DNA transposon activity is associated with increased mutation rates in genes of rice and other grasses.
DNA (class 2) transposons are mobile genetic elements which move within their 'host' genome through excising and re-inserting elsewhere. Although the rice genome contains tens of thousands of such elements, their actual role in evolution is still unclear. Analysing over 650 transposon polymorphisms in the rice species Oryza sativa and Oryza glaberrima, we find that DNA repair following transposon excisions is associated with an increased number of mutations in the sequences neighbouring the transposon. Indeed, the 3,000 bp flanking the excised transposons can contain over 10 times more mutations than the genome-wide average. Since DNA transposons preferably insert near genes, this is correlated with increases in mutation rates in coding sequences and regulatory regions. Most importantly, we find this phenomenon also in maize, wheat and barley. Thus, these findings suggest that DNA transposon activity is a major evolutionary force in grasses which provide the basis of most food consumed by humankind.
Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland.
Thomas
T
Wicker
Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA.
Yeisoo
Y
Yu
Plant Genome and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany.
Georg
G
Haberer
Plant Genome and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany.
Klaus F X
KF
Mayer
Dow AgroSciences, Indianapolis, Indiana 46268, USA.
Pradeep Reddy
PR
Marri
Dow AgroSciences, Indianapolis, Indiana 46268, USA.
Steve
0000-0002-3016-6795
S
Rounsley
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101 China.
Mingsheng
M
Chen
Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy.
Andrea
0000-0001-7574-0714
A
Zuccolo
Laboratoire Génome et Développement des Plantes, UMR5096 UPVD/CNRS, Université de Perpignan Via Domitia, 66860 Perpignan, France.
Olivier
O
Panaud
Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA.|International Rice Research Institute, Los Baños, 4031 Laguna, Philippines.|Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA.
Rod A
RA
Wing
Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland.
Stefan
S
Roffler
D001483:Base Sequence; D004251:DNA Transposable Elements / Q000235:genetics / Q000502:physiology*; D018744:DNA, Plant / Q000235:genetics; D018506:Gene Expression Regulation, Plant / Q000502:physiology*; D009154:Mutation; D012275:Oryza / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism*; D020641:Polymorphism, Single Nucleotide
D004251:DNA Transposable Elements; D018744:DNA, Plant; D010940:Plant Proteins