CG gene body DNA methylation changes and evolution of duplicated genes in cassava.
DNA methylation is important for the regulation of gene expression and the silencing of transposons in plants. Here we present genome-wide methylation patterns at single-base pair resolution for cassava (Manihot esculenta, cultivar TME 7), a crop with a substantial impact in the agriculture of subtropical and tropical regions. On average, DNA methylation levels were higher in all three DNA sequence contexts (CG, CHG, and CHH, where H equals A, T, or C) than those of the most well-studied model plant Arabidopsis thaliana. As in other plants, DNA methylation was found both on transposons and in the transcribed regions (bodies) of many genes. Consistent with these patterns, at least one cassava gene copy of all of the known components of Arabidopsis DNA methylation pathways was identified. Methylation of LTR transposons (GYPSY and COPIA) was found to be unusually high compared with other types of transposons, suggesting that the control of the activity of these two types of transposons may be especially important. Analysis of duplicated gene pairs resulting from whole-genome duplication showed that gene body DNA methylation and gene expression levels have coevolved over short evolutionary time scales, reinforcing the positive relationship between gene body methylation and high levels of gene expression. Duplicated genes with the most divergent gene body methylation and expression patterns were found to have distinct biological functions and may have been under natural or human selection for cassava traits.
Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095;
Haifeng
H
Wang
Donald Danforth Plant Science Center, St. Louis, MO 63132;
Getu
G
Beyene
Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095;
Jixian
J
Zhai
Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095;
Suhua
S
Feng
Donald Danforth Plant Science Center, St. Louis, MO 63132;
Noah
N
Fahlgren
Donald Danforth Plant Science Center, St. Louis, MO 63132;
Nigel J
NJ
Taylor
Donald Danforth Plant Science Center, St. Louis, MO 63132;
Rebecca
R
Bart
Donald Danforth Plant Science Center, St. Louis, MO 63132;
James C
JC
Carrington
Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095; Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095 jacobsen@ucla.edu israel.ausin@gmail.com.
Steven E
SE
Jacobsen
Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; jacobsen@ucla.edu israel.ausin@gmail.com.
Israel
I
Ausin
D019175:DNA Methylation; D020440:Gene Duplication; D002365:Manihot / Q000235:genetics*
DNA methylation; cassava; duplicate genes; gene expression