Inferring Ancestral Chloroplast Genomes with Inverted Repeat

Genome evolution is shaped not only by nucleotide substitutions, but also by structural changes including gene and genome duplications, insertions/deletions and gene order rearrangements. Reconstruction of phylogeny based on gene order changes has been limited to cases where equal gene content or few deletions can be assumed. Since conserved duplicated regions are present in many Chloroplast genomes, the inference of inverted repeats is needed in ancestral genome reconstruction. We apply GRAPPA-IR to reconstruct ancestral chloroplast genomes containing duplicated genes. A test of GRAPPA-IR using divergent chloroplast genomes from land plants and green algae recovers the phylogeny congruent with prior studies, while analysis that do not consider IR structure fail to obtain the accepted topology. The ancestral genome structure suggests that genome rearrangement in chloroplasts is probably limited by inverted repeats with a conserved core region. In addition, the boundaries of inverted repeats are hot spots for gene duplications or deletions.