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Microbiology and Biotechnology Letters

Genome Report(Note)

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Genome Report  |  Genome Report

Microbiol. Biotechnol. Lett. 2024; 52(2): 208-210

https://doi.org/10.48022/mbl.2403.03009

Received: March 19, 2024; Accepted: April 26, 2024

Complete Genome Sequence of Spirosoma sp. SC4-14 Isolated from the Rhizosphere of pepper (Capsicum annuum L.)

Jihye Jung*, Dawon Jo, Myoungjoo Riu, Seongho Ahn, and Do-Hyun Kim

Agricultural Microbiology Division, National Institute of Agricultural Sciences (NAAS), Rural Development Administration (RDA), Wanju 55365, Republic of Korea

Correspondence to :
Jihye Jung,         jhjung1224@korea.kr

Abstract

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Spirosoma sp. SC4-14 was isolated from the rhizosphere soil of pepper (Capsicum annuum L.). The genome of the strain SC4-14 consists of a single chromosome with one plasmid, total size of 8,104,799 bp and the DNA G+C-content is 48.2%. This chromosome contains 6,479 protein-coding sequences and 41 tRNA and 6 rRNA genes.

Keywords: Spirosoma sp. SC4-14, genome

Body

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Spirosoma species are commonly found in various environments, including soil [1−3], water, and extreme habitats such as dust, salt meadow, and herbicidecontaminated soil [4−6]. Some Spirosoma sp. have exhibited UV-radiation resistance [6, 7], indicating their potential for environmental applications as long-lasting microbes. In this study, we isolated Spirosoma sp. SC4- 14 from the rhizosphere of pepper (Capsicum annuum L.) infested with above-ground aphids. Comparative analysis revealed its similarity to S. terrae 15J9-4 (95.74%) [1], S. gilvum 15J10-9T5 (93.38%) [2], S. aerolatum KACC 17939 (92.93%) [8], S. aureum BT328 (92.93%) [3] and S. endbachense I-24 (92.79%) [9], based on 16S rRNA sequence comparison using EzBoCloud server [10]. We proposed Spirosoma sp. SC4-14 as a new strain belong to the genus Spirosoma and conducted whole genome sequencing.

Genomic DNA extraction was performed using Maxell® RSC Tissue DNA kit (Promega, USA), following the manufacturer’s instruction. The quality and quantity of DNA were assessed by using PicoGreen (Thermo Fisher Scientific, USA). High-quality and high-molecular-weight DNA samples were used to prepare size-selected SMRTbell templates with an optimal size range of approximately 7−12 kb. The library preparation involved sequencing 4 μg of input genomic DNA for PacBio Sequel IIe. The actual size distribution was determined using the Femto Pulse System (Agilent) for all size QC assessments. Genomic DNA was sheared using the Megaruptor® 3 (Diagenode) and purified with AMPure PB magnetic beads (Pacific Biosciences) for size selection. A 10 μl library was prepared using the PacBio SMRTbell prep kit 3.0, and SMRTbell templates were annealed using the Sequel II Bind Kit 3.2 and Int Ctrl 3.2. Sequencing was conducted using the Sequel II Sequencing Kit 2.0 and SMRT cell 8M Tray. SMRT cells (Pacific Biosciences) with a 15-hour movie time were captured for each SMRT cell using the PacBio Sequel IIe (Pacific Biosciences) sequencing platform by Macrogen (Republic of Korea). The subsequent steps followed the PacBio Sample Net-Shared Protocol, available at https://www.pacb.com. HiFi reads generated from the PacBio Sequel IIe system were assembled using the Genome Assembly application of SMRTlink 11.1.0.166339. Default options were used in the analysis, except for the expected genome size and downsampled coverage, set at 63M and 30X, respectively. To enhance assembly quality, the assembly result underwent three rounds of correction using high-quality adapter-trimmed Illumina reads by Pilon v1.21. Assembly quality was assessed using BUSCO (v 5.1.3) analysis with the eukaryota orthologs database v10. Predicted protein sets were annotated using InterProScan v5.30-69.0 and psiblast v2.4.0 with EggNOG DB v4.5.

The genome of Spirosoma sp SC4-14 was assembled with a total size of 8,104,799 bp, consisting of 2 contigs: a single chromosome of 7,756,329 bp and one plasmid with 348,470 bp (Table 1). The GC content is 48.2%, with 6 rRNAs and 41 tRNAs identified (Table 1). The genome of Spirosoma sp. SC4-14 contains 6,797 genes and 6,749 protein-coding sequences (CDS) (Table 1). The genome map of Spirosoma sp. SC4-14 was depicted in Fig. 1.

Table 1 . Genetic features of Spirosoma sp. SC4-14.

FeaturesSpirosoma sp. SC4-14
Chromosome size (bp)7,756,329
Plasmid size (bp)348,470
G + C content (%)48.2
Total number of genes6,797
Protein-coding genes6,749
Number of rRNAs6
Number of tRNAs41
Accession number (Genbank)CP147518 and CP147519


Figure 1.Genome Map of Spirosoma sp. SC4-14. Chromosome (A) and plasmid (B) map of Spirosoma sp. SC4-14. Characteristics are depicted from outside to center: CDS on the forward and reverse strands, tRNA (light green), rRNA (red), GC content (exterior light green peak for higher GC percentage, interior lavender peak for higher C content), and GC skew (positive value indicates G dominance, negative value indicates C dominance).

Nucleotide Sequence Accession Number

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The whole genome sequence of strain SC4-14 described in this study has been deposited in the NCBI database under accession number CP147518 (Chromosome) and CP147519 (Plasmid 1).

Acknowledgments

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This research was supported by grants from the Agenda Project (Project No. PJ01727502) of the Rural Development Administration (RDA), Republic of Korea.

Conflict of Interest

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The authors have no financial conflicts of interest to declare.

References

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