The chloroplast genomes of Euglena viridis and Euglenaformis [Euglena] proxima were sequenced and analyzed against the chloroplast genomes of other previously sequenced algal taxa. The chloroplast genome of E. viridis was sequenced in order to explore intrageneric chloroplast evolution, and our results revealed that while the chloroplast genome of E. viridis closely resembled that of Euglena gracilis, it did show significant differences. The chloroplast genome of E. viridis was far more compact, had a gene cluster that was reversed in both gene order and strand orientation, had a region that was comprised almost entirely of open reading frames, and had substantially fewer introns than E. gracilis. However, despite these differences, it was clear that the majority of chloroplast evolution in the genus Euglena probably occurred before its divergence from the rest of the photosynthetic euglenoids. The chloroplast genome of E. proxima was sequenced in an attempt to clarify its relationship to the rest of the photosynthetic euglenoids. Genetic data obtained from the chloroplast genome sequence were used in phylogenomic analyses to compare 78 chloroplast-encoded genes from E. proxima with those found in six photosynthetic euglenoids and three prasinophytes. The results of these analyses were consistent with the results of previous phylogenetic analyses using a small number of small subunit and large subunit rDNA genes and supported the position of E. proxima as sister to all of the Euglenaceae. Based on these data, E. proxima was removed from the genus Euglena, and a new genus, Euglenaformis, was erected for this taxon.
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