Advances in the use of next-generation sequence data in plant systematics and evolution

In just the past 20 years the use of molecular markers in systematics, evolution, and horticulture has progressed from using sequences of a few individual genes for a few taxa to using larger and larger sequence sets that are accumulating due to the routine sequencing of complete plastid genomes, transcriptomes, and even complete nuclear genomes. Here we highlight two areas in which the advances in molecular markers are transforming plant evolutionary biology: 1) assembling and exploring the plant tree of life, and 2) using genomic tools to make any “non-model” research organism more of a “model.” Recent technological advances in sequencing (i.e., next-generation sequencing) and the development of computational methods and resources have made it possible to compile and analyze enormous molecular data sets for phylogenetic analyses, and the resulting topologies have in turn provided unprecedented insights into plant evolution. In the angiosperms, for example, we have obtained new insights into many of the enigmatic deep-level relationships as well as the rapid radiations that have characterized angiosperm evolution. In addition, computational advances in phylogenetics enable analyses with thousands of terminals, which help elucidate large-scale patterns of evolution within plants. Recent advances in high-throughput sequencing technology also afford the opportunity to accelerate dramatically our ability to examine genome evolution in non-model species. For example, in Tragopogon (Asteraceae), an evolutionary model for the study of recent and recurrent polyploidization, we have used a genomic approach to survey gene loss and expression changes that follow polyploidization