Analysis of the chloroplast genome of Phalaenopsis aphrodite

The complete nucleotide sequence of the chloroplast genome of the Taiwan moth orchid (Phalaenopsis aphrodite subsp. formosana) was determined. The circular, double-stranded DNA of 148,964 bp comprises a pair of inverted repeats of 25,732 bp, which are separated by a small single copy (SSC) and a large single copy (LSC) region of 11,543 and 85,957 bp, respectively. The genome contains 76 protein coding genes, four ribosomal RNA genes, 30 tRNA genes, and 24 putative open reading frames (ORFs). Seventeen genes are intron-containing, including 6 tRNA and 11 protein coding genes. Unlike other chloroplast genomes of photosynthetic angiosperms, which have a complete set of genes in the 11 subunits of NADH dehydrogenase, the chloroplast genome of Phalaenopsis completely lacks the ndhA, ndhH, and ndhF genes. The other eight ndh genes have various degrees of nucleotide insertion/deletion, and they are all frameshifted. This loss results in the SSC region in Phalaenopsis being the shortest among known photosynthetic angiosperms.