Distribution of specific ORF s, sequences showing similarity with the other pepper mtDNA, tobacco mtDNA and FS4401 plastid genome, repeated sequences in FS4401 and Jeju mtDNA. Locations of ORFs (longer than 300 bp) that are specific to FS4401 (above) or Jeju (below) are shown on FS4401 or Jeju mtDNA, respectively. Red-colored ORFs are specifically present only in one of genomes or carry structural rearrangements. Blue-colored ORFs show polymorphism in length or sequence compared to its counterpart. Known genes are depicted in grey. The sequences showing similarity between genomes were determined based on alignment generated using default parameters of the BLASTN algorithm and is depicted by black rectangles or bars. The distribution of repeated sequences in each genome (>100 bp; > 95%) is depicted with black bars and rectangles. The name of ORFs indicates the number of amino acids in encoded proteins except for the case of ‘orf507’ for which the number of nucleotides in the ORF was adopted to name the ORF in consistent with the previous research .