Korean Journal of Microbiology (2020) Vol. 56, No. 1, pp. 89-91 pISSN 0440-2413
DOI https://doi.org/10.7845/kjm.2020.9077 eISSN 2383-9902
Copyright ⓒ 2020, The Microbiological Society of Korea
Draft genome sequence of Glaciihabitans arcticus RP-3-7 T isolated from Arctic 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
극지에서 분리된 박테리아 Glaciihabitans arcticus RP-3-7 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 18, 2020; Accepted March 6, 2020)
*For correspondence. E-mail: [email protected];
Tel.: +82-33-730-0403; Fax: +82-33-730-0433
Glaciihabitans arcticus RP-3-7
Twas originally isolated from soil of the Arctic region in Cambridge Bay, NU, Canada. In this study, we report the draft genome sequence of a bacterium Glaciihabitans arcticus RP-3-7
Tobtained using the Illumina HiSeq platform. The genome comprised of 3,172,742 bp with the G + C content of 66.9%, the genome included 3,068 genes among them, 2,984 genes are protein-coding genes.
Keywords: Glaciihabitans arcticus, Arctic soil, draft genome, Illumina HiSeq, psychrotolerant
Glaciihabitans arcticus is a strictly aerobic, rod-shaped, Gram-positive strain, non-spore-forming, oxidase and catalase positive bacterium. Colonies on R2A (Reasoner’s 2A) agar are pale yellow-coloured, entire, convex, and circular (Dahal and Kim, 2019). The diagnostic diamino acid of the cell-wall peptidoglycan is DAB (2, 4-diaminobutyric acid). G. arcticus RP-3-7
Tis a psychrotolerant bacterium that optimally grow at 15–20°C (Dahal and Kim, 2019).
Genomic DNA was extracted using DNeasy Blood and Tissue kits (Qiagen). Whole-genome shotgun sequencing of G.
arcticus was performed by Macrogen, using Illumina HiSeq platform. Obtained sequence was assembled by A5-miseq.
After analysis, whole genome sequence was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (Tatusova et al., 2016) and the Rapid Annotations using Subsystems Technology (RAST) server (Aziz et al., 2008).
Furthermore, circular genomic feature map was constructed using CGView server (Grant and Stothard, 2008). The whole genome sequence of strain RP-3-7
Twas 3,172,742 bp long with 2 contigs with an N50 value of 2,926,791 bp and the genome coverage of 233.0x. The G + C content of the genome was 66.9 mol%. A total of 3,068 genes, 2,984 protein-coding genes, 3 rRNAs, 46 tRNAs, and 32 pseudogenes were predicted (Table 1 and Fig. 1).
G. arcticus genome contained CDSs (coding sequences) for
proteins that are known to be associated with adaptation to cold
temperatures cold-shock proteins CspA and CspC (accessions,
TBN56659 and TBN57591). Carbon storage related genes
glycogen debranching enzyme (glgX) and glycogen synthase
were also found in the genome. In addition, cell wall/membrane
alternation related gene 3-oxoacyl-[acyl-carrier-protein] reductase
was detected in the genome. These genes help to adapt the
90 ∙ Dahal et al.
미생물학회지 제56권 제1호
Table 1. Genome features of Glaciihabitans arcticus RP-3-7
TAttribute Value
Genome size (bp) 3,172,742
GC content (mol%) 66.9
No. of contigs 2
N50 2,926,791
No. of proteins 2984
Total genes 3,068
CDSs (total) 3,016
Protein-coding genes 2,984
Genes (RNA) 52
Complete rRNAs (5S, 16S, 23S) 3 (1, 1, 1)
tRNAs 46
ncRNAs 3
Pseudo Genes (total) 32
CDSs (without protein) 32
Genome coverage 233.0×
Fig. 1. Graphical circular genome map of Glaciihabitans arcticus RP-3-7
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.
microorganism in cold environment (Goordial et al., 2015). The genome also contained antibiotic biosynthesis monooxygenase genes and several proteases genes such as trypsin-like serine protease, RIP metalloprotease, zinc-dependent metalloprotease, serine protease, CPBP family intramembrane metalloproteases, rhomboid family intramembrane serine proteases, and ATP- dependent CIp proteases and so on. The genome contained multidrug efflux SMR transporter, multidrug DMT transporter permease, and multidrug ABC transporter ATPase related genes. Gene annotation by the RAST server identified the presence of 263 subsystems for the G. arcticus genome.
The annotation and analysis of secondary metabolite bio- synthesis genes by using antiSMASH (Blin et al., 2019) revealed, G. arcticus contains betalactone, NRPS-like, terpene, and T3PKS most similar known cluster of alkylresorcinol.
This is the first genome sequence of G. arcticus and this
Draft genome sequence of G. arcticus RP-3-7
T∙ 91
Korean Journal of Microbiology, Vol. 56, No. 1 sequence information will provide the understanding of genome
diversity of G. arcticus strains and also help to understand the cold adaption by psychrotolerant species.
Nucleotide sequence accession number
This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession number SISG00000000.
The version described in this paper is version SISG01000000.
적 요
이 연구에서는 캐나다의 극지환경에서 분리된 저온내성균 Glaciihabitans arcticus RP-3-7
T의 게놈 서열을 분석하였다.
이 게놈은 G + C 함량이 66.9%인 3,172,742 bp으로 구성되어 있고 3,068개의 유전자와 2,984개의 단백질 코딩 유전자를 포 함하고 있다.
Acknowledgments
This research was supported by Sangji University Research Fund, 2020.
References
