Abstract
BackgroundRNA editing is a posttranscriptional modification process that alters the RNA sequence so that it deviates from the genomic DNA sequence. RNA editing mainly occurs in chloroplasts and mitochondrial genomes, and the number of editing sites varies in terrestrial plants. Why and how RNA editing systems evolved remains a mystery. Ginkgo biloba is one of the oldest seed plants and has an important evolutionary position. Determining the patterns and distribution of RNA editing in the ancient plant provides insights into the evolutionary trend of RNA editing, and helping us to further understand their biological significance.ResultsIn this paper, we investigated 82 protein-coding genes in the chloroplast genome of G. biloba and identified 255 editing sites, which is the highest number of RNA editing events reported in a gymnosperm. All of the editing sites were C-to-U conversions, which mainly occurred in the second codon position, biased towards to the U_A context, and caused an increase in hydrophobic amino acids. RNA editing could change the secondary structures of 82 proteins, and create or eliminate a transmembrane region in five proteins as determined in silico. Finally, the evolutionary tendencies of RNA editing in different gene groups were estimated using the nonsynonymous-synonymous substitution rate selection mode.ConclusionsThe G. biloba chloroplast genome possesses the highest number of RNA editing events reported so far in a seed plant. Most of the RNA editing sites can restore amino acid conservation, increase hydrophobicity, and even influence protein structures. Similar purifying selections constitute the dominant evolutionary force at the editing sites of essential genes, such as the psa, some psb and pet groups, and a positive selection occurred in the editing sites of nonessential genes, such as most ndh and a few psb genes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0944-8) contains supplementary material, which is available to authorized users.
Highlights
RNA editing is a posttranscriptional modification process that alters the RNA sequence so that it deviates from the genomic DNA sequence
We explored the RNA editing sites of the protein-encoding genes in the G. biloba chloroplast genome, and identified 255 editing sites in 82 transcripts, which is the highest number of RNA editing cases reported in seed plants
G. biloba chloroplast transcripts undergo several editing events Based on the sequence alignments between DNAs and cDNAs, we identified 255 editing sites in 82 proteincoding genes in the G. biloba chloroplast genome, and all of the editing sites were C-to-U conversions
Summary
RNA editing is a posttranscriptional modification process that alters the RNA sequence so that it deviates from the genomic DNA sequence. RNA editing mainly occurs in chloroplasts and mitochondrial genomes, and the number of editing sites varies in terrestrial plants. RNA editing was first documented in the coxII gene of a trypanosome. RNA editing was found for the first time in the coxII of Triticum aestivum [3]. RNA editing mainly occurs in the protein-encoding genes of mitochondria and chloroplasts. He et al BMC Plant Biology (2016) 16:257 and it mostly converts C to U, hornwort and fern have abundant U to C editing. RNA editing has been associated with cytoplasmic male sterility [21, 22]. Cao et al found editing efficiencies are significantly reduced at the accD-794, accD-1568 and ndhF-290 sites, which could lead to etiolating and the delayed greening phenotype at the young seeding stage in A. thaliana [24]
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