Distribution of ancestral gene pairs among the 12 prasinophyte cpDNAs examined in this study. We selected all the gene pairs that are shared by at least two prasinophytes from distinct lineages and also by one or both of the streptophytes Mesostigma and Chlorokybus. In addition, when one of the genes in a given gene pair was missing from several prasinophyte lineages or from the two streptophytes, gene pairs conserved in a single prasinophyte lineage or missing from streptophytes were selected. The presence of a gene pair is denoted by a dark blue box; a gray box indicates that at least one gene is missing due to gene loss. The gene pairs forming larger conserved clusters are grouped and individual genes that were cleanly deleted from some of these clusters are indicated on the right of the figure. Species names are abbreviated as in Table 1.