Whole plastid transcriptomes reveal abundant RNA editing sites and differential editing status in Phalaenopsis aphrodite subsp. formosana

Abstract

BackgroundRNA editing is a process of post-transcriptional level of gene regulation by nucleotide modification. Previously, the chloroplast DNA of Taiwan endemic moth orchid, P. aphrodite subsp. formosana was determined, and 44 RNA editing sites were identified from 24 plastid protein-coding transcripts of leaf tissue via RT-PCR and then conventional Sanger sequencing. However, the RNA editing status of whole-plastid transcripts in leaf and other distinct tissue types in moth orchids has not been addressed. To sensitively and extensively examine the plastid RNA editing status of moth orchid, RNA-Seq was used to investigate the editing status of whole-plastid transcripts from leaf and floral tissues by mapping the sequence reads to the corresponding cpDNA template. With the threshold of at least 5% C-to-U or U-to-C conversion events observed in sequence reads considered as RNA editing sites.ResultsIn total, 137 edits with 126 C-to-U and 11 U-to-C conversions, including 93 newly discovered edits, were identified in plastid transcripts, representing an average of 0.09% of the nucleotides examined in moth orchid. Overall, 110 and 106 edits were present in leaf and floral tissues, respectively, with 79 edits in common. As well, 79 edits were involved in protein-coding transcripts, and the 58 nucleotide conversions caused the non-synonymous substitution. At least 32 edits showed significant (≧20%) differential editing between leaf and floral tissues. Finally, RNA editing in trnM is required for the formation of a standard clover-leaf structure.ConclusionsWe identified 137 edits in plastid transcripts of moth orchid, the highest number reported so far in monocots. The consequence of RNA editing in protein-coding transcripts mainly cause the amino acid change and tend to increase the hydrophobicity as well as conservation among plant phylogeny. RNA editing occurred in non-protein-coding transcripts such as tRNA, introns and untranslated regulatory regions could affect the formation and stability of secondary structure, which might play an important role in the regulation of gene expression. Furthermore, some unidentified tissue-specific factors might be required for regulating RNA editing in moth orchid.Electronic supplementary materialThe online version of this article (doi:10.1186/s40529-017-0193-7) contains supplementary material, which is available to authorized users.

The complete plastome of macaw palm [Acrocomia aculeata (Jacq.) Lodd. ex Mart.] and extensive molecular analyses of the evolution of plastid genes in Arecaceae

“…The number of RNA editing sites predicted here for protein-coding genes in palm species is high in comparison with others monocots, as rice (21 sites), maize (26 sites), and orchids (79 sites) (Corneille et al 2000;Chen et al 2017). Therefore, future analyses will be important to validate these putative sites identified in Arecoideae species.…”

“…From the total sites, 87 are shared among all species sampled in this study and 74 are completely or partially edited in C. nucifera (Huang et al, 2013), which suggest high conservation of the RNA editing mechanism within Arecoideae. Interestingly, most RNA editing sites predicted here change the encoded amino acid from polar to apolar, increasing the protein hydrophobicity which can affect structural features such as the creation of new transmembrane regions (He et al 2016;Chen et al 2017). Thereby, the general editing process is biased towards to increase the hydrophobicity of plastid proteins, which may be involved in protein-protein interactions and transmembrane domains present in the plastid protein complexes.…”

“…Like most angiosperms, all editing sites identified are C-to-U conversions, at the first or second position of the codons (Takenaka et al 2013;He et al 2016). RNA editing sites at the third position of the codon are less common, generally resulting in synonymous substitutions and having low frequency (He et al 2016;Chen et al 2017). From the total sites, 87 are shared among all species sampled in this study and 74 are completely or partially edited in C. nucifera (Huang et al, 2013), which suggest high conservation of the RNA editing mechanism within Arecoideae.…”

“…Following the evolution of higher plants several RNA editing sites were lost maintaining a relative conserved number of editing sites in angiosperms (Tillich et al 2006;Takenaka et al 2013;He et al 2016). Plastid RNA editing sites have been identified in mRNA, introns, and untranslated regions, being implicated primordially as error correctors, but also acting in regulatory functions and producing variants of proteins to adapt to different physiological needs (Takenaka et al 2013;Tseng et al 2013;He et al 2016;Chen et al 2017).…”

“…Nevertheless, the diversification rate over time within palm genera seems to increase and a convergent evolution has been reported among palm species adapted to shaded areas (Ma et al 2015;Faurby et al 2016). Despite most plastid genes are conserved, several evolutionary events have been described such as new RNA editing sites, loss of introns, high divergence of genes, and positive signatures (Sen et al 2012;Williams et al 2015;He et al 2016;Chen et al 2017). In grasses, one-third of the plastid genes underwent positive selection, which shows a relationship between gene evolution and environmental conditions regarding the photosynthetic apparatus (Piot et al 2017).…”