Unveiling the Evolutionary History and Structural Dynamics of Dioscorea bulbifera L. and Congeners through matK Gene In silico Analysis

Abstract

Aerial yam (Dioscorea bulbifera) is a valuable tuber crop with numerous health benefits. However, due to insufficient conservation and breeding efforts, its genetic diversity is threatened, risking genetic erosion and the loss of wild relatives. This study examines genetic relationships using the chloroplast matK gene. Nucleotide sequences from the NCBI database were analyzed with MEGA 6 for phylogenetic and maternal lineage assessments. GC content was calculated using Genscan, domain architecture was evaluated with SMART tools, and tertiary protein structures were predicted via Phyre2.  Phylogenetic analyses revealed distinct groupings of Dioscorea species into three primary clades, with D. bulbifera positioned within the third clade, indicating its conserved genetic lineage. High bootstrap values supported the robustness of the phylogenetic tree, while maternal lineage analysis positioned D. bulbifera as a likely ancestral clade within the genus. Guanine-cytocine content ranged from 31.78% to 32.40%, with D. bulbifera showing the highest value, indicating increased molecular stability. The matK protein contained two primary domain types. Most species had a single low-complexity domain, but D. transversa exhibited transmembrane and low-complexity domains, and D. pseudojaponica showed two low-complexity domains. Predicted protein structures revealed conserved folding patterns, although D. arcuatinervis lacked beta sheets, implying adaptive divergence.  This study highlights the evolutionary importance of D. bulbifera and the matK gene, emphasising their relevance for phylogenetics, conservation, and breeding strategies within the Dioscorea genus. Future studies can employ genome-wide analyses and transcriptomics to investigate the regulatory mechanisms of matK gene expression and its role in Dioscorea genus evolution and biotechnology.