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Draft genome sequence of Flexivirga aerilata ID2601ST isolated from automobile air conditioning system
Korean J. Microbiol. 2021;57(4):300-302
Published online December 31, 2021
© 2021 The Microbiological Society of Korea.

So-Yi Chea1, Ji Yeon Han1, Jae-Hyung Ahn2, and Dong-Uk Kim1*

1Department of Biological Science, College of Life and Environment, Sangji University, Wonju 26339, Republic of Korea
2Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea
Correspondence to: E-mail: dukim@sangji.ac.kr;
Tel.: +82-33-730-0403; Fax: +82-33-730-0433
Received November 15, 2021; Revised December 21, 2021; Accepted December 22, 2021.
Abstract
A Gram-staining-positive, aerobic bacterium, non-motile, nearly- coccoid strain, designated ID2601ST, was isolated from the surface of the climatronic evaporator core, which is in the automobile. The strain ID2601ST grow optimally at 35°C, pH 7.0 and without NaCl. In this study, we report the draft genome sequence of a Flexivirga aerilata ID2601ST obtained using the Illumina MiSeq platform. The genome comprised of 4,007,297 bp which was assembled in 6 contigs. The N50 value of strain ID2601ST was 2,524,017 bp with genome coverage of 258.07 X. The G + C content of 69.8%, the genome included 3,784 genes were predicted, among them, 3,673 genes are protein-coding genes. Also, the genome of F. aerilata (= KCTC 49353T = NBRC 114622T) contained genes encoding enzymes necessary for phenylalanine, tyrosine, and tryptophan biosynthesis. Moreover, the gene encoding dTDP-4-dehydrorhamnose 3,5- epimerase, which synthesizes the antibiotic streptomycin, was found.
Keywords : Flexivirga aerilata, car evaporator core, draft genome, Illumina MiSeq
Body

The genus Flexivirga in the family Dermacoccaceae was proposed in 2011 (Anzai et al., 2011). Flexivirga has been isolated from a variety of sources, ranging from bird feces and plant leaves to environments containing activated sludge and around wastewater treatment facilities (Anzai et al., 2011; Gao et al., 2016; Kang et al., 2016; Keum et al., 2020). Flexivirga aerilata is an aerobic, Gram-positive, and nearly coccoid strain, which is nonspore-forming and nonmotile. The catalase test was positive, but the oxidase test was negative. The colony morphology was light yellow in color, smooth, and opaque, with a convex entire margin (Chaudhary et al., 2021). Peptidoglycans of the cell wall contained alanine, glutamic acid, glycine, serine, and lysine. Flexivirga aerilata ID2601ST is grown optimally on R2A medium at 35°C and pH 7.0 (Chaudhary et al., 2021). It was also confirmed by the salt tolerance test that it is grown optimally without NaCl.

A genomic library was prepared using the TruSeq Nano DNA kit and qPCR according to the Illumina qPCR Quantification Protocol Guide. Whole-genome shotgun sequencing of F. aerilata was performed using an Illumina MiSeq platform by Macrogen. The de novo assembly of reads was performed using SPAdes version 3.14.0, after which the entire 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). The total number of sequenced bases of ID2601ST was 1,243,838,554 bp, and following sequence assembly, it was finally determined to be 4,007,297 bp. The GC content of the genome was 69.79%, and a total of 3,784 genes, consisting of 3,673 protein-coding genes, 3 rRNAs, 48 tRNAs, and 53 pseudogenes, were predicted (Table 1).

Genome features of Flexivirga aerilata ID2601ST

Attribute Value
Genome size (bp) 4,007,297
GC content (mol%) 69.79
No. of contigs 6
N50 2,524,017
Protein-coding genes 3,673
CDSs (total) 3,726
Genes (RNA) 58
rRNAs 2, 3, 2 (5S, 16S, 23S)
tRNAs 48
ncRNAs 3
Pseudo genes (total) 53
CDSs (without protein) 53
Genome coverage (X) 258.07


Flexivirga aerilata contained coding sequences for proteins related to the Ars-R/SmtB family of transcription factors (HJ588_10330), which are metal regulators regulating metal efflux and detoxification mechanisms. The gene encoding 4-hydroxyphenylpyruvate dioxygenase (HJ588_13480), which is the Fe(II)-dependent, nonheme oxygenase that catalyzes the second step of tyrosine catabolism, was identified in the genome. In addition, a gene that encodes phytoene dehydrogenase, which is essential for the enzymatic degradation of 1,1'-(2,2,2-trichloroethane-1,1-diyl)bis(4-chlorobenzene) (DDT) was found. The genome also contained genes encoding enzymes necessary for phenylalanine, tyrosine, and tryptophan biosynthesis, such as histidinol-phosphate aminotransferase, chorismate synthase, indole-3-glycerol phosphate synthase, tryptophan synthase beta chain, 3-phosphoshikimate 1-carboxyvinyltransferase, and arogenate dehydrogenase. Interestingly, the gene encoding dTDP-4-dehydrorhamnose 3,5-epimerase (HJ588_04560), which synthesizes the antibiotic streptomycin, was found. Furthermore, gene annotation using the RAST server identified the presence of 283 subsystems of the F. aerilata genome. Information on genome annotations is available at the Pathosystems Resource Integration Center (PATRIC) (Davis et al., 2020).

This is the first published genome sequence of F. aerilata. This high-quality sequence information will provide a better understanding of the genome diversity of F. aerilata strains.

Nucleotide sequence accession number

Flexivirga aerilata ID2601ST was deposited in the Korean Collection for Type Cultures (= KCTC 49353T) and whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession number KP326340. The version described in this paper is version JABENB010000000.

적 요

ID2601ST로 명명된 균주는 그람 염색 양성 호기성 세균으로 비운동성으로 구균에 가까운 형태를 나타내며 자동차공조시스템의 증발기 표면에서 분리되었으며 해당 균주는 35°C, pH 7.0, NaCl이 없는 곳에서 최적으로 성장한다. 이번 연구에서 Illumina MiSeq 플랫폼을 사용하여 얻은 박테리아 Flexivirga aerilata ID2601ST의 유전체 염기서열을 보고한다. 해당 균주의 유전체는 6개의 contig로 구성된 4,007,297 bp의 크기를 가지며 N50 값은 2,524,017 bp로 258.07 X의 배율로 분석되었다. G + C 함량은 69.8%로 3,784개의 유전자를 포함하는 게놈이 예측되었으며, 이 중 3,673개의 유전자가 단백질 코딩 유전자로 예상된다. 또한, F. aerilata (= KCTC 49353T = NBRC 114622T)의 유전체는 페닐 알라닌, 티로신 및 트립토판 생합성에 필요한 효소를 코팅하는 유전자를 포함한다. 뿐만 아니라 항생제 스트렙토마이신을 합성하는 dTDP-4-dehydrorhamnose 3,5-epimerase를 코딩하는 유전자를 암호화한다.

Acknowledgments

This work was supported by Sangji University Research Fund and Rural Development Administration (Project No. PJ014897032020).

Conflict of Interest

The authors have no conflict of interest to report.

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