Comprehensive plastome analysis in prickly pear cactus (Opuntia, Cactaceae), a key genus for sustainable fuel and food: Uncovering evolutionary dynamics and germplasm

Opuntia , a genus in Cactaceae, holds considerable economic significance due to its diverse uses. However, species identification and understanding of phylogenetic relationships within this genus are challenging, given the extensive morphological variation and frequent hybridization. This study analyzed plastomes from 40 Opuntia and 32 additional species within Cactaceae, focusing on plastome structure, gene content, and evolutionary dynamics. Our findings reveal significant structural variations and changes in gene content across Opuntia plastomes, with sizes ranging from 121,985 bp to 152,717 bp. These variations are primarily driven by the contraction and expansion of Inverted Repeat (IR) regions, which range from 338 to 30,530 bp. We identified 101 species-specific SSRs across the Opuntia plastomes, along with six high-resolution plastid markers ( ndhJ - trnF , atpE - trnM-CAU , psaJ - rpl33 , ndhC - rbcL , psaA - ycf3 , atpB - rbcL ), which offer potential tools for accurate germplasm identification. Our phylogenomic framework within Cactaceae traced the ancestral IR states of Opuntia through divergence time and ancestral trait reconstruction, which suggests an origin in the Late Miocene (approximately 8.54 million years ago). Initial slight IR contraction was observed, followed by diversification involving extreme contraction and expansion events. These events, potentially adaptive responses to climate changes, are proposed based on patterns of IR variation and documented climate shifts during the Late Tertiary and Quaternary periods These findings provide key molecular markers that could help resolve taxonomic challenges within the Opuntia genus and enhance our understanding of Opuntia plastome evolution. This study offers comprehensive genomic resources for this economically significant genus, laying a foundation for future species identification and breeding applications. • Opuntia vital for agriculture & bioenergy, but face challenges for species identification. • IR variations in Opuntia plastomes show complex genomics and arid adaptability. • Opuntia -specific markers aid species identification and germplasm characterization. • Phylogenomics reveal Opuntia dynamics, aiding taxonomy and phylogeny clarity.