Abstract: Using bioinformatics methods, multi-dimensional analysis was performed on the chloroplast matK gene of Rubus chingii Hu, including open reading frame prediction, amino acid composition and physicochemical property analysis, hydrophilicity/hydrophobicity assessment, signal peptide prediction, subcellular localization, and spatial structure modeling.Meanwhile, phylogenetic analysis and evolutionary tree construction were conducted for 14 species based on matK gene sequences. The results showed that the matK gene of Rubus chingii Hu was 1 512 bp in length and encoded 503 amino acids. The matK protein was localized in chloroplasts with 95% confidence level, had an isoelectric point of 9.73 (indicating an alkaline protein), and showed an instability index of 42.52 and a hydrophilicity coefficient of -0.152, classifying it as an unstable hydrophilic protein.No signal peptide was detected in the matK protein. The secondary structure of matK protein primarily consisted of random coils (246 residues), α-helices (171 residues), and extended strands (86 residues), with random coils accounting for the highest proportion (48.90%) and extended strands the lowest (17.10%). The tertiary structure achieved a GMQE score of 0.61 with 93.64% sequence similarity. Phylogenetic analysis based on matK gene sequences revealed that Rubus chingii Hu and 13 other species were classified into three clusters. Rubus chingii Hu formed a clade with Rubus rosifolius, Rubus ursinus, and Rubus ellipticus, showing the closest genetic relationship with Rubus rosifolius.

Key words: bioinformatics, Rubus chingii Hu, matK gene, diversity analysis