Abstract
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.
Highlights
Chloroplasts are semi-autonomous organelles that were derived from a cyanobacterial endosymbiont and entered the eukaryotic cell ancestor as an endosymbiont around one billion years ago [1,2]
The three chloroplast genomes encoded an identical set of 133 genes with 19 of which were duplicated in the inverted repeats (IRs) regions and 114 are unique (Figure 1)
Ycf15 was not observed in the examined chloroplast genome of gymnosperms and other species outside angiosperms; of ten species representing early diverging lineages of angiosperms, only five were found to contain an intact ycf15; in the next-diverging thirteen lineages of monocots under investigation, ycf15 became either disabled or absent from the related species; in eudicots, we found that intact ycf15 genes were mainly distributed at basal group of asterids together with some taxa of rosids
Summary
Chloroplasts are semi-autonomous organelles that were derived from a cyanobacterial endosymbiont and entered the eukaryotic cell ancestor as an endosymbiont around one billion years ago [1,2]. In spite of its small size, the gene expression system of chloroplasts is far more complex than that of their cyanobacterial progenitor [4,5,6]. Transcripts of higher plants chloroplast genomes undergo a variety of complex maturation events, including cis- and transsplicing, cleavage of polycistronic messages, processing of 59 and 39 ends, and RNA editing [5]. Plant chloroplast genomes contain many dispersedly distributed non-functional copies or pseudogenes fragments with numbers varied among different genomes, e.g. the Pelargonium6hortorum genome harbors at least 30 pseudogenes that account for ,1/5 of its total genes [7]. It has long been considered that the most chloroplast functional genes are generally transcribed as single polycistronic transcripts with subsequently processed into smaller mature RNAs [5,8]. We still lack a genome-wide profile concerning the transcripton of these non-functional elements or pseudogenes in the chloroplast genome
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