ABSTRACT
Bacillus spizenii strain SHT-15 was isolated from the rhizosphere soil in Shihezi, Xinjiang, China. This study presents the whole-genome sequencing of strain SHT-15, revealing a genome size of 4.082 Mb, which comprises 4,185 predicted protein-coding sequences and 96 RNA genes.
KEYWORDS: Bacillus spizenii, cotton Verticillium wilt, antibacterial ability, coding sequence, genome sequencing
ANNOUNCEMENT
Bacillus spizenii, a gram-positive bacterium, is renowned for secreting antimicrobial peptides and other substances inhibiting plant pathogens (1). It also acts as a biosurfactant, enhancing anti-pathogenic efficacy. The B. spizenii is extensively studied in molecular and cell biology due to its large genome and genetic versatility (2, 3).
In Shihezi City, Xinjiang, China, the rhizosphere antagonistic bacterium SHT-15 was isolated from healthy cotton plants to control cotton verticillium wilt (4). Using the dilution plating method, soil samples were diluted to 10−6, spread onto TSA medium plates, and incubated at 33°C for 24 h. The antibacterial activity was determined by the plate confrontation method, and dominant antagonistic strains were purified on nutrient agar medium. Pot experiments with a 2×108 CFU/mL bacterial suspension showed that SHT-15 achieved a 89.23% control efficiency against tomato root rot caused by Fusarium oxysporum during the seedling stage.
The 16S rRNA gene sequence similarity was calculated using DNAMAN 8.0 software with primers 27F (5-AGAGTTTGATCCTGGCTCAG-3) and 1492R (5- ACGGCTACCTTGTTACGACTT-3), revealing a 99.52% identity with B. spizenii (NR_112686.1) (5). Additionally, a BLAST search in the NCBI NT database confirmed that the closest matching sequence was B. spizenii (NR_112686.1).
Genomic DNA of B. spizenii SHT-15 was extracted using the Ezup Column Bacterial Genomic DNA Extraction Kit. Bioinformatics analysis was performed on data from the Illumina platform. Quality checks and trimming were conducted using FastQC v0.11.7 (6) and Trimmomatic v0.39 (7). The clean short reads were assembled into complete genomes using SOAPdenovo v. 2.04 (8) and polished with Pilon v1.22 (9), and Quast v5.0.2 (10) evaluated the genome assembly quality. CheckM v1.1.6 (11) assessed completeness and contamination. The draft genome was annotated using the Rapid Annotation System Technology (RAST) (12) Pipeline and NCBI PGAP v6.5 (13) and assessed against the Genome Taxonomy Database using GTDB-Tk v1.7.0 (14).
The whole genome of B. spizenii SHT-15 consisted of a 4,081,549 bp chromosome with 279,920 reads, 3,920 protein-coding sequences, 30 rRNA genes, 86 tRNA genes, and a G+C content of 44.69%. Among 4,034 CDS, 767 are associated with transporters, 1,132 encode transmembrane proteins, and 421 relate to virulence, potentially explaining its inhibitory effect on cotton verticillium wilt (Fig. 1). Future studies will investigate the inhibition mechanism of B. spizenii SHT-15 on cotton verticillium wilt.
Fig 1.
Genome-wide mapping of B. spizenii SHT-15. Note: The outermost circle of the circle graph is the identification of genome size; the second and third circles are CDS on the positive and negative chains, and different colors represent the functional classification of different COGs of CDS; the fourth circle is rRNA and tRNA; the fifth circle is GC content. The outward red part indicates that the GC content in this region is higher than the average GC content of the whole genome. The higher the peak value is, the greater the difference between the average GC content is. The inward blue part indicates that the GC content in this region is lower than the average GC content of the whole genome. The higher the peak value is, the greater the difference between the average GC content and the average GC content is. The innermost circle is the GC-Skew value, and the specific algorithm is G-C / G+C, which can assist in judging the leading chain and the lagging chain. In general, the leading chain GC skew > 0, the lagging chain GC skew.
ACKNOWLEDGMENTS
This work was supported by the Xinjiang Major Science and Technology Projects (Grant No. 2022A02005-3) and the Key R&D Project of Xinjiang Uygur Autonomous Region, China (Grant No. 2022B02053-2) awarded to Yingwu Shi, as well as the Project of Fund for Stable Support to Agricultural Sci-Tech Renovation in Xinjiang (Grant Nos. xjnkywdzc2025003-06-02-01 and xjnkywdzc-2024003-66) awarded to Nuraliya Ablimit and Yue Sheng, respectively.
Zhichao Meng, Formal analysis, Investigation, Software, Writing – original draft | Xinxiang Niu, Data curation, Formal analysis, Investigation, Methodology, Writing – review and editing | Hongmei Yang, Data curation, Formal analysis, Investigation, Writing – review and editing | Min Chu, Investigation, Writing – review and editing | Ning Wang, Investigation, Writing – review and editing | Huifang Bao, Investigation, Writing – review and editing | Faqiang Zhan, Investigation, Writing – review and editing | Rong Yang, Investigation, Writing – review and editing | Kai Lou, Investigation, Writing – review and editing | Shuang Dou, Investigation, Writing – review and editing | Zhao Zhang, Investigation, Writing – review and editing | Yun Chen, Investigation, Writing – review and editing | Yingwu Shi, Conceptualization, Data curation, Formal analysis, Funding acquisition, Project administration, Resources, Supervision, Writing – review and editing.
Contributor Information
Yignwu Shi, Email: syw1973@126.com.
Vanja Klepac-Ceraj, Wellesley College, Wellesley, Massachusetts, USA.
DATA AVAILABILITY
The whole-genome shotgun project for B. spizenii SHT-15 has been deposited at DDBJ/ENA/GenBank under the accession CP167793, and the version described in this paper is version CP167793. The raw reads are available under the BioProject accession number PRJNA1149500, and the BioSample accession number is SAMN43249788. The sequence data obtained in this work have been deposited in the NCBI Sequence Read Archive under the accession number SRR33847918. Additionally, the assembled genome sequence is available in GenBank under accession number GCA_041501465.1.
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The whole-genome shotgun project for B. spizenii SHT-15 has been deposited at DDBJ/ENA/GenBank under the accession CP167793, and the version described in this paper is version CP167793. The raw reads are available under the BioProject accession number PRJNA1149500, and the BioSample accession number is SAMN43249788. The sequence data obtained in this work have been deposited in the NCBI Sequence Read Archive under the accession number SRR33847918. Additionally, the assembled genome sequence is available in GenBank under accession number GCA_041501465.1.