86 Chloroplast genome phylogenetics: facts and opinions

Recent progress in sequencing genomes from primary and secondary plastids provided various data including genomic complexities, gene sequences, gene complements, gene cluster organizations and rearrangements as well as secondary gene losses/gene relocations. They are considered to reflect evolutionary traits at different phylogenetic levels. However, current views of the validity of individual data sets are controversial and sometimes appear to reflect opinions rather than facts. Here I will present the plastid genomes of the Xanthophyte Vaucheria bursata and the brown alga Dictyota dichotoma and compare these genomes with those of other algae containing secondary plastids of rhodophytic origin. Gene complement analysis will focus on differential gene losses across evolutionary lineages and gene cluster rearrangements as a consequence of numerous inversions unknown from land plants. It will be discussed whether rearranged gene clusters common to two lineages, to the exclusion of others, may reflect parsimonious events or simply resulted from random independent processes. Although specific characters are encountered among all plastid genomes sequenced to date, the plastid genomes of Vaucheria and Dictyota confirm the presence of a basal set of 46 protein coding genes common to all plastid genomes of algae and metaphytes that have been used to infer a monophyletic origin of primary plastids and their evolutionary offsprings.