Abstract
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.
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Data availability
All data generated or analysed during the current study are included in this published article, NCBI repository (Accession No. OL701493) [and its supplementary information files].
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Acknowledgements
The authors thank the Director of Agharkar Research Institute for encouragement and facilities. Financial support received from Science and Engineering Research Board-Department of Science and Technology (SERB-DST) vide Project no. CRG/2020/000910 to carry out this research is duly acknowledged. Partial support received by the Department of Science & Technology, New Delhi, to GS via Inspire fellowship vide ref. no. IF210309 is also acknowledged. We also thank Prof. M. M. Sardesai and Dr. M.N. Datar for their help in the sample collection.
Funding
This work was supported by the Science and Engineering Research Board-Department of Science and Technology (SERB-DST) vide Project no. CRG/2020/000910. Partial support was received from the Department of Science & Technology, New Delhi, to GS via Inspire fellowship vide ref. no. IF210309.
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All authors contributed to the study's conception and design. GS and SM curated the data and performed the analysis. GS drafted the initial manuscript. RKC and SM reviewed and revised the manuscript. RKC acquired funding for this research. All authors read and approved the final manuscript as submitted.
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Sukhramani, G., Maurya, S. & Choudhary, R.K. Plastome comparison reveals hotspots of nucleotide diversity and positive selection pressure on accD, matK, psaA and rbcL genes in Smilacaceae. Braz. J. Bot 47, 145–161 (2024). https://doi.org/10.1007/s40415-023-00973-x
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DOI: https://doi.org/10.1007/s40415-023-00973-x