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Background  Photosynthetic euglenids acquired their plastid by secondary endosymbiosis of a prasinophyte-like green alga. But unlike its prasinophyte counterparts, the plastid genome of the euglenid  Euglena gracilis  is riddled with introns that interrupt almost every protein-encoding gene. The atypical group II introns and twintrons (introns-within-introns) found in the  E. gracilis  plastid have been hypothesized to have been acquired late in the evolution of euglenids, implying that massive numbers of introns may be lacking in other taxa. This late emergence was recently corroborated by the plastid genome sequences of the two basal euglenids,  Eutreptiella gymnastica  and  Eutreptia viridis , which were found to contain fewer introns.    Methodology/Principal Findings  To gain further insights into the proliferation of introns in euglenid plastids, we have characterized the complete plastid genome sequence of  Monomorphina aenigmatica , a freshwater species occupying an intermediate phylogenetic position between early and late branching euglenids. The  M. aenigmatica  UTEX 1284 plastid genome (74,746 bp, 70.6% A+T, 87 genes) contains 53 intron insertion sites, of which 41 were found to be shared with other euglenids including 12 of the 15 twintron insertion sites reported in  E. gracilis .    Conclusions  The pattern of insertion sites suggests an ongoing but uneven process of intron gain in the lineage, with perhaps a minimum of two bursts of rapid intron proliferation. We also identified several sites that represent intermediates in the process of twintron evolution, where the external intron is in place, but not the internal one, offering a glimpse into how these convoluted molecular contraptions originate.

Evidence for Transitional Stages in the Evolution of Euglenid Group II Introns and Twintrons in the Monomorphina aenigmatica Plastid Genome