Using Comparative Data to Reconstruct the Evolution of the Foxtail Millet (Setaria italica) Chromosomes

Setaria italica (foxtail millet) belongs to the grass family, subfamily Panicoideae, tribe Paniceae.  Because foxtail millet is diploid (2n=2x=18), has a small genome (C=515 Mb) and is taxonomically closely related to several species with large and complex genomes that are of interest as bioenergy feedstocks, the foxtail millet genome was shotgun sequenced in 2010 using Sanger technology.  The sequence has been assembled into 9 pseudomolecules, corresponding to the 9 foxtail millet chromosomes and is anchored to a 1000-loci genetic map.  Gene and repeat distribution in the foxtail millet genome is comparable to that in other small genomes.  We conducted comparative analyses of the Setaria genome with the sorghum, rice and B. distachyon sequence assemblies.  These analyses showed that sorghum has undergone considerably less chromosomal rearrangements than foxtail millet, or the lineage leading to foxtail millet, since the divergence of the two species from a common ancestor 26 million years ago.  To more precisely determine the timing of those rearrangements, we extended the comparative analysis to include switchgrass using sequence information from a newly generated switchgrass consensus map as comparative data points.  Most of the rearrangements appear to have occurred in the last 13 mya.  A model depicting the evolution of the foxtail millet chromosomes will be presented.