Cyanophora is the glaucophyte model taxon. Following the sequencing of the nuclear genome of C. paradoxa, studies based on single organelle and nuclear molecular markers revealed previously unrecognized species diversity within this glaucophyte genus. Here, we present the complete plastid (ptDNA) and mitochondrial (mtDNA) genomes of C. kugrensii, C. sudae, and C. biloba. The respective sizes and coding capacities of both ptDNAs and mtDNAs are conserved among Cyanophora species with only minor differences due to specific gene duplications. Organelle phylogenomic analyses consistently recover the species C. kugrensii and C. paradoxa as a clade and C. sudae and C. biloba as a separate group. The phylogenetic affiliations of the four Cyanophora species are consistent with architectural similarities shared at the organelle genomic level. Genetic distance estimations from both organelle sequences are also consistent with phylogenetic and architecture evidence. Comparative analyses confirm that the Cyanophora mitochondrial genes accumulate substitutions at 3‐fold higher rates than plastid counterparts, suggesting that mtDNA markers are more appropriate to investigate glaucophyte diversity and evolutionary events that occur at a population level. The study of complete organelle genomes is becoming the standard for species delimitation and is particularly relevant to study cryptic diversity in microbial groups.

中文翻译：

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蓝藻（Glaucophyta）物种细胞器基因组的高序列差异但有限的结构重排

Cyanophora 是蓝藻模型分类群。在对 C. paradoxa 的核基因组进行测序之后，基于单个细胞器和核分子标记的研究揭示了该蓝藻属内以前未被认识的物种多样性。在这里，我们介绍了 C. kugrensii、C. sudae 和 C. biloba 的完整质体 (ptDNA) 和线粒体 (mtDNA) 基因组。ptDNAs 和 mtDNAs 各自的大小和编码能力在蓝藻物种中是保守的，由于特定的基因重复，只有很小的差异。细胞器系统基因组学分析始终将 C. kugrensii 和 C. paradoxa 作为一个进化枝，将 C. sudae 和 C. biloba 作为一个单独的组。四种蓝藻物种的系统发育从属关系与在细胞器基因组水平上共享的结构相似性一致。两种细胞器序列的遗传距离估计也与系统发育和结构证据一致。比较分析证实，蓝藻线粒体基因以比质体对应物高 3 倍的速率积累替代，这表明 mtDNA 标记更适合研究在种群水平上发生的绿藻多样性和进化事件。完整细胞器基因组的研究正在成为物种定界的标准，并且与研究微生物群中的神秘多样性特别相关。表明 mtDNA 标记更适合研究在种群水平上发生的绿藻多样性和进化事件。完整细胞器基因组的研究正在成为物种定界的标准，并且与研究微生物群中的神秘多样性特别相关。表明 mtDNA 标记更适合研究在种群水平上发生的绿藻多样性和进化事件。完整细胞器基因组的研究正在成为物种定界的标准，并且与研究微生物群中的神秘多样性特别相关。