Charting the landscape of organellar genome evolution in eustigmatophyte algae

Organellar genomes are both a resource for reconstructing organismal phylogenies and interesting subjects for evolutionary studies. Herein, we focused on the organellar genomes of eustigmatophytes (eustigs), a class of the algal phylum Ochrophyta with a growing biotechnological potential, and massively expanded the existing limited sample by 51 new organellar genomes. Analyses of this large dataset provided a robustly resolved eustig phylogeny and important insights into the evolution of unique features of eustig organellar genomes. Eustig plastomes are rather stable in terms of the gene content and order, with only minor differences stemming from differential gene loss and rare lineage-specific gain. In contrast, eustig mitogenomes vary broadly in their gene order, the content of "accessory" genes, and substitution rates. Notably, the new data illuminated the origin of some of the organellar genes previously deemed eustig-specific. Thus, the plastid gene ycf95 most likely is an extremely divergent version of ycf35, and the mitochondrial genes orfX and orfY evolved, respectively, by rps4 duplication and extreme divergence of rps1 ortholog. Most interestingly, we identified five previously unrecognized orthogroups of mysterious mitochondrial orfs that are patchily distributed across eustigs yet likely evolved in the ancestor of this class. These orfs have no discernible homologs outside eustigmatophytes but are predicted to encode multipass membrane proteins with a soluble C-terminal domain. Finally, our results revise some of the previous conclusions regarding the mitochondrial translation in eustigs and suggest the recruitment of a group of unusual tRNAs for a translation-independent function in the genus Vischeria.