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Prasinophytes form a paraphyletic assemblage of early diverging green algae, which have the potential to reveal the traits of the last common ancestor of the main two green lineages: (i) chlorophyte algae and (ii) streptophyte algae. Understanding the genetic composition of prasinophyte algae is fundamental to understanding the diversification and evolutionary processes that may have occurred in both green lineages. In this study, we sequenced the chloroplast genome ofPyramimonas parkeaeNIES254 and compared it with that ofP. parkeaeCCMP726, the only other fully sequencedP. parkeaechloroplast genome. The results revealed thatP. parkeaechloroplast genomes are surprisingly variable. The chloroplast genome ofNIES254 was larger than that ofCCMP726 by 3,204 bp, theNIES254 large single copy was 288 bp longer, the small single copy was 5,088 bp longer, and theIRwas 1,086 bp shorter than that ofCCMP726. Similarity values of the two strains were almost zero in four large hot spot regions. Finally, the strains differed in copy number for three protein‐coding genes:ycf20,psaC, andndhE. Phylogenetic analyses using 16S and 18SrDNAandrbcLsequences resolved a clade consisting of these twoP. parkeaestrains and a clade consisting of these plus otherPyramimonasisolates. These results are consistent with past studies indicating that prasinophyte chloroplast genomes display a higher level of variation than is commonly found among land plants. Consequently, prasinophyte chloroplast genomes may be less useful for inferring the early history of Viridiplantae than has been the case for land plant diversification.

Proliferating cell nuclear antigen (PCNA) plays critical roles in eukaryoticDNAreplication and replication‐associated processes. It is typically encoded by one or two gene copies (pcna) in eukaryotic genomes. Recently reported higher copy numbers ofpcnain some dinoflagellates raised a question of how this gene has uniquely evolved in this phylum. Through real‐timePCRquantification, we found a wide range ofpcnacopy number (2–287 copies) in 11 dinoflagellate species (n = 38), and a strong positive correlation betweenpcnacopy number and genome size (log₁₀–log₁₀transformed). Intraspecificpcnadiverged up to 21% and are dominated by nonsynonymous substitutions, indicating strong purifying selection pressure on and hence functional necessity of this gene. By surveyingpcnacopy numbers in eukaryotes, we observed a genome size threshold at 4 pgDNA, above which more than twopcnacopies are found. To examine whether retrotransposition is a mechanism ofpcnaduplication, we measured the copy number of retroposedpcna, taking advantage of the 22‐nt dinoflagellate‐specific spliced leader (DinoSL) capping the 5′ end of dinoflagellate nuclear‐encodedmRNAs, which would exist in the upstream region of a retroposed gene copy. We found that retroposedpcnacopy number increased with totalpcnacopy number and genome size. These results indicate co‐evolution of dinoflagellatepcnacopy number with genome size, and retroposition as a major mechanism ofpcnaduplication in dinoflagellates. Furthermore, we posit that the demand of faithful replication and maintenance of the large dinoflagellate genomes might have favored the preservation of the retroposedpcnaas functional genes.