Gene organization of the C. japonica chloroplast genome (see Table 1). Genes shown outside the circle are transcribed clockwise, while those located inside are transcribed counter-clockwise. Intron-containing genes are indicated by asterisks. Red boxes, ribosomal RNA genes; black boxes, transfer RNA genes; light orange boxes, large subunit of ribosomal protein genes; dark orange boxes, small subunit of ribosomal protein genes; dark purple boxes, DNA dependent RNA polymerase genes; dark green boxes, rbcL gene; yellowish-green boxes, subunits of photosystem I genes; green boxes, subunits of photosystem II genes; light blue boxes, subunits of cytochrome genes; dark blue boxes, subunits of ATP synthase genes; light yellow boxes, ORF genes; dark yellow boxes, subunits of NADH dehydrogenase genes; light purple boxes, chlorophyll biosynthesis genes. The pseudogene is indicated by ψ (pseudo-).