Complete Genome Sequence of Brucella Anthropi Strain T16R-87 Isolated from Tomato (Solanum Lycopersicum L.) Rhizosphere

Complete genome sequence of Brucella anthropi strain T16R-87 isolated from tomato (Solanum lycopersicum L.) rhizosphere

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

토마토 근권에서 분리된 Brucella anthropi T16R-87 균주의 유전체 염기서열

이신애 ･ 상미경 ･ 송재경 ･ 권순우 ･ 원항연* 국립농업과학원 농업생물부 농업미생물과

(Received November 9, 2020; Revised December 15, 2020; Accepted December 16, 2020)

Brucella anthropi strain T16R-87 was isolated from the rhizo- the root nodules of Lupinus honoratus and induces nodulation sphere of tomato plants. This bacterium showed plant growth- in lupinus plant, was reclassified as a heterotypic synonym of promoting activity under abiotic and biotic stress conditions, B. anthropi based on whole-genome sequences (Trujillo et al., including drought, salinity, and bacterial wilt disease. Its genome 2005; Gazolla Volpiano et al., 2019). Brucella anthropi strain consists of two circular chromosomes with 2,645,855 bp and T16R-87 was isolated from the rhizosphere of tomato plants 2,090,924 bp. The genomic G + C content was 55.96%. In total, the genome includes 4,501 genes, 12 rRNAs, and 59 tRNAs. cultivated in a greenhouse in Buyeo, Republic of Korea Genes related to antioxidant activity, proline and siderophore (36°17'36.34"N 126°55'54.19"E) (Lee et al., 2016). Strain biosynthesis, and phosphonate degradation, which may contribute T16R-87 conferred plant tolerance to salinity and drought to the promotion of plant growth under environmental stresses, stresses and enhanced the resistance to bacterial wilt disease were also found in the genome. caused by Ralstonia solanacearum (unpublished data). To Keywords: Brucella, abiotic stress, genome sequence, plant understand the molecular mechanisms of B. anthropi strain growth-promoting rhizobacteria T16R-87 beneficial functions for plant growth and health, we analyzed its whole-genome sequence. Strain T16R-87 was cultured on Reasoner’s 2A (R2A) agar Brucella anthropi was first described by Holmes et al. (1988) medium and its genomic DNA was extracted using a QIAamp as a species belonging to the novel genus Ochrobactrum within DNA mini kit (Qiagen), according to the manufacturer’s the family Brucellaceae. Recently, Hördt et al. (2020) proposed protocols. Whole-genome sequencing was performed using the the reclassification of Ochrobactrum to Brucella based on PacBio RSII and Illumina HiSeq platforms at Macrogen Inc. genome analysis of type strains. Brucella species have been The sequences generated by PacBio RSII were assembled de isolated from various sources, including soil, plants, rhizosphere, novo using RS HGAP assembly version 3.0 (Chin et al., 2013) industrial environments, animals, and humans (Hu et al., 2020). and HiSeq reads were subsequently used for error correction of T Among them, B. lupini strain LUP21 , which was isolated from the draft genome assemblies using Pilon version 1.21 (Walker et al., 2014). Gene prediction and functional annotations were *For correspondence. E-mail: [email protected]; Tel.: +82-63-238-3042; Fax: +82-63-238-3834 carried out using the NCBI Prokaryotic Genomes Annotation Complete genome sequence of Brucella anthropi T16R-87 ∙ 431

Table 1. Genome features of Brucella anthropi T16R-87

Genome feature Chromosome 1 Chromosome 2 Total Genome size (bp) 2,645,955 2,090,924 4,736,879 G + C content (%) 56.26 55.58 55.96 Total genes 2,575 1,926 4.501 tRNAs 42 17 59 rRNAs (5S, 16S, 23S) 6 (2, 2, 2) 6 (2, 2, 2) 12 (4, 4, 4) Pseudogenes 103 GenBank accession No. CP044970 CP044971

Pipeline (Tatusova et al., 2016) and Rapid Annotation Sub- beneficial effects of plant growth-promoting bacteria on plants system Technology (RAST server) (Aziz et al., 2008). Genes and may lead to the development of biotechnical applications involved in secondary metabolite production were analyzed in agriculture. using antiSMASH version 4.0.0 (Blin et al., 2017). The complete genome of the B. anthropi T16R-87 consists Nucleotide sequence accession numbers of two circular chromosomes with 2,645,855 and 2,090,924 bp, Brucella anthropi T16R-87 has been deposited in the Korean respectively. The secondary chromosome contains a repABC Agricultural Culture Collection under accession number KACC origin similar to the type strain B. anthropi ATCC 49188T. The 92178P and the complete genome sequence has been deposited G + C content of the strain T16R-87 is 55.96%. A total of 4,501 in NCBI under the GenBank accession numbers CP044970 and genes, 12 rRNAs (4 each of 5S, 16S, and 23S rRNAs), 59 CP044971. tRNAs, 4 ncRNAs, and 102 pseudogenes were predicted (Table 1). This genome possesses four genes encoding antioxidant enzymes, including superoxide dismutase (SOD) and catalase 적 요 (CAT), which can reduce reactive oxygen species (ROS) that are produced under various stress conditions and cause cell 토마토 근권에서 분리한 Brucella anthropi T16R-87 균주 damage. The gene cluster phnGHJKL, related to a carbon- 는 가뭄과 고염 등의 환경 스트레스 조건에서 토마토 생육을 phosphorus (C-P) lyase was identified in the T16R-87 genome. 촉진시키고, 풋마름병에 대한 저항성을 나타내었다. 이 균주 C-P lyase degrades phosphonate into phosphate and alkane, 는 2,645,855 bp와 2,090,924 bp 크기의 2개의 원형 염색체로 increasing biologically available phosphate for plants (Shariati 구성되어 있으며, G + C 함량은 55.96%이다. 유전체는 4,501 et al., 2017). Moreover, strain T16R-87 contains three genes 개 유전자를 포함하고 있으며 항산화 활성, 프롤린 생합성, 유 involved in proline biosynthesis (proA, proB, and proC), 기인 분해, 시드로포어 생성 등에 관여하는 유전자를 확인하 suggesting that proline, an effective osmolyte, may protect 였다. 이들 유전자는 식물 생육 촉진과 관련되어 있을 것으로 plants from abiotic stresses, such as drought, salinity, and 판단된다. extreme temperatures (Ashraf and Foolad, 2007). Based on antiSMASH analyses, seven gene clusters related to the biosynthesis of secondary metabolites, including terpenes, arylpolyenes, Acknowledgments β-lactones, acyl amino acids, N-acetylglutaminylglutamine amide, ectoine, and a siderophore, were predicted. The siderophore This study was carried out with the support of “Research identified in the T16R-87 genome was ochrobactin, which may act Program for Agricultural Science & Technology Development as a biocontrol agent in plants by reducing the iron availability (Project No. PJ01351901)” from the National Institute of for phytopathogens (Ahmed and Holmstrom, 2014). Agricultural Sciences, Rural Development Administration, In conclusion, the genome sequence of T16R-87 provides Republic of Korea. information on the molecular mechanisms underlying the

Korean Journal of Microbiology, Vol. 56, No. 4 432 ∙ Lee et al.

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