Figure 1

Gene map of the Gossypium hirsutum chloroplast genome. The thick lines indicate the extent of the inverted repeats (IRa and IRb), which separate the genome into small (SSC) and large (LSC) single copy regions. Genes on the outside of the map are transcribed in the clockwise direction and genes on the inside of the map are transcribed in the counterclockwise direction. Numbered lines around the map indicate the location of repeated sequences found in the cotton genome (see Table 1 for details). The SSC region is in the reverse orientation relative to tobacco [80]. This does not reflect any differences in gene order for cotton but simply reflects the well-known phenomenon that the SSC exists in two orientations in chloroplast genomes [84].