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.
Highlights
The chloroplast, the green plastid that is found only in plant and algal cells, is a major cellular organelle for photosynthesis and plays important roles in many aspects of plant physiology and development, such as the biosynthesis of phytohormones, amino acids, fatty acids, and vitamins, the storage of a variety of products, the assimilation of sulfur and nitrogen, and function as a global sensor of abiotic stresses [1]
The results showed that there are six introncontaining tRNA genes in the chloroplasts of both dicot and monocot plants
Monocot plants contain ten introncontaining mRNA genes, whereas dicot plants harbor twelve intron-containing genes with two additional intron-containing genes in addition to the ten intron-containing mRNA genes found in monocot plants
Summary
The chloroplast, the green plastid that is found only in plant and algal cells, is a major cellular organelle for photosynthesis and plays important roles in many aspects of plant physiology and development, such as the biosynthesis of phytohormones, amino acids, fatty acids, and vitamins, the storage of a variety of products, the assimilation of sulfur and nitrogen, and function as a global sensor of abiotic stresses [1] The chloroplast is a double membrane-bound organelle that contains the thylakoid system where the process of light reaction of photosynthesis occurs. It has been demonstrated that chloroplast gene expression is regulated mainly at the posttranscriptional level, such as RNA splicing, RNA processing, RNA editing, RNA degradation, and translation [14,15,16]
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