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Microbiol Resour Announc
Microbiol Resour Announc
mra
Microbiology Resource Announcements
2576-098X
American Society for Microbiology 1752 N St., N.W., Washington, DC

39162470
mra00458-24
10.1128/mra.00458-24
mra.00458-24
Genome Sequences
environmental-microbiologyEnvironmental MicrobiologyDraft genome sequence of Priestia megaterium strain IMGN3 derived from soil
Choi Sejin 1 2 Conceptualization Data curation Investigation Writing – original draft
Jung Hoseong 1 2 Investigation Writing – review and editing
Kim Yeongjun 1 2 Data curation Formal analysis Investigation Validation
Han Jeong A. 3 Resources Supervision
https://orcid.org/0000-0002-6506-9725
Kim Eun Yu 1 2 4 5 Funding acquisition Supervision Writing – review and editing eunyu.kim@dukekunshan.edu.cn

https://orcid.org/0000-0002-1640-7601
Lee Ho-Seok 1 2 Conceptualization Investigation Project administration Supervision Writing – review and editing hoseoklee@khu.ac.kr

1 Center for Genome Engineering, Institute for Basic Science , Daejeon, South Korea
2 Department of Biology, College of Sciences, Kyung Hee University , Seoul, South Korea
3 Gyeonggido Agricultural Research & Extension Services , Hwaseong, South Korea
4 Division of Natural and Applied Sciences, Duke Kunshan University , Kunshan, Jiangsu, China
5 Environment Research Center, Duke Kunshan University , Kunshan, Jiangsu, China
Editor Dunning Hotopp Julie C. University of Maryland School of Medicine , Baltimore, Maryland, USA

Address correspondence to Eun Yu Kim, eunyu.kim@dukekunshan.edu.cn
Address correspondence to Ho-Seok Lee, hoseoklee@khu.ac.kr
Sejin Choi and Hoseong Jung contributed equally to this article. The authors order was determined based on seniority.

The authors declare no conflict of interest.

9 2024
20 8 2024
20 8 2024
13 9 e00458-2411 5 2024
30 7 2024
Copyright © 2024 Choi et al.
2024
Choi et al.
https://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

ABSTRACT

Priestia megaterium sp. strain IMGN3 was isolated from the soil in South Korea. Here, we report its draft genome sequence, comprising 12 contigs with a total sequence length of 5.64 Mbp. This genome will provide valuable resources for future genomic studies, particularly focusing on plant growth promotion and biocontrol.

KEYWORDS

Priestia megaterium
plant growth-promoting bacterium
biocontrol agent
Duke Kunshan University (DKU) Startup Fund Kim Eun Yu Institute for Basic Science (IBS) IBS-R021-D1-2024-a00 Lee Ho-Seok National Research Foundation of Korea (NRF) RS-2024-00338015 Lee Ho-Seok cover-dateSeptember 2024
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pmcANNOUNCEMENT

Priestia megaterium (previously known as Bacillus megaterium) is an aerobic, rod-shaped, Gram-positive bacterium that adapts to diverse environments (1). In biotechnology, it has been researched as a potential host for industrial protein synthesis because of its high cloning host capacity and simple cultivation methods (2). Moreover, it is an ideal organism for environmental applications with its plant growth-promoting ability and potential as a biocontrol agent (BCA) (3), which promotes sustainable agriculture practices (4–6). This announcement will serve as a resource for comparative genomics, enhancing our comprehension of similar microbes and plant-microbiome interactions.

The new P. megaterium strain was isolated from a soil sample collected at a depth of 15 cm in the Yangpyeong Province (37.59707, 127.59836) of the Republic of Korea in 2019. The soil was diluted, spread onto TSA, and incubated for 16 h at 37°C. The culture was subsequently streaked two times under the same medium and conditions to obtain a single colony.

Genomic DNA was extracted using the Maxwell RSC Tissue DNA kit protocol and divided into two portions for different sequencing methods. One portion was sheared with the Megaruptor 3 (Diagenode) and purified using AMPure PB magnetic beads (Pacific Biosciences) for size selection. The PacBio sequencing library was prepared using the PacBio SMRTbell prep kit 3.0. HiFi sequencing was conducted on the PacBio Sequel II, yielding 92,291 reads. The mean length of HiFi reads was 9,077 bp, with an N50 value of 9,770 bp.

Second, the other portion was used to prepare the Illumina sequencing library using the TruSeq DNA Nano Library Prep Kit (Illumina, Inc., San Diego, CA, USA). Sequencing was performed on the Illumina HiSeq X Ten platform using a 2 × 150 paired-end protocol, generating total od 14,826,316 reads. Additionally, quality filtering and adaptor trimming were performed using Trimmomatic v0.38 (7), ensuring a phred score of 30 or higher in 90% of the bases.

The HiFi reads were employed for de novo assembly, performed using HGAP v4 (8) to generate the draft genome assembly, and the Illumina reads were used to refine and polish the genome assembly with Pilon v1.21 (9) three times. The final draft genome of IMGN3 comprised 12 contigs totaling 5,639,441 bp, with an average coverage of 148.4×, 37.8% GC content, and an N50 value of 5,137,220 bp. To assess assembly quality, BUSCO v5.1.3 (10) analysis indicated a high completeness of 99.19%.

Prokka v1.14.6 (11) was utilized to predict genes, resulting in 5,918 predicted genes, including 5,724 coding sequences, 146 tRNA genes, and 47 rRNA genes. Annotation was conducted using psiblast v2.7.1 (12) against the EggNOG DB v4.5 (13). The assembled draft genome was compared to the Genome Taxonomy Database (GTDB) via GTDB-Tk v2.3.2 (14) and assigned to P. megaterium. In each step, default parameters were used except where otherwise noted.

Genome annotation revealed functional genes for nitrogen fixation and production of beneficial compounds like polyamines, polyketides, and phenazine (15). These findings underscore the potential of this species in bioremediation and plant growth promotion.

ACKNOWLEDGMENTS

The authors would like to express our gratitude to the members of the IMGN Lab. This research was supported by a grant from the Institute for Basic Science (IBS-R021-D1-2024-a00), the National Research Foundation of Korea (NRF) grant funded by the Korean Government (MSIT) (RS-2024-00338015), and by the Startup Fund at Duke Kunshan University.

DATA AVAILABILITY

The annotated draft genome sequences of P. megaterium IMGN3 strain have been deposited at DDBJ/ENA/GenBank under the accession JBBLUG000000000. The version described in this paper is JBBLUG010000000. The raw reads are available under the BioProject accession number PRJNA1091902, with BioSample accession number SAMN40615794, and the Sequence Read Archive information for this project is SRR28604260 and SRR28604261.
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REFERENCES

1 Gupta RS, Patel S, Saini N, Chen S. 2020. Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the subtilis and cereus clades of species. Int J Syst Evol Microbiol 70 :5753–5798. doi:10.1099/ijsem.0.004475 33112222
2 Vary PS, Biedendieck R, Fuerch T, Meinhardt F, Rohde M, Deckwer WD, Jahn D. 2007. Bacillus megaterium--from simple soil bacterium to industrial protein production host. Appl Microbiol Biotechnol 76 :957–967. doi:10.1007/s00253-007-1089-3 17657486
3 Ortíz-Castro R, Valencia-Cantero E, López-Bucio J. 2008. Plant growth promotion by Bacillus megaterium involves cytokinin signaling. Plant Signal Behav 3 :263–265. doi:10.4161/psb.3.4.5204 19704649
4 Bach E, Rangel CP, Ribeiro IDA, Passaglia LMP. 2022. Pangenome analyses of Bacillus pumilus, Bacillus safensis, and Priestia megaterium exploring the plant-associated features of bacilli strains isolated from canola. Mol Genet Genomics 297 :1063–1079. doi:10.1007/s00438-022-01907-0 35612623
5 Biedendieck R, Knuuti T, Moore SJ, Jahn D. 2021. The “beauty in the beast”-the multiple uses of Priestia megaterium in biotechnology. Appl Microbiol Biotechnol 105 :5719–5737. doi:10.1007/s00253-021-11424-6 34263356
6 Liu JM, Liang YT, Wang SS, Jin N, Sun J, Lu C, Sun YF, Li SY, Fan B, Wang FZ. 2023. Antimicrobial activity and comparative metabolomic analysis of Priestia megaterium strains derived from potato and dendrobium. Sci Rep 13 :5272. doi:10.1038/s41598-023-32337-6 37002283
7 Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics 30 :2114–2120. doi:10.1093/bioinformatics/btu170 24695404
8 Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10 :563–569. doi:10.1038/nmeth.2474 23644548
9 Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9 :e112963. doi:10.1371/journal.pone.0112963 25409509
10 Manni M, Berkeley MR, Seppey M, Zdobnov EM. 2021. BUSCO: assessing genomic data quality and beyond. Curr Protoc 1 :e323. doi:10.1002/cpz1.323 34936221
11 Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30 :2068–2069. doi:10.1093/bioinformatics/btu153 24642063
12 Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. 2009. BLAST+: architecture and applications. BMC Bioinformatics 10 :421. doi:10.1186/1471-2105-10-421 20003500
13 Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, Jensen LJ, von Mering C, Bork P. 2016. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res 44 :D286–93. doi:10.1093/nar/gkv1248 26582926
14 Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. 2022. GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics 38 :5315–5316. doi:10.1093/bioinformatics/btac672 36218463
15 Dimkić I, Janakiev T, Petrović M, Degrassi G, Fira D. 2022. Plant-associated Bacillus and Pseudomonas antimicrobial activities in plant disease suppression via biological control mechanisms - a review. Physiol Mol Plant Pathol 117 :101754. doi:10.1016/j.pmpp.2021.101754
