Mitochondrial genome structure, phylogenetic analyses and substitution rate estimation of the Oedogoniales

The order Oedogoniales comprises three genera, <i>Oedogonium, Oedocladium</i> and <i>Bulbochaete</i>, which were classified based on traditional morphological criteria, and includes more than 600 described species. This group is economically important in astaxanthin production and the energy sector. However, only one mitochondrial genome (mitogenome) has been reported so far. This study determined the mitochondrial genomes of seven Oedogoniales species, including six <i>Oedogonium</i> species and <i>Oedocladium prescottii</i>. Comparative analyses between the newly determined mitogenomes and the previously reported <i>Bulbochaete rectangularis</i> var. <i>hiloensis</i> mitogenome showed that all eight mitogenomes comprised 12 protein-coding genes (PCGs) and two rRNAs; however, the mitogenomes differed in their genome sizes, GC content, tRNAs, non-coding regions and introns. Synteny analysis of the eight mitogenomes revealed a high degree of syntenic conservation in general, with some rearrangements and inversions. The average nucleotide identity (ANI) analysis of the eight mitogenomes indicated <i>Oedogonium dentireticulatum</i> showed high similarity with <i>Oedogonium</i> sp3 (ANI of 96.32%). Most of the PCGs of the eight mitogenomes presented the conventional start codon ATG and stop codon TAR (TAA/TAG/TGA), and the synonymous codon preferences were conserved. Phylogenetic results indicated that <i>Oedogonium</i> was polyphyletic, and species of <i>Oedocladium</i> clustered with <i>Oedogonium</i>, while the position of <i>B. rectangularis</i> var. <i>hiloensis</i> was uncertain for the incongruent phylogenetic results. Statistical analyses of substitution rates demonstrated no significant differences among the three genera, and the dN/dS ratios based on branch model showed that <i>cob, cox</i>1 and <i>nad</i>4 of <i>Oedocladium prescottii</i> and <i>B. rectangularis</i> var. <i>hiloensis</i> were putative fast-evolving genes. These findings suggested that the traditional taxonomy of Oedogoniales did not define natural groups, and that species of <i>Oedocladium</i> and <i>Bulbochaete</i> may have undergone rapid evolution.