The draft genome of the C(3) panicoid grass species Dichanthelium oligosanthes

BACKGROUND: Comparisons between C(3) and C(4) grasses often utilize C(3) species from the subfamilies Ehrhartoideae or Pooideae and C(4) species from the subfamily Panicoideae, two clades that diverged over 50 million years ago. The divergence of the C(3) panicoid grass Dichanthelium oligosanthes from the independent C(4) lineages represented by Setaria viridis and Sorghum bicolor occurred approximately 15 million years ago, which is significantly more recent than members of the Bambusoideae, Ehrhartoideae, and Pooideae subfamilies. D. oligosanthes is ideally placed within the panicoid clade for comparative studies of C(3) and C(4) grasses. RESULTS: We report the assembly of the nuclear and chloroplast genomes of D. oligosanthes, from high-throughput short read sequencing data and a comparative transcriptomics analysis of the developing leaf of D. oligosanthes, S. viridis, and S. bicolor. Physiological and anatomical characterizations verified that D. oligosanthes utilizes the C(3) pathway for carbon fixation and lacks Kranz anatomy. Expression profiles of transcription factors along developing leaves of D. oligosanthes and S. viridis were compared with previously published data from S. bicolor, Zea mays, and Oryza sativa to identify a small suite of transcription factors that likely acquired functions specifically related to C(4) photosynthesis. CONCLUSIONS: The phylogenetic location of D. oligosanthes makes it an ideal C(3) plant for comparative analysis of C(4) evolution in the panicoid grasses. This genome will not only provide a better C(3) species for comparisons with C(4) panicoid grasses, but also highlights the power of using high-throughput sequencing to address questions in evolutionary biology. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-016-1080-3) contains supplementary material, which is available to authorized users.