Plastid Genomes of Seed Plants

The field of comparative plastid genomics has burgeoned during the past decade, largely due to the availability of rapid, less expensive genome sequencing technologies. Currently there are 200 plastid genomes (plastomes) publicly available with 65% of these from seed plants. Comparative analyses have demonstrated that there is an overall stability in plastome architecture, gene and intron content, and gene order across seed plants. However, a number of unrelated lineages of both gymnosperms and angiosperms do not follow this pattern and have experienced considerable genomic upheaval. Within angiosperms these lineages with highly rearranged plastomes exhibit three other phenomena: highly accelerated rates of nucleotide substitutions, an increase in the number of dispersed repeats, many of which are associated with rearrangement endpoints, and biparental plastid inheritance. The correlation between genomic upheaval and these other phenomena suggest that aberrant DNA repair mechanisms may be involved in destabilizing these plastid genomes. Experimental studies support this idea because knocking out DNA repair genes destabilizes plastomes. Further studies of nuclear-plastid interactions, especially in seed plant lineages with highly rearranged plastomes, are needed to clarify the causes of the plastome instability. The large number of plastome sequences has also provided valuable data for resolving phylogenetic relationships among seed plants. This is especially true for angiosperms where these data have been instrumental in clarifying relationships among the early diverging clades, an endeavor that had stymied plant biologists for over a decade. The most recent plastome phylogenies clearly identify Amborella as the earliest diverging lineage of flowering plants and provide strong support for the position of magnoliids as sister to a large clade that includes eudicots and monocots. This robust phylogenetic estimate provides an evolutionary framework for examining patterns and rates of change in plastid genomes across angiosperms.