Genomic Insights into the Evolution of Angiosperms

Whole-genome sequencing has provided new insights into the dynamics of genomes across the angiosperms. With increased parallelization of sequencing reactions, more species can be explored at the genomic level than ever before. However, a better understanding of the relationships between species at the genomic level is still dependent on the assembly of genomic sequences into contiguous sequence information so that genes can be ordered along chromosomes. This information is particularly important for analyzing gene families and ancient genome duplication events. Comparison of the collinear order of genes between species reveals copy number variation (CNV), where the function of some copies remain very conserved and others diverge. An example of conservation of function is the linkage between a copy of a miRNA169 gene and a CONSTANS-LIKE gene across the monocot barrier, which possibly could explain a linkage drag between two different but interconnected pathways. Although certain miRNA169 genes are involved in drought tolerance, others could have a role in the carbon flow in stems. CNV appears to also explain in part neoteny, where juvenile to adult transition in rapidly growing aquatic plants is suppressed. In particular interesting is CNV that affects RNA editing because cis- and trans-acting functions are separated into different compartments of cells. CNV of the pentatricopeptide repeat protein (PPR) gene family in the nuclear genome, one of the largest in plants that edits the sequence of organelle mRNAs, does not correlate with the phylogeny of species. It rather suggests gene losses can occur in different phylogenetic lineages.