Sequencing and Analysis of the Complete Organellar Genomes ofPrototheca wickerhamii

Of theProtothecagenus,Protothecawickerhamiihas the highest clinical significance in humans. However, neither nuclear nor organellar genomes of this species were sequenced until now. The hitherto determined and analyzed mitochondrial and plastid genomes of the allegedP. wickerhamiispecies belong in fact to another species, recently namedPrototheca xanthoriae. This study provides a first insight into the organellar genomes of a trueP. wickerhamii(type strain ATCC 16529). TheP. wickerhamiimitochondrion had a 53.8-kb genome, which was considerably larger than that ofProtothecaciferrii(formerlyPrototheca zopfiigen. 1) andPrototheca bovis(formerlyPrototheca zopfiigen. 2), yet similarly functional, with the differences in size attributable to a higher number of introns and the presence of extra unique putative genes. The 48-kb plastid genome ofP. wickerhamii, compared to autotrophic Trebouxiophyceae, was highly reduced due to the elimination of the photosynthesis-related genes. The gene content of the plastid genome ofP. wickerhamiiwas, however, very similar to other colorlessProtothecaspecies. Plastid genome-based phylogeny reinforced the polyphyly of the genusPrototheca, withHelicosporidiumandAuxenochlorellabranching within clades ofProtothecaspecies. Phylogenetic reconstruction also confirmed the close relationship ofP. wickerhamiiandP. xanthoriae, which is reflected in the synteny of their organellar genomes. Interestingly, the entire set ofatpgenes was lost inP. wickerhamiiplastid genome while being preserved inP. xanthoriae.