Chloroplast Gene Order and the Divergence of Plants and Algae, from the Normalized Number of Induced Breakpoints

Normalizing the number of breakpoints between two genomes, previously reduced by deleting the genes specific to one or the other, gives a rapidly calculated index of gene order evolution which is not based on any assumptions about the relative importance of various possible rearrangement processes. This is used to compare chloroplast genomes with known gene orders, with a focus on recently sequenced members of the algal class Prasinophycae. Phylogenies based on pairwise comparisons highlight the paraphyly and polyphyly of this class, with Mesostigma viride branching near the time of divergence of the streptophytes and chlorophytes, possibly within the former, Nephroselmis olivacea branching near the base of the Chlorophyte lineage, and Pedinomonas minor diverging relatively recently from other Chlorophyte classes.