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Microbiology and Biotechnology Letters

Genome Report(Note)

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Genome Report  |  Genome Report

Microbiol. Biotechnol. Lett. 2023; 51(3): 303-305

Received: August 1, 2023; Revised: September 4, 2023; Accepted: September 7, 2023

Complete Genome Sequence of Priestia megaterium Hyangyak-01 Isolated from Rhizosphere Soil of Centella asiatica

Kyeongmo Lim1, HyungWoo Jo2,3, Jerald Conrad Ibal4, Min-Chul Kim4, Hye-Been Kim2, Dong-Geol Lee2,3, Seunghyun Kang2, and Jae-Ho Shin1,4,5*

1Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
2COSMAX BTI, R&I Center, Seongnam 13486, Republic of Korea
3Department of Microbiology, Dankook University, Cheonan 31116, Republic of Korea
4NGS Core Facility, 5Department of Integrative Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea

Correspondence to :
Jae-Ho Shin,

In this study, we report the complete genome sequence of Priestia megaterium strain HyangYak-01, which was isolated from the rhizosphere soil of Centella asiatica. The genome consists of 5,086,279 bp of sequences with 38.2 percent GC content and 5,111 coding genes. The genome contains several important genes related to plant growth-promoting activities, which were also confirmed with in vitro media assays.

Keywords: Priestia megaterium, plant growth-promoting rhizobacteria, Centella asiatica, sustainable agriculture

Centella asiatica, commonly known as Indian pennywort, is an important medicinal plant using as traditional medicine in Southeast Asia [1]. Active compounds extracted from C. asiatica leaves have been widely used for medical and cosmetic purposes, especially triterpenoids such as madecassoside and asiaticoside [2]. Maximizing the yield of its active compounds can directly lead to increased profits. Among the numerous ways to increase yields, we focused on plant growth-promoting rhizobacteria (PGPR) in this study. Under the worldwide carbon neutrality challenge, PGPR is attracting attention as a potential alternative fertilizer for sustainable agriculture. Priestia megaterium, formerly known as Bacillus megaterium, is a well-known PGPR [3]. In this study, we isolated and genetically analyzed a potential PGPR agent to increase the advantage in C. asiatica.

P. megaterium HyangYak-01 was isolated from the rhizosphere soil of C. asiatica. Planted field was Cosmax HyangYak herb garden, located at 11−37, Yugugyebonggil, Yugu-eup, Gongju-si, Chungcheongnam-do, Korea. Isolates were identified based on the 16S rRNA gene. The identified strain was subsequently used for genomic DNA extraction for whole-genome sequencing. Bacterial genome was extracted using the Promega Wizard Genomic DNA Purification Kit (Promega, USA) following the provided protocol. Extracted DNA was checked to confirm quantity and quality using Qubit fluorometer 2.0 (Waltham, USA) and NanoDrop Onec (Thermo Fisher Scientific, USA). Sequencing was performed with two different platforms to obtain both short and long sequencing reads for hybrid assembly. Long read sequences were sequenced using the Oxford Nanopore MinION Mk1C platform using flow cell (R10.4.1) and barcoding kit 24 V14 (Oxford Nanopore Technologies, UK). Short-read sequencing was performed with the DNBSEQ-G400RS platform (MGI Tech, China) using the PE50 kit. Both sequencing was performed at NGS Core Facility (Kyungpook National University, Daegu, South Korea). Sequencing raw reads were assembled with the Maryland Super Read Cabog Assembler (MaSuRCA, version 4.1.0). The assembled contigs were scaffolded with the Contig Scaffolding tool using Algebraic rearrangements (CSAR) and polished with Polypolish. Polished genome was subsequently confirmed to be complete with the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). The completed genome was finally annotated with functional genes to confirm the existence of PGP-related genes and visualized with Proksee web.

The completed genome has a total length of 5,086,279 bp with 38.2% G + C content. The total gene count is 5,289, including 5,111 protein-coding sequences (CDS), 48 pseudogenes, 44 ribosomal RNAs, 126 transfer RNAs, and 8 other RNAs (Table 1). Several plant growth-promoting activities-related genes were found from result of functional gene annotation (Fig. 1). Regarding auxin-producing activity, genes related to tryptophan-dependent pathways of bacterial indole-3-acetic acid were found such as aldH and trp genes [4]. For urease activity, ure genes were found, which involved in the urease operon [5, 6]. Lastly, regarding phosphate solubilization activity, genes related to the bacterial phosphorus cycle were found such as phnW and pho genes [7, 8].

Table 1 . Genetic features of P. megaterium HyangYak-01.

Genomic Size5,086,279 bp
GC contents38.2%
Total genes5289
Ribosomal RNAs44
Transfer RNAs126
Other RNAs8

Figure 1.Circular representation of P. megaterium HyangYak-01 using Proksee. Plant growth-promoting activity related genes were highlighted on the figure.

The genome sequence of P. megaterium Hyangyak-01 have been deposited in NCBI under the accession number PRJNA956741.

This work was carried out with the support of COSMAX BTI, “Cooperative Research Program for Agriculture Science & Technology Development (Project No. PJ015697)” Rural Development Administration, Republic of Korea, Korea Basic Science Institute (National research Facilities and Equipment center) grant funded by the Ministry of Education (2021R1A6C101A416) and a project to train professional personnel in biological materials by the Ministry of Environment.

The authors have no financial conflicts of interest to declare.

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