Complete Genome Sequence of Labrys Sp. KNU-23 Isolated from Ginseng Soil in the Republic of Korea

Complete genome sequence of Labrys sp. KNU-23 isolated from ginseng soil in the Republic 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

한국의 인삼 토양에서 분리한 Labrys sp. KNU-23의 완전 해독된 게놈 서열

김민지1 ･ 박영준1 ･ 박민규1 ･ 박창언1,2 ･ 조영재1 ･ 세투 바지에 태글1 ･ 신재호1,3* 1경북대학교 응용생명과학과, 2경북대학교 조류생태환경연구소, 3경북대학교 농생명융합공학과

(Received October 8, 2020; Revised November 12, 2020; Accepted November 12, 2020)

Labrys sp. KNU-23 is a Gram-negative, aerobic, rod-shaped, have potential plant growth-promoting activity (Visioli et al., tryptophan-producing, urea-decomposing bacterium that was 2018). In this study, Labrys sp. KNU-23 was isolated from gin- isolated from ginseng soil in Bonghwa-gun, Republic of Korea. seng soil in Bonghwa-gun, Republic of Korea (N 37.0036.8°, This study reports the complete genome sequence of strain E 128.4950.9°). KNU-23. The complete genome comprises two circular chro- A single colony of this strain was inoculated in R2A medium mosomes of 5,388,854 bp and 2,162,438 bp with a GC content of 64 and 62.1%, respectively. The whole genome was pre- and incubated at 30°C for 24 h at 200 rpm. Subsequently, dicted to have 6,868 protein coding genes. In addition, urea- manual extraction of genomic DNA was performed (Sambrook decomposing and tryptophan-producing genes that are associated et al., 1989). Quantity and quality of the extracted DNA was with plant growth-promoting activity were identified. There- analyzed using a Qubit 3.0 fluorometer (Thermo Fisher fore, Labrys sp. KNU-23 is likely to be an agriculturally useful Scientific) and a Nanodrop One spectrophotometer (Thermo strain. Fisher Scientific), respectively. Whole-genome sequencing Keywords: Labrys sp., tryptophan, urease 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) Labrys species are Gram-negative, aerobic capsulated, non- (Tatusova et al., 2016) and the Rapid Annotations using Sub- motile, non-sporulating, and morphologically different bacteria system Technology server (Aziz et al., 2008). (Nguyen et al., 2015). Some members of the genus Labrys have The 16S rRNA sequence of strain KNU-23 was compared previously been isolated from rhizospheric ecosystem (Chou et with 16S rRNA sequences available by the BLAST search (Fig. al., 2007; Nguyen et al., 2015). Labrys sp. has been reported to 1). The total number of subreads from the raw sequencing reads following adapter removal was 9,841 with a mean length of *For correspondence. E-mail: [email protected]; 7,258 bp. De novo assembly of the subreads was conducted Tel.: +82-53-950-5716; Fax: +82-53-953-7233 Complete genome sequence of Labrys sp. KNU-23 ∙ 411

Fig 1. Phylogenetic tree based on 16S rRNA sequences of Labrys species and strain KNU-23. using the HGAP 4.0 program (Chin et al., 2013). The complete because ureA, ureB, and ureC genes were found in the genome, genome of strain KNU-23 was deposited in GenBank under which encode the quaternary structured urease (Table 2). accession numbers CP043488.1 and CP043489.1. The genome Furthermore, the genome contains trpA, trpB, trpC, and trpD, comprised two chromosomes, one 5,388,854 bp in length and which encode subunits of tryptophan synthase and anthranilate the other 2,162,438 bp in length. A total of 6,868 genes were phosphoribosyltransferase, which are related to tryptophan predicted, and 64 RNA genes (9 rRNAs and 51 tRNAs) were synthesis (Table 2). These findings indicate that the strain identified (Table 1). KNU-23 can synthesize tryptophan as a precursor of auxin for The genome contains several coding genes related to plant plant growth hormone (Spaepen et al., 2011). These findings growth-promoting activity, such as tryptophan and urease indicate that Labrys sp. KNU-23 is a highly potent bacterial biosynthesis which are the important features as plant growth strain for agricultural purposes. promoting bacteria (Ibal et al., 2018). The strain KNU-23 has the ability to catalyze the hydrolysis of urea into ammonia Nucleotide sequence data and strain accession number

The complete genome sequence was deposited in GenBank Table 1. Genome features of Labrys sp. KNU-23 chromosomes under accession numbers CP043488.1 and CP043489.1. The Genome feature Chromosome 1 Chromosome 2 strain is available in Korean Collection for Type Cultures under Genome size (bp) 5,388,854 2,162,438 the accession number KCTC 13849BP. GC content (%) 63.96 62.13 Total number of genes 4,945 1,923 Number of 4,803 1,911 protein-coding genes 적 요 rRNA 36 tRNA 45 6 한국 봉화의 인삼 경작지에서 분리된 Labrys sp. KNU-23 균주는 그람 음성의 호기성 균이며, 우레아 분해 및 트립토판 Table 2. The list of plant growth promoting genes in the genome of Labrys 생합성능을 가지고 있다. 이 균주의 유전체는 두 개의 원형 sp. KNU-23 chromosome으로 이루어져 있었다. 각각의 chromosome은 Gene Size (bp) Protein Locus-tag 64.0%와 62.1%의 GC 비율을 가지며, 길이는 5,388,854 bp와 ureA 302 Urease subunit gamma FZC33_06640 2,162,438 bp인 것으로 확인되었다. 이 균주의 유전체에는 총 ureB 695 Urease subunit beta FZC33_01610 6,868개의 단백질 코딩 유전자가 있는 것으로 예측되었다. 또 1,706 FZC33_01615 ureC Urease subunit alpha 한 식물 생장 촉진 활성과 관련된 우레아 분해 및 트립토판 생 305 FZC33_05455 trpA 827 Tryptophan synthase subunit alpha FZC33_24525 산 관련 유전자가 있었다. 따라서 인삼 경작지에서 분리된 trpB 1,217 Tryptophan synthase subunit beta FZC33_24530 Labrys sp. KNU-23 균주는 농업 유용 미생물로서 활용 가능성 trpC 803 Indole-3-glycerol phosphate synthase FZC33_10995 이 있다. trpD 1,010 Anthranilate phosphoribosyltransferase FZC33_10990

Korean Journal of Microbiology, Vol. 56, No. 4 412 ∙ Kim et al.

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