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Comparative DNA sequence analyses of Pyramimonas parkeae (Prasinophyceae) chloroplast genomes
Author(s) -
Satjarak Anchittha,
Graham Linda E.
Publication year - 2017
Publication title -
journal of phycology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.85
H-Index - 127
eISSN - 1529-8817
pISSN - 0022-3646
DOI - 10.1111/jpy.12515
Subject(s) - biology , genome , phylogenomics , chloroplast dna , evolutionary biology , phylogenetic tree , chloroplast , phylogenetics , genetics , clade , gene
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 NIES 254 and compared it with that of P. parkeae CCMP 726, the only other fully sequenced P. parkeae chloroplast genome. The results revealed that P. parkeae chloroplast genomes are surprisingly variable. The chloroplast genome of NIES 254 was larger than that of CCMP 726 by 3,204 bp, the NIES 254 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 CCMP 726. 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.