skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: The draft genome of the C 3 panicoid grass species Dichanthelium oligosanthes

Abstract

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. Here, 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 4more » photosynthesis. In conclusion, 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.« less

Authors:
 [1];  [2];  [3];  [4];  [3];  [5];  [4];  [3];  [3]
  1. Donald Danford Plant Science Center, St. Louis, MO (United States); Univ. of Illinois Urbana-Champaign, Urbana, IL (United States)
  2. Donald Danford Plant Science Center, St. Louis, MO (United States); Univ. of Nebraska-Lincoln, Lincoln, NE (United States)
  3. Donald Danford Plant Science Center, St. Louis, MO (United States)
  4. Washington State Univ., Pullman, WA (United States)
  5. Donald Danford Plant Science Center, St. Louis, MO (United States); St. Jude Children's Research Hospital, Memphis, TN (United States)
Publication Date:
Research Org.:
Univ. of Illinois, Urbana-Champaign, Urbana, IL (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1395571
Grant/Contract Number:  
FG02-12ER16337; SC0008510
Resource Type:
Accepted Manuscript
Journal Name:
Genome Biology (Online)
Additional Journal Information:
Journal Name: Genome Biology (Online); Journal Volume: 17; Journal Issue: 1; Journal ID: ISSN 1474-760X
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; Dichanthelium oligosanthes; PACMAD; Panicoid grass; Photosynthesis; Carbonic anhydrase

Citation Formats

Studer, Anthony J., Schnable, James C., Weissmann, Sarit, Kolbe, Allison R., McKain, Michael R., Shao, Ying, Cousins, Asaph B., Kellogg, Elizabeth A., and Brutnell, Thomas P. The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes. United States: N. p., 2016. Web. doi:10.1186/s13059-016-1080-3.
Studer, Anthony J., Schnable, James C., Weissmann, Sarit, Kolbe, Allison R., McKain, Michael R., Shao, Ying, Cousins, Asaph B., Kellogg, Elizabeth A., & Brutnell, Thomas P. The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes. United States. doi:10.1186/s13059-016-1080-3.
Studer, Anthony J., Schnable, James C., Weissmann, Sarit, Kolbe, Allison R., McKain, Michael R., Shao, Ying, Cousins, Asaph B., Kellogg, Elizabeth A., and Brutnell, Thomas P. Fri . "The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes". United States. doi:10.1186/s13059-016-1080-3. https://www.osti.gov/servlets/purl/1395571.
@article{osti_1395571,
title = {The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes},
author = {Studer, Anthony J. and Schnable, James C. and Weissmann, Sarit and Kolbe, Allison R. and McKain, Michael R. and Shao, Ying and Cousins, Asaph B. and Kellogg, Elizabeth A. and Brutnell, Thomas P.},
abstractNote = {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. Here, 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. In conclusion, 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.},
doi = {10.1186/s13059-016-1080-3},
journal = {Genome Biology (Online)},
number = 1,
volume = 17,
place = {United States},
year = {2016},
month = {10}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 6 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

The developmental dynamics of the maize leaf transcriptome
journal, October 2010

  • Li, Pinghua; Ponnala, Lalit; Gandotra, Neeru
  • Nature Genetics, Vol. 42, Issue 12, p. 1060-1067
  • DOI: 10.1038/ng.703

Fast and SNP-tolerant detection of complex variants and splicing in short reads
journal, February 2010


The B73 Maize Genome: Complexity, Diversity, and Dynamics
journal, November 2009

  • Schnable, P. S.; Ware, D.; Fulton, R. S.
  • Science, Vol. 326, Issue 5956, p. 1112-1115
  • DOI: 10.1126/science.1178534