Comprehensive analysis of chloroplast intron-containing genes and conserved splice sites in dicot and monocot plants

Abstract

Despite the increasing knowledge on the importance of the intron splicing of chloroplast genes during plant growth and stress responses, identification of intron-containing chloroplast genes and determination of splice sites in chloroplast introns are still lacking. Here, we carried out a comprehensive analysis of the chloroplast genome sequences in important plants and crops, including four dicots (Arabidopsis thaliana, Coffea arabica, Nicotiana tabacum, and Panax schinseng) and four monocots (Musa acuminata, Oryza sativa, Triticum aestivum, and Zea mays). The results showed that both dicot and monocot chloroplast genomes harbor 6 intron-containing tRNAs (trnA, trnG, trnI, trnK, trnL, and trnV) and 10-12 intron-containing mRNAs (atpF, rpl2, rpl16, rps16, ndhA, ndhB, petB, petD, rpoC1, rps12, ycf3, and clpP). Notably, rpoC1 and clpP lacked introns in monocot plants, except M. acuminata. Analysis of the nucleotide sequences of chloroplast introns revealed that the 5’-splice sites, 3’-splice sites, and branch-point sites of the chloroplast introns were highly conserved among dicots and monocots. Notably, the 5’-splice sites and 3’-splice sites of the chloroplast introns were similar to those of the nuclear U12 introns, whereas the branch-point sites of the chloroplast introns were homologous to those of the nuclear U2 introns. Taken together, these results indicated that the chloroplast genomes contained strictly limited intron-containing genes with conserved splice sites, suggesting that splicing of chloroplast introns was important for chloroplast biogenesis and function in both dicot and monocot plants.