Fig. 2: Codon alterations caused by editing in CDS regions, and the distributions of CDS-recoding sites and the corresponding recoded amino acids.

A Amino acid and codon alterations of 253 editing sites in CDS regions. Red and gray arrows denote codon alterations with more and less than 10 editing events, respectively. Edited RNA bases are underlined in codons. Amino acids in membrane structures and water drops denote hydrophobic and hydrophilic amino acids, respectively. Asterisks denote stop codons. Ala Alanine, Arg Arginine, Cys Cysteine, Gln Glutamine, His Histidine, Ile Isoleucine, Leu Leucine, Met Methionine, Phe Phenylalanine, Pro Proline, Ser Serine, Thr Threonine, Trp Tryptophan, Tyr Tyrosine, Val Valine. B Normalized CDS-recoding site counts in different grouped genes/proteins/complexes as well as their corresponding hydrophobic amino acid counts before and after editing. Purple bars denote normalized CDS-recoding site counts in protein-coding genes. Numbers in the left bars denote total normalized CDS-recoding site counts in different types of proteins or complexes (complex I, III, IV, V, Cyt c biogenesis proteins, ribosomal proteins and other proteins from up to down). Normalized counts of hydrophobic amino acids corresponding to editing sites before and after editing in protein-coding genes are shown as blue and red bars, respectively. Numbers in the right bars denote normalized hydrophobic amino acid counts after editing in different types of proteins or complexes. Normalized editing site counts (or normalized hydrophobic amino acid counts) in protein-coding genes (or proteins, or complexes) is denoted as “CDS-recoding site counts (or hydrophobic amino acid counts)/total length of CDS in the corresponding protein-coding gene (or protein, or complex) × 1000”. C Recoded amino acids caused by RNA editing with mapped positions in the 3D structure of apocytochrome b (COB). The abbreviation used is: IMM, inner mitochondrial membrane.