The draft genome of the C₃ panicoid grass species Dichanthelium oligosanthes

Authors

Anthony J. Studer, Donald Danforth Plant Science Center
James C. Schnable, University of Nebraska-LincolnFollow
Sarit Weissmann, Donald Danforth Plant Science Center
Allison R. Kolbe, Washington State University
Michael R. McKain, Donald Danforth Plant Science Center
Ying Shao, Donald Danforth Plant Science Center
Asaph B. Cousins, Washington State University
Elizabeth A. Kellogg, Donald Danforth Plant Science CenterFollow
Thomas P. Brutnell, Donald Danforth Plant Science Center

ORCID IDs

James C. Schnable

Document Type

Article

Date of this Version

2016

Citation

Studer et al. Genome Biology (2016) 17:223

Comments

© The Author(s). 2016 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License

Abstract

Background: Comparisons between C₃ and C₄ grasses often utilize C₃ species from the subfamilies Ehrhartoideae or Pooideae and C₄ species from the subfamily Panicoideae, two clades that diverged over 50 million years ago. The divergence of the C₃ panicoid grass Dichanthelium oligosanthes from the independent C₄ 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 C₃ and C₄ 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 C₃ 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 C₄ photosynthesis.

Conclusions: The phylogenetic location of D. oligosanthes makes it an ideal C₃ plant for comparative analysis of C₄ evolution in the panicoid grasses. This genome will not only provide a better C₃ species for comparisons with C₄ panicoid grasses, but also highlights the power of using high-throughput sequencing to address questions in evolutionary biology.