The chloroplasts of three exemplar taxa of photosynthetic euglenoids, have been sequenced and compared, providing an overview of chloroplast evolution in this highly diverse group of organisms which acquired their chloroplast through secondary endosymbiosis. The use of synteny mapping has shown that the chloroplast genomes of euglenoids are not fully collinear, and significant gene rearrangements have occurred across the lineage. The gene rearrangements however, have occurred largely through the repositioning of conserved gene clusters. Gene content among the taxa was similar with only a few variations noted including rpl32, psaI, psaM, rrn5, rpoA and roaA genes. Comparisons between the euglenoid chloroplast genomes also highlighted significant differences in genome sizes, due mainly to expansion/shrinkage of intergenic space and an overall increase in intron number. Further comparisons with the chloroplast genome of Euglena gracilis and green algal taxa provided insight into chloroplast genome evolution within the Euglenophyta. Phylogenies based upon 55 chloroplast genes are nearly identical to those based on nuclear encoded genes, indicating similar evolutionary pathways. Sequence comparisons and phylogenetic analyses have also provided evidence that the putative green algal chloroplast donor lineage was a scaly green algal flagellate belonging to the Prasinophyceae and that the chloroplast was acquired through a single endosymbiotic event.
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