Expanded diversity of pedinophytes provides a window into the evolution of the genetic code in organelles

Mitochondria and plastids of various lineages exhibit genetic code alterations. However, the knowledge of the diversity and occurrence, mechanistic underpinnings, and evolutionary origins of codon reassignments in organelles remains incomplete. To address this gap, we focused on organelles of the neglected green algal class Pedinophyceae, as well as pedinophyte-derived secondary plastids of green-coloured dinoflagellates (peDinoflagellates). We isolated and characterized a novel pedinophyte, herein formally described as Oistococcus okinawensis gen. et sp. nov., and phenotypically documented the previously sequenced but morphologically uncharacterized strain YPF-701, herein described as Akinorimonas japonica gen. et sp. nov. Based on phylogenetic analyses, both new taxa were classified into the expanded family Resultomonadaceae. We sequenced the organellar genomes of O. okinawensis, and utilizing existing raw (meta)genomic data we assembled organellar genome sequences from other previously unexplored pedinophyte lineages. Bioinformatic analyses of the expanded set of pedinophyte organellar genomes painted a complex picture of their genetic code landscape. Concerning mitochondria, the stop-to-Trp reassignment of the UGA codon turned out to have evolved multiple times in pedinophytes, and the Arg-to-Ala reassignment of AGA/AGG codons was shown to be apomorphic for the whole order Marsupiomonadales. The latter has additionally converted UUA and UUG into termination codons, relying on specific mutations in the mtRF1a protein. All pedinophyte mitochondria seem to decode AUA as methionine rather than the standard isoleucine, and an analogous reassignment seems to be evolving also in plastids of two separate pedinophyte lineages. Finally, apart from the previously reported Ile-to-Met AUA reassignment, peDinoflagellate plastids have switched the meaning of the AGA/AGG codons from arginine to another amino acid (most likely alanine), and have modified their pRF2 protein to mediate translation termination at UUA/UCA codons. Pedinophyte(-derived) organelles present a broad spectrum of codon reassignments and provide important insights into the emergence and mechanisms of non-standard codon translation.