The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes

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.

doi:10.1186/s13059-016-1080-3

Title: The draft genome of the C₃ panicoid grass species Dichanthelium oligosanthes

Journal Article · Fri Oct 28 00:00:00 EDT 2016 · Genome Biology (Online)

DOI:https://doi.org/10.1186/s13059-016-1080-3· OSTI ID:1395571

Studer, Anthony J. ^[1]; Schnable, James C. ^[2]; Weissmann, Sarit ^[3]; Kolbe, Allison R. ^[4]; McKain, Michael R. ^[3]; Shao, Ying ^[5]; Cousins, Asaph B. ^[4]; Kellogg, Elizabeth A. ^[3]; Brutnell, Thomas P. ^[3]

Donald Danford Plant Science Center, St. Louis, MO (United States); Univ. of Illinois Urbana-Champaign, Urbana, IL (United States)
Donald Danford Plant Science Center, St. Louis, MO (United States); Univ. of Nebraska-Lincoln, Lincoln, NE (United States)
Donald Danford Plant Science Center, St. Louis, MO (United States)
Washington State Univ., Pullman, WA (United States)
Donald Danford Plant Science Center, St. Louis, MO (United States); St. Jude Children's Research Hospital, Memphis, TN (United States)

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.

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Research Organization:: Univ. of Illinois, Urbana-Champaign, Urbana, IL (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: FG02-12ER16337; SC0008510

OSTI ID:: 1395571

Journal Information:: Genome Biology (Online), Vol. 17, Issue 1; ISSN 1474-760X

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 26 works

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES
Dichanthelium oligosanthes
PACMAD
Panicoid grass
Photosynthesis
Carbonic anhydrase

The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes Studer, Anthony; Schnable, James; Weissmann, Sarit https://doi.org/10.6084/m9.figshare.c.3597854 The current record is supplemented by this dataset	dataset	October 2016
The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes [Supplemental Data] Studer, Anthony; Schnable, James; Weissmann, Sarit https://doi.org/10.6084/m9.figshare.c.3597854.v1 The current record is supplemented by this dataset	dataset	October 2016
Additional file 2: Table S1. of The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes Studer, Anthony; Schnable, James; Weissmann, Sarit https://doi.org/10.6084/m9.figshare.c.3597854_d1 The current record is supplemented by this text	text	January 2016
Additional file 2: Table S1. of The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes Studer, Anthony; Schnable, James; Weissmann, Sarit https://doi.org/10.6084/m9.figshare.c.3597854_d1.v1 The current record is supplemented by this figure	figure	October 2016
Additional file 5: of The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes Studer, Anthony; Schnable, James; Weissmann, Sarit https://doi.org/10.6084/m9.figshare.c.3597854_d2 The current record is supplemented by this text	text	January 2016
Additional file 5: of The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes Studer, Anthony; Schnable, James; Weissmann, Sarit https://doi.org/10.6084/m9.figshare.c.3597854_d2.v1 The current record is supplemented by this dataset	dataset	October 2016
Additional file 1: Figure S1. of The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes Studer, Anthony; Schnable, James; Weissmann, Sarit https://doi.org/10.6084/m9.figshare.c.3597854_d3 The current record is supplemented by this text	text	January 2016
Additional file 1: Figure S1. of The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes Studer, Anthony; Schnable, James; Weissmann, Sarit https://doi.org/10.6084/m9.figshare.c.3597854_d3.v1 The current record is supplemented by this dataset	dataset	October 2016
Additional file 4: of The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes Studer, Anthony; Schnable, James; Weissmann, Sarit https://doi.org/10.6084/m9.figshare.c.3597854_d4 The current record is supplemented by this text	text	January 2016
Additional file 4: of The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes Studer, Anthony; Schnable, James; Weissmann, Sarit https://doi.org/10.6084/m9.figshare.c.3597854_d4.v1 The current record is supplemented by this dataset	dataset	October 2016
Additional file 3: Table S2. of The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes Studer, Anthony; Schnable, James; Weissmann, Sarit https://doi.org/10.6084/m9.figshare.c.3597854_d5 The current record is supplemented by this text	text	January 2016
Additional file 3: Table S2. of The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes Studer, Anthony; Schnable, James; Weissmann, Sarit https://doi.org/10.6084/m9.figshare.c.3597854_d5.v1 The current record is supplemented by this figure	figure	October 2016

Title: The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes

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