Complete Genome Sequence of Plant Growth-Promoting Bacterium Pedobacter Ginsengisoli T01R-27 Isolated from Tomato (Solanum Lycopersicum L.) Rhizosphere

Complete genome sequence of plant growth-promoting bacterium Pedobacter ginsengisoli T01R-27 isolated from tomato (Solanum lycopersicum L.) rhizosphere

Shin Ae Lee, Hyeon Su Kim, Tae-Wan Kim, Mee Kyung Sang, Jaekyeong Song, and Hang-Yeon Weon* Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju 55365, Republic of Korea

토마토 근권에서 분리한 식물생육촉진 세균 Pedobacter ginsengisoli T01R-27 균주의 유전체 염기서열

이신애 ･ 김현수 ･ 김태완 ･ 상미경 ･ 송재경 ･ 원항연* 국립농업과학원 농업생물부 농업미생물과

(Received September 25, 2019, Revised November 1, 2019; Accepted November 4, 2019)

Pedobacter ginsengisoli strain T01R-27 was isolated from the from soil and various other environments such as water, lake rhizosphere of tomato plants in Korea. The bacteria showed sediment, glacier, and wood (Yuan et al., 2018). Although plant growth promoting activity under abiotic stress condi- Pedobacter was found to be highly abundant in the rhizosphere tions, including salinity, heat, and cold. The genome of the (the soil region associated with plant roots) and endosphere strain consists of a circular chromosome with 5,373,360 bp (inside plant tissue) of wheat and grass plants have been with G + C content of 37.82%. The genome includes 4,399 coding genes, 16 rRNAs, and 53 tRNAs. Genes related to root reported (Yin et al., 2013; Wemheuer et al., 2017), its bene- colonization, antioxidant activity, proline biosynthesis, and ficial functions for plant growth and the underlying molecular phytohormone modulations were found in the genome, which mechanisms are largely unknown. may contribute to the promotion of plant growth under en- Strain T01R-27 was isolated from the rhizosphere of tomato vironmental stresses. plants cultivated in a greenhouse in Jeju, Korea (33.459765 N Keywords: Pedobacter, abiotic stress, genome sequence, plant 126.363764 E). It is closely related to Pedobacter ginsengisoli T growth-promoting bacteria strain Gsoli 104 , with 98.31% 16S rRNA gene sequence similarity. We tested its beneficial effect on plant growth under abiotic stress conditions and observed that strain T01R-27 The genus Pedobacter, which belongs to the family Sphingo- conferred plant tolerance under high osmotic stress and both bacteriaceae, was first described by Steyn et al. (1998) with the low (10°C) and high (40°C) temperatures. following general characteristics: Gram-negative rods, strictly Strain T01R-27 was cultured on Reasoner’s 2A (R2A) agar aerobic, non-motile, and non-spore forming (Steyn et al., medium and the genomic DNA was extracted using a QIAamp 1998). To date, Pedobacter species have mainly been isolated DNA mini kit (Qiagen), according to the manufacturer’s protocols. Whole-genome sequencing was carried out using *For correspondence. E-mail: [email protected]; Tel.: +82-63-238-3042; Fax: +82-63-238-3834 the Pacific Biosciences (PacBio) RSII single-molecule real- 426 ∙ Lee et al.

TM time (SMRT) sequencing platform with a 20 kb SMRTbell extreme temperatures. This study provides basic information to template at ChunLab Inc. All generated reads were assembled reveal the additional molecular mechanisms underlying the de novo using FALCON version 2.3.0 (Chin et al., 2016). Gene beneficial effect of T01R-27 on plants. prediction and functional annotations were carried out using the NCBI Prokaryotic Genomes Annotation Pipeline (Tatusova Nucleotide sequence accession numbers et al., 2016) and the Rapid Annotation Subsystem Technology Pedobacter ginsengisoli T01R-27 has been deposited in the (RAST server) (Aziz et al., 2008). Korean Agricultural Culture Collection under accession num- The complete genome of the P. ginsengisoli T01R-27 ber KACC 92177P and the complete genome sequence has consists of a 5,373,360 bp circular chromosome with G + C been deposited in NCBI under the GenBank accession number content of 37.82%. A total of 4,399 coding sequences, 16 rRNAs, CP024091. 53 tRNAs, 3 ncRNAs, and 77 pseudogenes were predicted (Table 1). The genome of P. ginsengisoli T01R-27 possesses 11 gld genes (gldA, gldB, gldD, gldF, gldG, gldH, gldJ, gldK, 적 요 gldL, gldM, and gldN) that are associated with gliding motility and genes encoding plant cell-wall degrading enzymes, such as 토마토 근권에서 분리한 Pedobacter ginsengisoli T01R-27 pectate lyase, xylanase, and glucanase, that may help bacteria 균주는 고온, 저온, 고염류와 같은 환경 스트레스 조건에서 토마 penetrate into plant tissue by degrading the plant cell-wall 토 생육을 촉진시키는 효과를 나타내었다. 이 균주는 5,373,360 components. Strain T01R-27 contains genes NhaA and Kup bp 크기의 원형 염색체로 구성되어 있으며, G + C 함량은 + + that encode the Na /H antiporter and potassium transporter 37.82%이다. 유전체에는 4,399개 단백질 유전자가 있었고, 뿌 + + that are responsible for pumping out Na and K , respectively, 리 정착, 항산화 활성, 프롤린 생합성, 식물호르몬 조절 등에 관 in the cell. We also found 6 genes encoding antioxidant enzymes 여하는 유전자를 포함하고 있었다. 이들 유전자는 식물생육촉 including superoxide dismutase (SOD), catalase (CAT), and 진 기작과 관련되어 있을 것으로 판단된다. peroxidase (PRX). The enzymes can reduce reactive oxygen species (ROS) that are produced under various stress conditions and result in significant cell damage. The gene encoding Acknowledgements 1-aminocyclopropane-1-carboxylate (ACC) deaminase was detected in the genome, which is a well-known enzyme involed This study was made possible by the support of “Cooperative in plant growth promotion activity by modulating a phyto- Research Program for Agricultural Science & Technology hormone, ethylene. We found three genes involved in proline Development (Project No. PJ01093903)”, Rural Development biosynthesis (proA, proB, and proC) in the T01R-27 genome, Administration, Republic of Korea. suggesting that the proline, an effective osmolyte, may protect plants from abiotic stresses such as drought, salinity, and References

Table 1. Genome features of Pedobacter ginsengisoli T01R-27 Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, et al. 2008. The Genome feature Value RAST server: rapid annotations using subsystems technology. Genome size (bp) 5,373,360 BMC Genomics 9, 75. Number of contigs 1 Chin CS, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT, Clum G + C content (%) 37.82 A, Dunn C, O'Malley R, Figueroa-Balderas R, Morales-Cruz A, Protein-coding genes 4,399 et al. 2016. Phased diploid genome assembly with single- – tRNAs 53 molecule real-time sequencing. Nat. Methods 13, 1050 1054. Steyn PL, Segers P, Vancanneyt M, Sandra P, Kersters K, and Joubert rRNAs (5S, 16S, 23S) 16 (6, 5, 5) JJ. 1998. Classification of heparinolytic bacteria into a new genus, Pseudogenes 77

미생물학회지 제55권 제4호 Complete genome sequence of P. ginsengisoli T01R-27 ∙ 427

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Korean Journal of Microbiology, Vol. 55, No. 4