Intrageneric chloroplast genome comparison in the genus Euglena (Phylum: Euglenophyta) with annotated chloroplast genomes of Euglena hiemalis and Euglena clara

The genus Euglena is composed of six subclades with a diversity of chloroplast morphologies, unlike that found in the other genera of Euglenaceae. This genus contains five published chloroplast genomes (cpGenome) and the colorless plastid genome (ptGenome) of the non-photosynthetic euglenoid Euglena longa within the same subclade as Euglena gracilis. Previous studies of cpGenomes revealed that Euglena viridis and E. gracilis, although in separate subclades, had few cpGenome differences, while Euglena mutabilis maintained the same gene order but was mirror-inverted except for the rRNA cluster. However, we expanded the number of cpGenomes available in Euglena by sequencing and annotating the cpGenomes of Euglena clara, the earliest diverging species in the E. gracilis and E. longa subclade and Euglena hiemalis, the putative sister species to E. longa. Analysis of these newly annotated cpGenomes showed them to be largely similar in gene content, conserved gene clusters (operons), and G + C/A + T percentage to previously published Euglena cpGenomes. The only extensive gene rearrangements observed were between cpGenomes and the ptGenome in subclade B. However, a unique feature of the subclade was multi-copies of the rRNA operon. Also, homologous twintrons in psbD and psbF to E. gracilis were observed in E. hiemalis. Overall, these results revealed a conserved intrageneric cpGenome for Euglena species.