Chloroplast Genome Diversity in the Phototrophic Euglenoids, with Emphasis on Genome Structure, Synteny and Intron Evolution

摘要

To shed light on chloroplast genome evolution in the phototrophic euglenoids the cpGenomes of Euglena mutabilis (SAG 1224-9b), Trachelomonas grandis (SAG 204.80) and Eutreptiella pomquetensis (CCMP 1491) were isolated, sequenced and annotated. The chloroplastgenomes were investigated intensively and compared to other cpGenomes of phototrophic euglenoids, with special focus on genome size and structure, number and localization ofrRNA operons as well as introns. As a cause for genome size differences three major reasonshave been identified. First, the intergenic space between the cpGenomes of different taxavaried greatly, even between closely related species. Second, the rRNA operon numbersbetween different taxa were not uniform. Third, the different intron numbers and intron typesbetween different taxa led to the main reason for size differences in euglenoids cpGenomes.Comprehensive trends of intron number and intron type have been detected in closely as wellas distantly related euglenoids. These trends can be used to explain intron density and quantityas well as high or low similarities in the evolution of introns in all phototrophic euglenoids.The expansion and evolution of psbC introns can partly be elucidated by assumed horizontalintron transfers in the chloroplast of euglenoids after the split from Eutreptiales andEuglenales.Findings concerning the emergence and evolution of group III introns supported thehypothesis that group III introns are degenerated group II introns. Surprisingly, thecpGenomes of the basally branching Eutreptiales are free of group III introns, although theresults indicated that their evolution began in Eutreptiales as intermediate stages of group IIand III introns (mini group II introns).Furthermore, a new phylogenomic analysis of phototrophic euglenoids was performed andcompared to recently published phylogenetic analyses. As a new approach genome-levelcharacters from all known cpGenomes of euglenoids have been used as a tool to complementthe phylogenomic analysis. Metacharacter analyses yielded gene arrangement, clusterarrangement and rRNA operons as viable metacharacters with partly important modificationsbetween the taxa. Significant cluster rearrangement was identified in several clades thatmatched the phylogenetic reconstruction. Using the rRNA operon as a metacharacter revealeda trend of loss of one rRNA copy following the diversification of Euglenales. Basallybranching Eutreptiales contained two copies, which is identical to the structure in the surmised chloroplast donor Pyramimonas parkeae. Only for both Euglena gracilis speciesand Strombomonas acuminata an independent acquirement of further rRNA operons wasrecognizable.The cpGenome of Eutreptiella pomquetensis showed the same quadripartite cpGenomestructure as Pyramimonas parkeae, corroborating the close relationship between these twotaxa. The present work provides a sound basis for further examinations of chloroplast genomeanalyses to get a more thorough understanding of intron evolution within the phototrophiceuglenoids. Likewise it represents a precursor for future studies concerning genome-levelfeatures in phototrophic euglenoids.