A variety of secondary metabolites contributing to plant growth are synthesized by bacterial nonribosomal peptide synthases (NRPSs). Among them, the NRPS biosynthesis of surfactin is regulated by the SrfA operon. To explore the molecular mechanism for the diversity of surfactins produced by bacteria within the genus Bacillus, we performed a genome-wide identification study focused on three critical genes of the SrfA operon—SrfAA, SrfAB and SrfAC—from 999 Bacillus genomes (belonging to 47 species). Gene family clustering indicated the three genes can be divided into 66 orthologous groups (gene families), of which a majority comprised members of multiple genes (e.g., OG0000009 had members of all three SrfAA, SrfAB and SrfAC genes), indicating high sequence similarity among the three genes. Phylogenetic analyses also found that none of the three genes formed monophyletic groups, but were usually arranged in a mixed manner, suggesting the close evolutionary relationship among the three genes. Considering the module structure of the three genes, we propose that self-duplication, especially tandem duplications, might have contributed to the initial establishment of the entire SrfA operon, and further gene fusion and recombination as well as accumulated mutations might have continuously shaped the different functional roles of SrfAA, SrfAB and SrfAC. Overall, this study provides novel insight into metabolic gene clusters and operon evolution in bacteria.

Hibiscus, which belongs to the Malvaceae family, is primarily distributed in tropical and subtropical regions. Hibiscus species are known for their large, visually striking flowers, which are highly valued for ornamental purposes and are widely admired. Despite this diversity, the mitochondrial DNA of Hibiscus species remains largely unexplored. Here, we assembled chromosome-level mitochondrial genomes (mitogenomes) of H. schizopetalus, H. syriacus, H. hamabo, and Talipariti tiliaceum (Hibiscus tiliaceum) using Illumina short reads (Illumina, Inc., San Diego, CA, USA) and PacBio long reads (Pacific Biosciences of California, Inc., Menlo Park, CA, USA), and conducted comparative genomic analyses. Our findings revealed that the mitogenomes of Hibiscus species exhibited structural complexity, including variable sizes and multi-molecular configurations, while maintaining high conservation in codon usage bias and GC content. Repeat sequence analysis suggested that repeat-mediated homologous recombination played a critical role in frequent recombination events in the mitogenomes. In addition, phylogenetic analysis showed that Hibiscus species did not form a monophyletic clade, and H. hamabo and T. tiliaceum were positioned in sister clades, which was consistent with the results of synteny analysis. To sum up, our study provides valuable resources for phylogenetic research and makes significant contributions to exploring further genetic mechanisms and biodiversity of Hibiscus species.