Whole-genome sequence data of Bacillus tropicus strain MHES12 isolated from the rhizosphere of tomato in a drought-prone ecosystem in Bangladesh

Abstract

We report the whole-genome sequence data of Bacillus tropicus strain MHES12 isolated from the rhizosphere of tomato plants grown in a drought-prone ecosystem in Rajshahi, Bangladesh (24.44,067° N, 88.40,943° E). Genomic DNA was extracted using the GeneJET Genomic DNA Purification Kit, quality-checked by NanoDrop 2000 and Qubit 4.0 Fluorometer (Thermo Fisher Scientific) and sequenced on the Illumina MiSeq platform (2 × 150 bp) using the Nextera DNA Flex Library Preparation Kit. Raw reads were quality-assessed with FastQC v0.11.3, trimmed with Trimmomatic v0.39 (Q30 = 94% R1, 79% R2 raw; 96% and 88% after trimming), and de novo assembled with SPAdes v4.2.0, yielding a draft genome of 5569,334 bp across 40 contigs at 63× total read coverage (52.9× after trimming), with a GC content of 35.1%, N50 value of 838,108 bp and N90 value of 124,199 bp. CheckM2 (Neural-Network specific model) reported 100% completeness and 0.05% contamination. Taxonomic placement was confirmed by FastANI (96.98% to B. tropicus N24 type strain), skani (97.21%), NCBI ANI (96.90%) and TYGS dDDH (d4 = 72.5%), all above the 95% ANI and 70% dDDH species-delimitation thresholds. An additional publicly available complete Bacillus tropicus genome (EMB20, GCA_023159405.1; PRJNA742863) from India shares 99.12% FastANI with MHES12, further supporting the species assignment. A maximum-likelihood core-genome phylogeny built from 1119 single-copy core genes across 21 Bacillus genomes places MHES12 in the B. tropicus clade with 100% SH-aLRT/ultrafast-bootstrap support. Genome annotation using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v6.11 predicted a total of 5829 genes, comprising 5707 coding sequences, 24 rRNA genes, 93 tRNA genes, 5 ncRNA genes, and 200 pseudogenes. antiSMASH v8.0 identified 10 biosynthetic gene clusters, including siderophore-associated clusters with petrobactin- and bacillibactin-like features, both of which were independently confirmed against reference operons in the Virulence Factor Database (VFDB), as well as ribosomally synthesized and post-translationally modified peptide (RiPP) clusters, a terpene cluster, and a beta-lactone synthetase cluster. As these biosynthetic cluster classes are commonly distributed among members of the B. cereus group, their identification is presented as a genome-based reference inventory rather than evidence of functional activity or pathogenicity. RAST subsystem analysis, cross-validated using eggNOG-mapper and Prokka, identified putative genomic determinants associated with osmotic and oxidative stress responses, as well as arsenic, chromium, copper, cadmium/zinc/cobalt, manganese, and iron homeostasis. These findings represent predicted genomic potential and should not be interpreted as evidence of phenotypic expression or experimentally verified resistance or stress tolerance. PathogenFinder2 predicted a low probability of human pathogenicity (score = 0.3912), below the 0.5 threshold. However, ABRicate analysis against the Virulence Factor Database (VFDB) identified the B. cereus group enterotoxin operons nheA/B/C, hblA/C/D, and cytK, which are widely distributed among environmental members of the B. cereus group. Nevertheless, the in silico detection of these genes alone does not establish a pathogenic phenotype, and their functional expression and potential pathogenic significance would require experimental validation. The annotated genome assembly (GenBank: JBXWLV000000000; version JBXWLV010000000) and raw sequencing reads (SRA: SRR36889416; BioProject: PRJNA1405269; BioSample: SAMN54739323) are publicly available for reuse in comparative genomics and B. cereus group taxonomy.