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.

鞘藻目（Oedogoniales）包含3个属，即鞘藻属（Oedogonium）、毛鞘藻属（Oedocladium）和根枝藻属（Bulbochaete），该类群基于传统形态学标准划分，目前已描述的物种超过600个。该类群在虾青素生产及能源领域具有重要经济价值。然而截至目前，仅报道过1个线粒体基因组（mitogenome）。本研究测定了7种鞘藻目物种的线粒体基因组，包括6种鞘藻属物种及普雷斯科特毛鞘藻（Oedocladium prescottii）。将新测定的线粒体基因组与已报道的矩形根枝藻希洛变种（Bulbochaete rectangularis var. hiloensis）的线粒体基因组进行比较分析，结果显示8个线粒体基因组均包含12个蛋白质编码基因（protein-coding genes, PCGs）和2个核糖体RNA（rRNAs），但在基因组大小、GC含量、转运RNA（tRNAs）、非编码区及内含子方面存在差异。对8个线粒体基因组的共线性分析表明，整体共线性保守程度较高，但存在部分重排与倒位事件。针对8个线粒体基因组的平均核苷酸一致性（average nucleotide identity, ANI）分析显示，齿状网鞘藻（Oedogonium dentireticulatum）与鞘藻属sp3（Oedogonium sp3）的相似性极高，ANI值达96.32%。8个线粒体基因组的多数蛋白质编码基因以标准起始密码子ATG和终止密码子TAR（TAA/TAG/TGA）起始，同义密码子偏好性较为保守。系统发育分析结果表明，鞘藻属为多系群，毛鞘藻属物种与鞘藻属物种聚为一支，而矩形根枝藻希洛变种的系统发育位置因不同分析结果存在冲突而无法确定。替换速率统计分析显示，3个属之间无显著差异；基于分支模型的dN/dS比值分析表明，普雷斯科特毛鞘藻和矩形根枝藻希洛变种的cob、cox1及nad4基因为推定的快速进化基因。本研究结果提示，鞘藻目的传统分类并未界定自然类群，毛鞘藻属和根枝藻属物种可能经历了快速进化。