Analysis of mitochondrial genomics and transcriptomics reveal abundant RNA edits and differential editing status in moth orchid, Phalaenopsis aphrodite subsp. formosana

Abstract

We determined the mitochondrial genome of an endemic moth orchid, Phalaenopsis aphrodite subsp. formosana, and annotated the mitochondrial genes, studied gene expression and investigated the RNA editing status. The mitochondrial DNA (mtDNA) of moth orchid is approximately 576,203 bp, with 27 % and 9% of sequences derived from nucleus and plastid, respectively. The mtDNA encodes 38 protein-coding, 9 tRNA and 3 ribosomal RNA genes of mitochondrial origin. Up to 1032 RNA edits, with 1020 C-to-U and 12 U-to-C conversions, were identified from mitochondrial transcripts of leaf and floral tissues, the highest number reported so far in angiosperms. Overall, 941 edits were involved in protein-coding transcripts, and the 686 nucleotide conversions caused non-synonymous substitution. RNA editing in protein-coding transcripts mainly altered the amino acids and tended to increase the hydrophobicity as well as conservation among plant phylogeny. The remaining 91 RNA edits occurred in non–protein-coding transcripts such as untranslated regulatory regions and introns; some would affect the stability of secondary structures, which might play an important role in regulating gene expression. The average efficiency of RNA editing was significantly higher for protein-coding than non–protein-coding transcripts 69.1 % vs 44.2 %). At least 135 edits showed significant (≥ 20 %) differential editing between leaf and floral tissues, which suggested that unidentified tissue-specific factors might be required for regulating RNA editing in moth orchid. In addition, the mitochondrial gene expression varied among genes, tissue types and developmental stages in moth orchid.