Abstract:
Plant genomes vary greatly in size, organization, and architecture. Such structural differences
may be highly relevant for inference of genome evolution dynamics and phylogeny. Indeed,
microsynteny—the conservation of local gene content and order—is recognized as a valuable
source of phylogenetic information, but its use for the inference of large phylogenies has been
limited. Here, by combining synteny network analysis, matrix representation, and maximum
likelihood phylogenetic inference, we provide a way to reconstruct phylogenies based on
microsynteny information. Both simulations and use of empirical data sets show our method
to be accurate, consistent, and widely applicable. As an example, we focus on the analysis of
a large-scale whole-genome data set for angiosperms, including more than 120 available
high-quality genomes, representing more than 50 different plant families and 30 orders. Our
‘microsynteny-based’ tree is largely congruent with phylogenies proposed based on more
traditional sequence alignment-based methods and current phylogenetic classifications but
differs for some long-contested and controversial relationships. For instance, our syntenybased tree finds Vitales as early diverging eudicots, Saxifragales within superasterids, and
magnoliids as sister to monocots. We discuss how synteny-based phylogenetic inference
can complement traditional methods and could provide additional insights into some
long-standing controversial phylogenetic relationships.
