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Background  Over the last few years multiple studies have been published showing a great diversity in size of chloroplast genomes (cpGenomes), and in the arrangement of gene clusters, in the Euglenales. However, while these genomes provided important insights into the evolution of cpGenomes across the Euglenales and within their genera, only two genomes were analyzed in regard to genomic variability between and within Euglenales and Eutreptiales. To better understand the dynamics of chloroplast genome evolution in early evolving Eutreptiales, this study focused on the cpGenome of  Eutreptiella pomquetensis , and the spread and peculiarities of introns.    Methods  The  Etl. pomquetensis  cpGenome was sequenced, annotated and afterwards examined in structure, size, gene order and intron content. These features were compared with other euglenoid cpGenomes as well as those of prasinophyte green algae, including  Pyramimonas parkeae .    Results and Discussion  With about 130,561 bp the chloroplast genome of  Etl. pomquetensis , a basal taxon in the phototrophic euglenoids, was considerably larger than the two other Eutreptiales cpGenomes sequenced so far. Although the detected quadripartite structure resembled most green algae and plant chloroplast genomes, the gene content of the single copy regions in  Etl. pomquetensis  was completely different from those observed in green algae and plants. The gene composition of  Etl. pomquetensis  was extensively changed and turned out to be almost identical to other Eutreptiales and Euglenales, and not to  P. parkeae . Furthermore, the cpGenome of  Etl. pomquetensis  was unexpectedly permeated by a high number of introns, which led to a substantially larger genome. The 51 identified introns of  Etl. pomquetensis  showed two major unique features: (i) more than half of the introns displayed a high level of pairwise identities; (ii) no group III introns could be identified in the protein coding genes. These findings support the hypothesis that group III introns are degenerated group II introns and evolved later.

Chloroplast genome expansion by intron multiplication in the basal psychrophilic euglenoidEutreptiella pomquetensis