title: Full transcription of the chloroplast genome in photosynthetic eukaryotes.
abstract: Prokaryotes possess a simple genome transcription system that is different from that of eukaryotes. In chloroplasts (plastids), it is believed that the prokaryotic gene transcription features govern genome transcription. However, the polycistronic operon transcription model cannot account for all the chloroplast genome (plastome) transcription products at whole-genome level, especially regarding various RNA isoforms. By systematically analyzing transcriptomes of plastids of algae and higher plants, and cyanobacteria, we find that the entire plastome is transcribed in photosynthetic green plants, and that this pattern originated from prokaryotic cyanobacteria - ancestor of the chloroplast genomes that diverged about 1 billion years ago. We propose a multiple arrangement transcription model that multiple transcription initiations and terminations combine haphazardly to accomplish the genome transcription followed by subsequent RNA processing events, which explains the full chloroplast genome transcription phenomenon and numerous functional and/or aberrant pre-RNAs. Our findings indicate a complex prokaryotic genome regulation when processing primary transcripts.
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650204, China.|University of the Chinese Academy of Sciences, Beijing 100039, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Shi
authors.affiliation: Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650093, China.
authors.forename: Shuo
authors.initials: S
authors.lastname: Wang
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650204, China.|University of the Chinese Academy of Sciences, Beijing 100039, China.
authors.forename: En-Hua
authors.initials: EH
authors.lastname: Xia
authors.affiliation: Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650093, China.
authors.forename: Jian-Jun
authors.initials: JJ
authors.lastname: Jiang
authors.affiliation: Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650093, China.
authors.forename: Fan-Chun
authors.initials: FC
authors.lastname: Zeng
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650204, China.|Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650093, China.
authors.forename: Li-Zhi
authors.initials: LZ
authors.lastname: Gao
mesh_terms: D000458:Cyanobacteria / Q000235:genetics; D056890:Eukaryota / Q000235:genetics*; D054628:Genome, Chloroplast; D008957:Models, Genetic; D010788:Photosynthesis; D018087:Plastids / Q000235:genetics; D017393:RNA Editing; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic