Comparative DNA sequence analyses of Pyramimonas parkeae (Prasinophyceae) chloroplast genomes

Abstract

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 of Pyramimonas parkeae NIES254 and compared it with that of P. parkeae CCMP726, the only other fully sequenced P. parkeae chloroplast genome. The results revealed that P. parkeae chloroplast genomes are surprisingly variable. The chloroplast genome of NIES254 was larger than that of CCMP726 by 3,204 bp, the NIES254 large single copy was 288 bp longer, the small single copy was 5,088 bp longer, and the IR was 1,086 bp shorter than that of CCMP726. 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, and ndhE. Phylogenetic analyses using 16S and 18S rDNA and rbcL sequences resolved a clade consisting of these two P. parkeae strains and a clade consisting of these plus other Pyramimonas isolates. 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.

Complete mitochondrial genomes of prasinophyte algae Pyramimonas parkeae and Cymbomonas tetramitiformis

“…). While such differences might suggest the possibility that the two investigated P. parkeae strains are different species, a phylogeny based on 18S rDNA, rbc L, and chloroplast 16S rDNA sequences indicated that the two strains together form a monophyletic group separate from other studied Pyramimonas strains (Satjarak and Graham ). Additional molecular data from other P. parkeae strains and Pyramimonas species would be useful for future examination of intraspecific variability in mitochondrial genomes and its relevance to evolutionary diversification patterns.…”

The Complete Plastid Genome of Magnolia zenii and Genetic Comparison to Magnoliaceae species

“…Rates of nucleotide substitution were previously shown to be several times slower in the plastid IR regions compared with SC regions in other angiosperms, suggesting that IR regions provide enhanced copy-correction activity [49]. Gene conversion has been shown to be biased towards copy-dependent repair mechanisms [50]. This phenomenon is possibly due to error correction occurring via gene conversion between Irs [51].…”

Comparison of Auxenochlorella protothecoides and Chlorella spp. Chloroplast Genomes: Evidence for Endosymbiosis and Horizontal Virus-like Gene Transfer

“…The availability of algal and higher plant chloroplast genome sequences has enhanced the understanding of their evolutionary relationships by strengthening the reliability of taxonomic classification [ 29 ] and facilitating reassessment of previous species classifications [ 30 ] to reveal new insights into global genomic and evolutionary relationships. Recent genome analyses have revealed subspecies divergence among C. sorokiniana variants [ 31 ], also contributing to a better understanding of gene composition, as well as photosynthetic and metabolic pathways conducive to genetic modification [ 32 , 33 ].…”