title: Transcriptional Slippage and RNA Editing Increase the Diversity of Transcripts in Chloroplasts: Insight from Deep Sequencing of Vigna radiata Genome and Transcriptome.
abstract: We performed deep sequencing of the nuclear and organellar genomes of three mungbean genotypes: Vigna radiata ssp. sublobata TC1966, V. radiata var. radiata NM92 and the recombinant inbred line RIL59 derived from a cross between TC1966 and NM92. Moreover, we performed deep sequencing of the RIL59 transcriptome to investigate transcript variability. The mungbean chloroplast genome has a quadripartite structure including a pair of inverted repeats separated by two single copy regions. A total of 213 simple sequence repeats were identified in the chloroplast genomes of NM92 and RIL59; 78 single nucleotide variants and nine indels were discovered in comparing the chloroplast genomes of TC1966 and NM92. Analysis of the mungbean chloroplast transcriptome revealed mRNAs that were affected by transcriptional slippage and RNA editing. Transcriptional slippage frequency was positively correlated with the length of simple sequence repeats of the mungbean chloroplast genome (R2=0.9911). In total, 41 C-to-U editing sites were found in 23 chloroplast genes and in one intergenic spacer. No editing site that swapped U to C was found. A combination of bioinformatics and experimental methods revealed that the plastid-encoded RNA polymerase-transcribed genes psbF and ndhA are affected by transcriptional slippage in mungbean and in main lineages of land plants, including three dicots (Glycine max, Brassica rapa, and Nicotiana tabacum), two monocots (Oryza sativa and Zea mays), two gymnosperms (Pinus taeda and Ginkgo biloba) and one moss (Physcomitrella patens). Transcript analysis of the rps2 gene showed that transcriptional slippage could affect transcripts at single sequence repeat regions with poly-A runs. It showed that transcriptional slippage together with incomplete RNA editing may cause sequence diversity of transcripts in chloroplasts of land plants.
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 11529, Taiwan; Department of Earth and Life Science, University of Taipei, Taipei 10048, Taiwan.
authors.forename: Ching-Ping
authors.initials: CP
authors.lastname: Lin
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 11529, Taiwan.
authors.forename: Chia-Yun
authors.initials: CY
authors.lastname: Ko
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 11529, Taiwan.
authors.forename: Ching-I
authors.initials: CI
authors.lastname: Kuo
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 11529, Taiwan.
authors.forename: Mao-Sen
authors.initials: MS
authors.lastname: Liu
authors.affiliation: AVRDC-The World Vegetable Center, Shanhua, Tainan 74199, Taiwan.
authors.forename: Roland
authors.initials: R
authors.lastname: Schafleitner
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 11529, Taiwan.
authors.forename: Long-Fang Oliver
authors.initials: LF
authors.lastname: Chen
mesh_terms: D002736:Chloroplasts / Q000235:genetics* / Q000378:metabolism; D007887:Fabaceae / Q000235:genetics* / Q000378:metabolism; D061125:Genes, Chloroplast; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D017393:RNA Editing; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: D012333:RNA, Messenger