The green algal ancestry of land plants as revealed by the chloroplast genome

The phylum Streptophyta comprises all land plants and six monophyletic groups of charophycean green algae. Which of these charophycean groups is the most closely related to land plants has long been debated. In 2001, a phylogenetic analysis of four genes encoded by three cellular compartments was inferred that robustly supports the placement of the Charales as sister to land plants as well as the notion that charophycean green algae evolved progressively toward an increasing cellular complexity. This view on the origin of land plants is now being challenged by recent analyses of chloroplast genome sequences from six charophyceans. Phylogenies inferred from multiple chloroplast genes and proteins support the hypothesis that the Charales are sister to a clade composed of the Coleochaetales, the Zygnematales, and land plants, thus implying a more complex evolutionary history for charophycean green algae. Analyses of four sets of genomic features (gene content, intron content, gene order, and insertions/deletions in coding regions) provided strong, independent evidence for the early emergence of the Charales and revealed that most of the features typical of land plant chloroplast genomes were inherited from their green algal ancestors. Here we review the information derived from these comparative genome analyses and present some additional, complementary analyses.