title: DNA methylation changes facilitated evolution of genes derived from Mutator-like transposable elements.
abstract: Mutator-like transposable elements, a class of DNA transposons, exist pervasively in both prokaryotic and eukaryotic genomes, with more than 10,000 copies identified in the rice genome. These elements can capture ectopic genomic sequences that lead to the formation of new gene structures. Here, based on whole-genome comparative analyses, we comprehensively investigated processes and mechanisms of the evolution of putative genes derived from Mutator-like transposable elements in ten Oryza species and the outgroup Leersia perieri, bridging ~20 million years of evolutionary history.
  
  
  
  Our analysis identified thousands of putative genes in each of the Oryza species, a large proportion of which have evidence of expression and contain chimeric structures. Consistent with previous reports, we observe that the putative Mutator-like transposable element-derived genes are generally GC-rich and mainly derive from GC-rich parental sequences. Furthermore, we determine that Mutator-like transposable elements capture parental sequences preferentially from genomic regions with low methylation levels and high recombination rates. We explicitly show that methylation levels in the internal and terminated inverted repeat regions of these elements, which might be directed by the 24-nucleotide small RNA-mediated pathway, are different and change dynamically over evolutionary time. Lastly, we demonstrate that putative genes derived from Mutator-like transposable elements tend to be expressed in mature pollen, which have undergone de-methylation programming, thereby providing a permissive expression environment for newly formed/transposable element-derived genes.
  
  
  
  Our results suggest that DNA methylation may be a primary mechanism to facilitate the origination, survival, and regulation of genes derived from Mutator-like transposable elements, thus contributing to the evolution of gene innovation and novelty in plant genomes.
authors.affiliation: Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.
authors.forename: Yeisoo
authors.initials: Y
authors.lastname: Yu
authors.affiliation: Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA.
authors.forename: Feng
authors.initials: F
authors.lastname: Tao
authors.affiliation: Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.
authors.forename: Jianwei
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.
authors.forename: Dario
authors.initials: D
authors.lastname: Copetti
authors.affiliation: Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.
authors.forename: Dave
authors.initials: D
authors.lastname: Kudrna
authors.affiliation: Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.
authors.forename: Jayson
authors.initials: J
authors.lastname: Talag
authors.affiliation: Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.
authors.forename: Seunghee
authors.initials: S
authors.lastname: Lee
authors.affiliation: Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.|T.T. Chang Genetics Resources Center, International Rice Research Institute, Los Baños, Laguna, 4031, Philippines.
authors.forename: Rod A
authors.initials: RA
authors.lastname: Wing
authors.affiliation: Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA. cfan@wayne.edu.
authors.forename: Chuanzhu
authors.initials: C
authors.lastname: Fan
mesh_terms: D019175:DNA Methylation / Q000235:genetics*; D004251:DNA Transposable Elements / Q000235:genetics*; D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D023281:Genomics; D012275:Oryza / Q000235:genetics*; D058727:RNA, Small Untranslated / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements; D058727:RNA, Small Untranslated
keywords: Comparative genomics; DNA methylation; GC content; MULEs; Molecular evolution; New genes; Oryza; Recombination rate