Korean Journal of Microbiology (2020) Vol. 56, No. 1, pp. 86-88 pISSN 0440-2413
DOI https://doi.org/10.7845/kjm.2020.9076 eISSN 2383-9902
Copyright ⓒ 2020, The Microbiological Society of Korea
Draft genome sequence of Flavobacterium silvisoli RD-2-33 T isolated from forest soil
Ram Hari Dahal
1, Dhiraj Kumar Chaudhary
1, Jaisoo Kim
1, and Dong-Uk Kim
2*
1
Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon 16227, Republic of Korea
2
Department of Biological Science, College of Science and Engineering, Sangji University, Wonju 26339, Republic of Korea
삼림토양에서 분리된 박테리아 Flavobacterium silvisoli RD-2-33 T 의 게놈 서열 초안
다할 램 하리
1･ 차우다리 디라즈 꾸마르
1･ 김재수
1･ 김동욱
2*
1
경기대학교 자연과학대학 생명과학과,
2상지대학교 이공과대학 생명과학과
(Received July 18, 2019; Revised February 17, 2020; Accepted March 6, 2020)
*For correspondence. E-mail: [email protected];
Tel.: +82-33-730-0403; Fax: +82-33-730-0433
Flavobacterium silvisoli was isolated from Kyonggi University forest soil during the study of bacterial diversity. In this study, we report the draft genome sequence of a bacterium Flavobacterium silvisoli RD-2-33
T(= KACC 21178
T= NBRC 113789
T) obtained using the Illumina MiSeq platform. The genome comprised of 2,894,048 bp with the G + C content of 38.6%, the genome included 2,612 genes among them, 2,543 genes are protein- coding genes.
Keywords: Flavobacterium, draft genome, forest soil, Illumina MiSeq
Flavobacterium silvisoli RD-2-33
Tis a mesophilic bacterium that are well grown on R2A and NA media and is aerobic, Gram-staining-negative, non-sporulating, rod-shaped, and yellow- pigmented. Colonies on R2A agar are 1~2 mm in diameter, entire, circular, and convex (Chaudhary et al., 2019). This is the first genome sequence of F. silvisoli and this genome will help to understand the genomic and phylogenetic analysis of F.
silvisoli. Strain RD-2-33
Thas been deposited in the Korean Agricultural Culture Collection (KACC, South Korea) and the
NITE Biological Resource Center (NBRC, Japan) as KACC 21178
Tand NBRC 113789
T, respectively.
For whole genomic analysis, F. silvisoli RD-2-33
Twas grown on R2A agar at 28°C for 3 days. Genomic DNA was extracted using DNeasy Blood and Tissue kits (Qiagen). The whole- genome shotgun sequencing of F. silvisoli was performed by Macrogen, using Illumina MiSeq platform. Thereafter, obtained sequence was assembled by A5-miseq. Annotation of genome was done using NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (https://www.ncbi.nlm.nih.gov/genome/annotation_prok/) (Tatusova et al., 2016) and the Rapid Annotations using Subsystems Technology (RAST) server (Aziz et al., 2008). In addition, circular genomic map of F. silvisoli RD-2-33
Twas constructed using CGView server (Grant and Stothard, 2008).
Whole-genome sequence of strain RD-2-33
Twas 2,894,048 bp long and was assembled in 39 contigs with an N50 value of 160,705 bp and genome coverage of 263.0x. The DNA G + C content was 38.6 mol%. The annotation result showed a total of 2,612 genes with 2,543 coding genes, 4 ncRNAs, and 21 pseudogenes (Table 1, Fig. 1).
The genome of F. silvisoli contained gene for antibiotic
biosynthesis monooxygenase and various hypothetical proteins.
Draft genome sequence of F. silvisoli RD-2-33
T∙ 87
Korean Journal of Microbiology, Vol. 56, No. 1 Fig. 1. Graphical circular genome map of Flavobacterium silvisoli RD-2-33
T. From outside to the center: Genes on forward strand, genes on reverse strand, RNA genes (tRNAs light green, rRNAs red, tmRNA blue), GC content, and GC skew.
Table 1. Genome features of Flavobacterium silvisoli RD-2-33
TAttribute Value
Genome size (bp) 2,894,048
DNA G + C content (mol%) 38.6
No. of contigs 39
No. of subsystems 231
N50 160,705
Genes (total) 2,612
CDSs (total) 2,564
Genes (coding) 2,543
CDSs (with protein) 2,543
Genes (RNA) 48
rRNAs (5S, 16S, 23S) 4, 2, 1
complete rRNAs (5S, 16S, 23S) 2, 1, 1
partial rRNAs (5S, 16S) 2, 1
tRNAs 37
ncRNAs 4
Pseudo Genes (total) 21
CDSs (without protein) 21
Pseudo Genes (ambiguous residues) 0 of 21
Pseudo Genes (frameshifted) 7 of 21
Pseudo Genes (incomplete) 9 of 21
Pseudo Genes (internal stop) 5 of 21
Genome coverage 263.0×
Several proteases genes such as ATP-dependent CIp proteases, RIP metalloprotease RSeP, tail-specific protease, acid protease, rhomboid family intramembrane serine proteases, zinc metallo- protease, and CPBP family intramembrane metalloprotease were detected. The genome had transporter related genes like ABC transporter ATP-binding proteins, efflux RND transporter periplasmic adaptor subunit, nicotinamide riboside transporter PnuC, DMT family transporters, cation transporter, MFS trans- porter, RND family transporters, efflux RND transporters, biopolymer transporter ExbD, metal transporter, urea transporter and so on. In addition, the genome contained gene for glycogen synthase, NAD(P)H-dependent glycerol-3-phosphate dehydro- genase, 1-acyl-sn-glycerol-3-phosphate acyltransferase, and diacylglycerol kinase family protein. The RAST server revealed the presence of 231 subsystem in the genome.
The analysis of secondary metabolite biosynthesis genes by
using antiSMASH (Blin et al., 2019) revealed, F. silvisoli
RD-2-33
Tcontained terpene and was most similar known
cluster of carotenoid with homology of 28%.
88 ∙ Dahal et al.
미생물학회지 제56권 제1호
Nucleotide sequence accession number
This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession number SJPE00000000.
The version described in this paper is version SJPE01000000.
적 요
이 연구에서는 경기대학교의 삼림토양에 대한 세균의 다양 성 연구 중에 분리된 Flavobacterium silvisoli RD-2-33
T의 게 놈 서열을 분석하였다. 이 게놈은 G + C 함량이 38.6%인 2,894,048 bp으로 구성되어 있고 2,612개의 유전자와 2,543개 의 단백질 코딩 유전자를 포함하고 있다.
Acknowledgments
This research was supported by Sangji University Research Fund, 2020.
References
