Evidence of Relaxed Selection in the Mitochondrial Genomes of Phototrophic Paulinella Lineages

Primary endosymbiosis resulting in the establishment of a photosynthetic organelle in eukaryotes, has occurred twice: more than 1.5 billion years ago in the common ancestor of Archaeplastida and 90-140 million years ago in the Paulinella lineage. The relatively recent, independent event in phototrophic Paulinella provides opportunities for investigating the earlier stages of primary plastid establishment. In Archaeplastida, plastid origin is so ancient that little can be inferred about the eukaryotic host in which endosymbiosis occurred. By contrast, the genus Paulinella includes nine heterotrophic species that are closely related to the phototrophic lineage which can be used to understand the impact of primary endosymbiosis on "host" cell evolution. Research on heterotrophic Paulinella is very limited, and analyses addressing the evolutionary impacts of primary endosymbiosis on the ancestral heterotrophic lineage have been lacking. In this study, we used long-read sequencing to determine the mitochondrial genome sequence from three taxa of heterotrophic Paulinella that formed a "bloom" in their native environment. We also determined the mitogenomes of two phototrophic Paulinella species. Along with two available mitogenomes, we conducted a comparative analysis of phototrophic and heterotrophic Paulinella mitogenomes and find that gene order rearrangements occurred more frequently in the phototrophic lineage. We detected signatures of relaxed selection in mitochondrial DNA from the phototrophic clade. This pattern likely reflects reduced effective population size (Ne) associated with plastid primary endosymbiosis, in line with the endosymbiotic ratchet hypothesis. We propose that the reduced Ne in phototrophic Paulinella strongly impacted mitogenome evolution in these species.