Phylogenetic Analysis and Protein Structure Characterization of the matK Gene in Sphenostylis stenocarpa and Related Legumes

Abstract

Legumes are essential for global nutrition and agriculture, providing significant protein, vital nutrients, and beneficial compounds. African yam bean (Sphenostylis stenocarpa), an important legume for agriculture and food security, faces challenges like high anti-nutritional factors, hard seed coats, long lifecycles, and photoperiod sensitivity. Their genetic diversity and that of related legumes remain underexplored. The Maturase K (matK) gene, a chloroplast marker with a high substitution rate, is widely used in studying genetic diversity and species evolution. This study focuses on the matK gene in legumes, specifically analysing S. stenocarpa and related species, to enhance understanding of their genetic diversity and potential for improvement. Nucleotide sequences for several leguminous species, including S. stenocarpa, Sphenostylis angustifolia, Vigna aconitifolia, Vigna angularis, Vigna umbellata, Vigna mungo, Cajanus cajan, Phaseolus vulgaris, and Glycine max were retrieved from NCBI database. Phylogenetic relationships were assessed using MEGA 6 software with Clustal W alignments and 1000 bootstrap resampling. The secondary and tertiary structures of proteins of the matK gene were predicted using the GORIV and Phyre2 tools, respectively. Phylogenetic analysis revealed two primary clusters: one containing exclusively P. vulgaris with high bootstrap support, and another encompassing the remaining legumes, further divided into sub-clusters with C. cajan distinct from Vigna species. Structural analysis showed S. stenocarpa exhibited the highest percentage of alpha helix (36.54%), while C. cajan displayed the lowest alpha helix and highest random coil. Notably, P. vulgaris had the highest percentage of extended strands (35.21%). Tertiary structure predictions indicated that while Vigna species shared similar folding patterns, P. vulgaris and C. cajan had unique tertiary structures. These findings underscore significant evolutionary differences among the legumes and highlight the potential for genetic enhancement of these important crops.