Plastome comparison reveals hotspots of nucleotide diversity and positive selection pressure on accD, matK, psaA and rbcL genes in Smilacaceae

The genus Smilax (Smilacaceae), commonly known as Sarsaparilla, comprises about 262 species with numerous medicinal and economic importance. Due to considerable morphological similarity, Smilax has been recognized as a taxonomically challenging group. In this study, we conducted a comprehensive analysis of the genomic architecture and nucleotide variation within the genus Smilax, comparing the newly sequenced plastome of Smilax zeylanica with ten other plastomes. Our analyses revealed a highly conserved gene structure, order, and orientation across the plastomes studied. Nonetheless, we identified eight highly divergent regions, namely rbcL-accD, petA-psbJ, psaJ-rpl33, ndhC-trnV UAC, accD-psaI, ndhF-rpl32, trnK UUU, and rps16-trnQ UUG. These highly diverse DNA regions could potentially be used as DNA super-barcodes for the precise identification of Smilax species. Furthermore, our study identified four positively selected genes—accD, matK, psaA, and rbcL. We also observed the loss of infA and pseudogenization of ycf15 and ycf68 genes within Smilacaceae. Additionally, the prediction of RNA editing sites revealed a high level of conservation across the genus Smilax. These findings provide valuable insights into adaptation, evolutionary dynamics, marker development, and barcode validation in Smilax, ultimately enhancing its therapeutic applications.