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Complete genome sequence of Variovorax sp. PMC12, a plant growth-promoting bacterium conferring multiple stress resistance in plants
Korean J. Microbiol 2018;54(4):471-473
Published online December 31, 2018
© 2018 The Microbiological Society of Korea.

Shin Ae Lee, Hyeon Su Kim, Yiseul 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
Correspondence to: E-mail: why@korea.kr; Tel.: +82-63-238-3042; Fax: +82-63-238-3834
Received October 22, 2018; Revised December 9, 2018; Accepted December 10, 2018.
Abstract

Variovorax sp. PMC12 is a rhizobacterium isolated from tomato rhizosphere and enhanced the plant resistance to abiotic and biotic stresses. Here we present the complete genome sequence of strain PMC12. The genome is comprised of two circular chromosomes harboring 5,873,297 bp and 1,141,940 bp, respectively. A total of 6,436 protein-coding genes, 9 rRNAs, 64 tRNAs, 3 ncRNAs, and 80 pseudogenes were identified. We found genes involved in 1-aminocyclopropane-1-carboxylate (ACC) deaminase, antioxidant activity, phosphate solubilization, and biosynthesis of proline and siderophore. Those genes may be related to capability of improving plant resistance to various stresses including salinity, cold temperature, and phytopathogen.

Keywords : Variovorax, plant growth-promoting rhizobacteria, plant stress
Body
embers of Variovorax are a Gram-nagative bacteria belonging to the family Comamonadaceae, the class Betaproteobacteria (Willems et al., 1991). They were initially isolated from contaminated soil and tolerate to various metals including Cd, Co, Cu, Ni, and Zn and capable of degrading a wide range of substrates (Willems et al., 1991; Belimov et al., 2005; Satola et al., 2013). In addition, some strains of Variovorax inhabit interior and exterior of plant roots and confer beneficial effect on plant growth (Han et al., 2011). It has been reported that V. paradoxus 5C-2 with 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity enhanced plant growth in arid soil (Belimov et al., 2009) and V. paradoxus S110 isolated form potato plant has been well studied its metabolic diversity and various properties associated with host plants (Han et al., 2011). In the previous study, strain PMC12 was isolated from tomato rhizosphere and exhibited potential for application as biostimulant and biocontrol agent; promoting tomato (Solanum lycopersicum L.) plant growth in abiotic stress conditions such as salinity and low temperature (10°C) and enhancing the resistance to bacterial wilt disease caused by Ralstonia solanacearum (Kim et al., 2018). To gain better knowledge about molecular mechanisms of Variovorax, we carried out complete genome sequencing of strain PMC12 and found out genes that are predicted to be involved in plant growth promotion under abiotic and biotic stress conditions.

The genome of strain PMC12 was sequenced using the PacBio RSII and Illumina HiSeq platforms at Microgen Inc. The sequences generated by PacBio RSII were assembled de novo using RSHGAP assembly version 3.0 (Chin et al., 2013) and HiSeq reads were subsequently used for error correction of the draft genome assemblies by using Pilon version 1.21 (Walker et al., 2014). Gene prediction and functional annotation were carried out using the NCBI prokaryotic genomes annotation pipeline (Tatusova et al., 2016) and the RAST server (Aziz et al., 2008). The genes involved in the secondary metabolite production were analyzed using antiSMASH version 4.0.0 (Blin et al., 2017).

The complete genome of strain PMC12 is composed of two circular chromosomes; one is a 5,873,297 bp chromosome with 67.6% G + C content and the other is an 1,141,940 bp chromosome with 67.7% G + C content (Fig. 1). The genome contains 6,436 protein-coding genes, 9 rRNAs, 64 tRNAs, 3 ncRNAs, and 80 pseudogenes (Table 1). Functional annotation reveals that the genome of strain PMC12 possesses a numbers of genes associated with plant growth promotion and stress tolerance. ACC deaminase gene (acdS) is well-known to promote plant growth by reducing phytohormone ethylene. The genes involved in proline biosynthesis (proA, proB, and proC) are related to produce organic osmoytes increasing plant stress tolerance. There are 7 genes encoding the antioxidant enzymes, superoxide dismutase (SOD), catalase (CAT), and peroxidase (PRX), that scavenge reactive oxygen species. Strain PMC12 possesses phnA and phnX genes involved in hydrolysis of phosphonoacetate and phosphonoacetaldehyde, respectively that could increase biologically available phosphate for plants. The homologous gene cluster for biosynthesis of variochelin, a lipopeptide siderophore (Kurth et al., 2016), were found in the chromosome 2 of strain PMC12 genome. This study will provide basic information for understanding of molecular mechanisms where rhizobacteria enhances plant growth under environmental stresses and resistance to bacterial wilt disease.

Fig. 1.

Circular maps of chromosomes 1 (A) and 2 (B) of Variovorax sp. PMC12. Each circle from outside to the center represents the GC skew, the black CDS on forward strand, CDS on reverse strand, tRNA, rRNA, GC content, and GC skew.


Genome features of Variovorax sp. PMC12

Genome featureChromosome 1Chromosome 2Total
Accession numberCP027773CP027774
Genome size (bp)5,873,2971,141,9407,015,237
G + C content (%)67.667.767.61
Protein-coding genes5,4389986,436
tRNAs62264
rRNAs (5S, 16S, 23S)9 (3, 3, 3)-9 (3, 3, 3)
Pseudogenes562480

Nucleotide sequence accession numbers

The genome sequences of two chromosomes described in this study were available under the accession numbers CP027773 and CP027774 in GenBank database.

적 요

본 연구에서 생물 및 비생물학적 스트레스에 내성을 유도하는 식물 생육 촉진 세균인 Variovarx sp. PMC12 균주의 유전체 염기서열을 분석하였다. PMC12 균주의 유전체는 5,873,297 bp와 1,141,940 bp 크기의 원형 염색체 2개로 구성되었다. 총 6,436개 단백질 유전자, rRNA 9개, tRNA 64개, ncRNA 3개와 유사유전자 80개가 확인되었다. 유전체상에서 발견된 1-aminocyclopropane-1-carboxylate (ACC) deaminase, 항산화 활성, 인산 가용화, 프롤린 생합성, 시드로포어 생합성과 관련된 유전자들은 PMC12 균주가 염, 온도, 병원균에 대한 스트레스에 대한 식물의 내성 유도와 관련되어 있을 것으로 판단된다.

Acknowledgements

This study was carried out with the support of “Research Program for Agricultural Science & Technology Development (Project No. PJ01185002)” from the National Institute of Agricultural Sciences, Rural Development Administration, Republic of Korea.

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December 2018, 54 (4)