Comparative Mitogenome Analysis of Colletotrichum Species Causing Anthracnose of Rubber Trees Unveils Distinct Species Complex-Specific Evolution Trajectories Within the Genus

<i>Colletotrichum</i> spp. are the causative agents of anthracnose of rubber trees, one of the most destructive diseases, resulting in substantial economic losses. To investigate the evolutionary characteristics of these pathogenic species, we first assembled the complete mitogenomes of four dominant pathogens, i.e., <i>C. siamense</i>, <i>C. fructicola</i>, <i>C. wanningense</i> and <i>C. bannaense</i>. Comparative analyses revealed that variations in their mitogenome size were primarily driven by intron expansion and expansion/contraction within the <i>cox1</i>, <i>cob</i> and <i>nad</i> genes. Moreover, we observed the strong conservation of gene content, mitochondrial DNA copy number, gene order and intron features within species complexes, but a clear divergence between them. Notably, further studies indicated that patterns such as genomic organization, selective pressures and codon usage were consistent across the genus, suggesting that <i>Colletotrichum</i> species complexes had followed distinct evolutionary trajectories, particularly in the arrangement of protein-coding genes. Therefore, this study systematically characterized the mitogenomes of the four major <i>Colletotrichum</i> species associated with rubber tree anthracnose and provided novel insights into the broad evolutionary mechanisms shaping <i>Colletotrichum</i> species complexes.