starts of Metrics

Share this article on :

Related articles in MBL

Most Searched Keywords ?

What is Most Searched Keywords?

  • It is most registrated keyword in articles at this journal during for 2 years.