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Plant chloroplast genes are usually co-transcribed while its posttranscriptional splicing is fairly complex and remains largely unsolved. On basis of sequencing the three complete  Camellia  (Theaceae) chloroplast genomes for the first time, we comprehensively analyzed the evolutionary patterns of  ycf15 , a plastid gene quite paradoxical in terms of its function and evolution, along the inferred angiosperm phylogeny. Although many species in separate lineages including the three species reported here contained an intact  ycf15  gene in their chloroplast genomes, the phylogenetic mixture of both intact and obviously disabled  ycf15  genes imply that they are all non-functional. Both intracellular gene transfer (IGT) and horizontal gene transfer (HGT) failed to explain such distributional anomalies. While, transcriptome analyses revealed that  ycf15  was transcribed as precursor polycistronic transcript which contained  ycf2 ,  ycf15  and antisense  trnL-CAA . The transcriptome assembly was surprisingly found to cover near the complete  Camellia  chloroplast genome. Many non-coding regions including pseudogenes were mapped by multiple transcripts, indicating the generality of pseudogene transcriptions. Our results suggest that plastid DNA posttranscriptional splicing may involve complex cleavage of non-functional genes.

plos one

Contradiction between Plastid Gene Transcription and Function Due to Complex Posttranscriptional Splicing: An Exemplary Study of ycf15 Function and Evolution in Angiosperms