Genome-wide <i>in silico</i> and <i>in vitro</i> mining to develop a novel cyclotide-based marker system in plants

Cyclotides are cysteine-rich cyclic peptides that have various activities and applications. Mining at the whole-genome scale facilitates profiling development of cyclotide-based markers. However, characterization cyclotide subfamilies a genome-scale in plants is an untapped area needs more studies. Here we developed four degenerate subfamily-specific (CSS) markers based on their subfamily’s semi-conserved sequence for identifying each subfamily separately. Initially, silico mining analysis was performed 15 plant genomes/transcriptomes. The PCR produced 476 amplicons Bracelet, Moebius, Hybrid Trypsin Inhibitor (TI) subfamilies. In results identified 903 mature domains (CMDs) analyzed genomes/transcriptomes addition, prevalence correlated positively with genome size, particularly Hybrid, followed by TI Bracelet CSS were validated vitro 19 genotypes/cultivars. generated total 175 bands, polymorphic percentage 98%–100%. Cluster showed distinct clusters cultivars/genotypes species. marker efficiency parameters demonstrated capability to determine genetic diversity among studied This study represents first report perform genome/transcriptome-wide characterize Cyclotide plants. proposed potential applications novel as effective system screening across multiple species no prior sequencing knowledge requirement. Additionally, it proposes innovative approach appropriate used drug design.