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Complete genome sequence of Labrys sp. KNU-23 isolated from ginseng soil in the Republic of Korea
Korean J. Microbiol. 2020;56(4):410-412
Published online December 31, 2020
© 2020 The Microbiological Society of Korea.

Min-Ji Kim1, Yeong-Jun Park1, Min-Kyu Park1, Chang Eon Park1,2, YoungJae Jo1, Setu Bazie Tagele1, and Jae-Ho Shin1,3*

1Department of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
2Insitute of Ornithology, Association of Ex-situ Conservation, Daegu 41566, Republic of Korea
3Department of Integrative Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea
Correspondence to: E-mail: jhshin@knu.ac.kr;
Tel.: +82-53-950-5716; Fax: +82-53-953-7233
Received October 8, 2020; Revised November 12, 2020; Accepted November 12, 2020.
Abstract
Labrys sp. KNU-23 is a Gram-negative, aerobic, rod-shaped, tryptophan-producing, urea-decomposing bacterium that was isolated from ginseng soil in Bonghwa-gun, Republic of Korea. This study reports the complete genome sequence of strain KNU-23. The complete genome comprises two circular chromosomes of 5,388,854 bp and 2,162,438 bp with a GC content of 64 and 62.1%, respectively. The whole genome was predicted to have 6,868 protein coding genes. In addition, ureadecomposing and tryptophan-producing genes that are associated with plant growth-promoting activity were identified. Therefore, Labrys sp. KNU-23 is likely to be an agriculturally useful strain.
Keywords : Labrys sp., tryptophan, urease
Body

Labrys species are Gram-negative, aerobic capsulated, non-motile, non-sporulating, and morphologically different bacteria (Nguyen et al., 2015). Some members of the genus Labrys have previously been isolated from rhizospheric ecosystem (Chou et al., 2007; Nguyen et al., 2015). Labrys sp. has been reported to have potential plant growth-promoting activity (Visioli et al., 2018). In this study, Labrys sp. KNU-23 was isolated from ginseng soil in Bonghwa-gun, Republic of Korea (N 37.0036.8°, E 128.4950.9°).

A single colony of this strain was inoculated in R2A medium and incubated at 30°C for 24 h at 200 rpm. Subsequently, manual extraction of genomic DNA was performed (Sambrook et al., 1989). Quantity and quality of the extracted DNA was analyzed using a Qubit 3.0 fluorometer (Thermo Fisher Scientific) and a Nanodrop One spectrophotometer (Thermo Fisher Scientific), respectively. Whole-genome sequencing was performed using the PacBio RSII system (Park et al., 2019) at Macrogen Inc.. In addition, the genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (Tatusova et al., 2016) and the Rapid Annotations using Subsystem Technology server (Aziz et al., 2008).

The 16S rRNA sequence of strain KNU-23 was compared with 16S rRNA sequences available by the BLAST search (Fig. 1). The total number of subreads from the raw sequencing reads following adapter removal was 9,841 with a mean length of 7,258 bp. De novo assembly of the subreads was conducted using the HGAP 4.0 program (Chin et al., 2013). The complete genome of strain KNU-23 was deposited in GenBank under accession numbers CP043488.1 and CP043489.1. The genome comprised two chromosomes, one 5,388,854 bp in length and the other 2,162,438 bp in length. A total of 6,868 genes were predicted, and 64 RNA genes (9 rRNAs and 51 tRNAs) were identified (Table 1).

Genome features of Labrys sp. KNU-23 chromosomes

Genome feature Chromosome 1 Chromosome 2
Genome size (bp) 5,388,854 2,162,438
GC content (%) 63.96 62.13
Total number of genes 4,945 1,923
Number of protein-coding genes 4,803 1,911
rRNA 3 6
tRNA 45 6


Fig. 1. Phylogenetic tree based on 16S rRNA sequences of Labrys species and strain KNU-23.

The genome contains several coding genes related to plant growth-promoting activity, such as tryptophan and urease biosynthesis which are the important features as plant growth promoting bacteria (Ibal et al., 2018). The strain KNU-23 has the ability to catalyze the hydrolysis of urea into ammonia because ureA, ureB, and ureC genes were found in the genome, which encode the quaternary structured urease (Table 2). Furthermore, the genome contains trpA, trpB, trpC, and trpD, which encode subunits of tryptophan synthase and anthranilate phosphoribosyltransferase, which are related to tryptophan synthesis (Table 2). These findings indicate that the strain KNU-23 can synthesize tryptophan as a precursor of auxin for plant growth hormone (Spaepen et al., 2011). These findings indicate that Labrys sp. KNU-23 is a highly potent bacterial strain for agricultural purposes.

The list of plant growth promoting genes in the genome of Labrys sp. KNU-23

Gene Size (bp) Protein Locus-tag
ureA 302 Urease subunit gamma FZC33_06640

ureB 695 Urease subunit beta FZC33_01610

ureC 1,706 Urease subunit alpha FZC33_01615
305 FZC33_05455

trpA 827 Tryptophan synthase subunit alpha FZC33_24525

trpB 1,217 Tryptophan synthase subunit beta FZC33_24530

trpC 803 Indole-3-glycerol phosphate synthase FZC33_10995

trpD 1,010 Anthranilate phosphoribosyltransferase FZC33_10990


Nucleotide sequence data and strain accession number

The complete genome sequence was deposited in GenBank under accession numbers CP043488.1 and CP043489.1. The strain is available in Korean Collection for Type Cultures under the accession number KCTC 13849BP.

적 요

한국 봉화의 인삼 경작지에서 분리된 Labrys sp. KNU-23 균주는 그람 음성의 호기성 균이며, 우레아 분해 및 트립토판 생합성능을 가지고 있다. 이 균주의 유전체는 두 개의 원형 chromosome으로 이루어져 있었다. 각각의 chromosome은 64.0%와 62.1%의 GC 비율을 가지며, 길이는 5,388,854 bp와 2,162,438 bp인 것으로 확인되었다. 이 균주의 유전체에는 총 6,868개의 단백질 코딩 유전자가 있는 것으로 예측되었다. 또한 식물 생장 촉진 활성과 관련된 우레아 분해 및 트립토판 생산 관련 유전자가 있었다. 따라서 인삼 경작지에서 분리된 Labrys sp. KNU-23 균주는 농업 유용 미생물로서 활용 가능성이 있다.

Acknowledgments

This work was carried out with the support of “Cooperative Research Program for Agriculture Science and Technology Development (Project No. PJ013383)” Rural Development Administration, Republic of Korea.

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