title: Contradiction between plastid gene transcription and function due to complex posttranscriptional splicing: an exemplary study of ycf15 function and evolution in angiosperms.
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.
authors.affiliation: Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Shi
authors.forename: Yuan
authors.initials: Y
authors.lastname: Liu
authors.forename: Hui
authors.initials: H
authors.lastname: Huang
authors.forename: En-Hua
authors.initials: EH
authors.lastname: Xia
authors.forename: Hai-Bin
authors.initials: HB
authors.lastname: Zhang
authors.forename: Li-Zhi
authors.initials: LZ
authors.lastname: Gao
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D028244:Camellia / Q000235:genetics*; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D017343:Genes, Plant / Q000235:genetics*; D054628:Genome, Chloroplast / Q000235:genetics*; D016013:Likelihood Functions; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D011544:Pseudogenes / Q000235:genetics; D012323:RNA Processing, Post-Transcriptional / Q000235:genetics / Q000502:physiology*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013045:Species Specificity