DOI QR코드

DOI QR Code

Draft Genome Sequences of Three Janthinobacterium lividum Strains Producing Violacein

  • Yu Jeong Lee (Department of Microbiology, Pukyong National University) ;
  • Jae-Cheol Lee (Division of Environmental Materials, Honam National Institute of Biological Resources (HNIBR)) ;
  • Kira Moon (Division of Environmental Materials, Honam National Institute of Biological Resources (HNIBR)) ;
  • Aslan Hwanhwi Lee (Division of Environmental Materials, Honam National Institute of Biological Resources (HNIBR)) ;
  • Byung Hee Chun (Department of Microbiology, Pukyong National University)
  • Received : 2023.11.17
  • Accepted : 2024.04.04
  • Published : 2024.06.28

Abstract

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

Acknowledgement

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

References

  1. Gillis M, Logan NA. 2015. Janthinobacterium. Bergey's Manual of Systematics of Archaea and Bacteria. pp. 1-12.
  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.
  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. https://doi.org/10.1089/cmb.2012.0021
  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. https://doi.org/10.1101/gr.186072.114
  5. Manni M, Berkeley MR, Seppey M, Zdobnov EM, 2021. BUSCO: assessing genomic data quality and beyond. Curr. Protoc. 1: e323.
  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. https://doi.org/10.1093/nar/gkw569
  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. https://doi.org/10.1128/JB.01688-14
  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. https://doi.org/10.1099/ijsem.0.000760
  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. https://doi.org/10.1007/s12275-021-1154-0
  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. https://doi.org/10.1093/nar/gkm882
  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. https://doi.org/10.1039/D0RA04815A