title: A Comparative Epigenomic Analysis of Polyploidy-Derived Genes in Soybean and Common Bean.
abstract: Soybean (Glycine max) and common bean (Phaseolus vulgaris) share a paleopolyploidy (whole-genome duplication [WGD]) event, approximately 56.5 million years ago, followed by a genus Glycine-specific polyploidy, approximately 10 million years ago. Cytosine methylation is an epigenetic mark that plays an important role in the regulation of genes and transposable elements (TEs); however, the role of DNA methylation in the fate/evolution of genes following polyploidy and speciation has not been fully explored. Whole-genome bisulfite sequencing was used to produce nucleotide resolution methylomes for soybean and common bean. We found that, in soybean, CG body-methylated genes were abundant in WGD genes, which were, on average, more highly expressed than single-copy genes and had slower evolutionary rates than unmethylated genes, suggesting that WGD genes evolve more slowly than single-copy genes. CG body-methylated genes were also enriched in shared single-copy genes (single copy in both species) that may be responsible for the broad and high expression patterns of this class of genes. In addition, diverged methylation patterns in non-CG contexts between paralogs were due mostly to TEs in or near genes, suggesting a role for TEs and non-CG methylation in regulating gene expression post polyploidy. Reference methylomes for both soybean and common bean were constructed, providing resources for investigating epigenetic variation in legume crops. Also, the analysis of methylation patterns of duplicated and single-copy genes has provided insights into the functional consequences of polyploidy and epigenetic regulation in plant genomes.
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602 (K.D.K., M.E.B., B.A., A.I.-O., C.C., M.G., S.A.J.);Department of Microbiology and Plant Biology, University of Oklahoma, Noman, Oklahoma 73019 (M.L.); andHudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806 (J.G.).
authors.forename: Kyung Do
authors.identifier: http://orcid.org/0000-0001-5296-2349
authors.initials: KD
authors.lastname: Kim
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602 (K.D.K., M.E.B., B.A., A.I.-O., C.C., M.G., S.A.J.);Department of Microbiology and Plant Biology, University of Oklahoma, Noman, Oklahoma 73019 (M.L.); andHudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806 (J.G.).
authors.forename: Moaine
authors.initials: M
authors.lastname: El Baidouri
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602 (K.D.K., M.E.B., B.A., A.I.-O., C.C., M.G., S.A.J.);Department of Microbiology and Plant Biology, University of Oklahoma, Noman, Oklahoma 73019 (M.L.); andHudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806 (J.G.).
authors.forename: Brian
authors.initials: B
authors.lastname: Abernathy
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602 (K.D.K., M.E.B., B.A., A.I.-O., C.C., M.G., S.A.J.);Department of Microbiology and Plant Biology, University of Oklahoma, Noman, Oklahoma 73019 (M.L.); andHudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806 (J.G.).
authors.forename: Aiko
authors.identifier: http://orcid.org/0000-0001-9378-3961
authors.initials: A
authors.lastname: Iwata-Otsubo
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602 (K.D.K., M.E.B., B.A., A.I.-O., C.C., M.G., S.A.J.);Department of Microbiology and Plant Biology, University of Oklahoma, Noman, Oklahoma 73019 (M.L.); andHudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806 (J.G.).
authors.forename: Carolina
authors.initials: C
authors.lastname: Chavarro
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602 (K.D.K., M.E.B., B.A., A.I.-O., C.C., M.G., S.A.J.);Department of Microbiology and Plant Biology, University of Oklahoma, Noman, Oklahoma 73019 (M.L.); andHudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806 (J.G.).
authors.forename: Michael
authors.initials: M
authors.lastname: Gonzales
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602 (K.D.K., M.E.B., B.A., A.I.-O., C.C., M.G., S.A.J.);Department of Microbiology and Plant Biology, University of Oklahoma, Noman, Oklahoma 73019 (M.L.); andHudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806 (J.G.).
authors.forename: Marc
authors.identifier: http://orcid.org/0000-0001-7419-9129
authors.initials: M
authors.lastname: Libault
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602 (K.D.K., M.E.B., B.A., A.I.-O., C.C., M.G., S.A.J.);Department of Microbiology and Plant Biology, University of Oklahoma, Noman, Oklahoma 73019 (M.L.); andHudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806 (J.G.).
authors.forename: Jane
authors.initials: J
authors.lastname: Grimwood
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602 (K.D.K., M.E.B., B.A., A.I.-O., C.C., M.G., S.A.J.);Department of Microbiology and Plant Biology, University of Oklahoma, Noman, Oklahoma 73019 (M.L.); andHudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806 (J.G.) sjackson@uga.edu.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Jackson
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D019175:DNA Methylation; D004251:DNA Transposable Elements; D044127:Epigenesis, Genetic; D057890:Epigenomics / Q000379:methods*; D063990:Gene Ontology; D017343:Genes, Plant / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics; D027805:Phaseolus / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification / Q000235:genetics; D011123:Polyploidy; D013025:Glycine max / Q000145:classification / Q000235:genetics*; D013045:Species Specificity; D026801:Synteny
chemical_list: D004251:DNA Transposable Elements; D010940:Plant Proteins