title: The Methylome of Soybean Roots during the Compatible Interaction with the Soybean Cyst Nematode.
abstract: The soybean cyst nematode (SCN; Heterodera glycines) induces the formation of a multinucleated feeding site, or syncytium, whose etiology includes massive gene expression changes. Nevertheless, the genetic networks underlying gene expression control in the syncytium are poorly understood. DNA methylation is a critical epigenetic mark that plays a key role in regulating gene expression. To determine the extent to which DNA methylation is altered in soybean (Glycine max) roots during the susceptible interaction with SCN, we generated whole-genome cytosine methylation maps at single-nucleotide resolution. The methylome analysis revealed that SCN induces hypomethylation to a much higher extent than hypermethylation. We identified 2,465 differentially hypermethylated regions and 4,692 hypomethylated regions in the infected roots compared with the noninfected control. In addition, 703 and 1,346 unique genes were identified as overlapping with hyper- or hypomethylated regions, respectively. The differential methylation in genes apparently occurs independently of gene size and GC content but exhibits strong preference for recently duplicated paralogs. Furthermore, a set of 278 genes was identified as specifically syncytium differentially methylated genes. Of these, we found genes associated with epigenetic regulation, phytohormone signaling, cell wall architecture, signal transduction, and ubiquitination. This study provides, to our knowledge, new evidence that differential methylation is part of the regulatory mechanisms controlling gene expression changes in the nematode-induced syncytium.
authors.affiliation: Department of Plant Sciences (A.R., J.H.R., J.L., P.R., M.M., V.P., C.N.S., T.H.), and Department of Entomology, Plant Pathology, and Nematology (T.L., M.S.), University of Tennessee, Knoxville, Tennessee 37996.
authors.forename: Aditi
authors.initials: A
authors.lastname: Rambani
authors.affiliation: Department of Plant Sciences (A.R., J.H.R., J.L., P.R., M.M., V.P., C.N.S., T.H.), and Department of Entomology, Plant Pathology, and Nematology (T.L., M.S.), University of Tennessee, Knoxville, Tennessee 37996.
authors.forename: J Hollis
authors.identifier: http://orcid.org/0000-0003-4046-1672
authors.initials: JH
authors.lastname: Rice
authors.affiliation: Department of Plant Sciences (A.R., J.H.R., J.L., P.R., M.M., V.P., C.N.S., T.H.), and Department of Entomology, Plant Pathology, and Nematology (T.L., M.S.), University of Tennessee, Knoxville, Tennessee 37996.
authors.forename: Jinyi
authors.initials: J
authors.lastname: Liu
authors.affiliation: Department of Plant Sciences (A.R., J.H.R., J.L., P.R., M.M., V.P., C.N.S., T.H.), and Department of Entomology, Plant Pathology, and Nematology (T.L., M.S.), University of Tennessee, Knoxville, Tennessee 37996.
authors.forename: Thomas
authors.identifier: http://orcid.org/0000-0003-4082-9502
authors.initials: T
authors.lastname: Lane
authors.affiliation: Department of Plant Sciences (A.R., J.H.R., J.L., P.R., M.M., V.P., C.N.S., T.H.), and Department of Entomology, Plant Pathology, and Nematology (T.L., M.S.), University of Tennessee, Knoxville, Tennessee 37996.
authors.forename: Priya
authors.initials: P
authors.lastname: Ranjan
authors.affiliation: Department of Plant Sciences (A.R., J.H.R., J.L., P.R., M.M., V.P., C.N.S., T.H.), and Department of Entomology, Plant Pathology, and Nematology (T.L., M.S.), University of Tennessee, Knoxville, Tennessee 37996.
authors.forename: Mitra
authors.initials: M
authors.lastname: Mazarei
authors.affiliation: Department of Plant Sciences (A.R., J.H.R., J.L., P.R., M.M., V.P., C.N.S., T.H.), and Department of Entomology, Plant Pathology, and Nematology (T.L., M.S.), University of Tennessee, Knoxville, Tennessee 37996.
authors.forename: Vince
authors.initials: V
authors.lastname: Pantalone
authors.affiliation: Department of Plant Sciences (A.R., J.H.R., J.L., P.R., M.M., V.P., C.N.S., T.H.), and Department of Entomology, Plant Pathology, and Nematology (T.L., M.S.), University of Tennessee, Knoxville, Tennessee 37996.
authors.forename: C Neal
authors.initials: CN
authors.lastname: Stewart
authors.affiliation: Department of Plant Sciences (A.R., J.H.R., J.L., P.R., M.M., V.P., C.N.S., T.H.), and Department of Entomology, Plant Pathology, and Nematology (T.L., M.S.), University of Tennessee, Knoxville, Tennessee 37996.
authors.forename: Meg
authors.identifier: http://orcid.org/0000-0003-2971-9353
authors.initials: M
authors.lastname: Staton
authors.affiliation: Department of Plant Sciences (A.R., J.H.R., J.L., P.R., M.M., V.P., C.N.S., T.H.), and Department of Entomology, Plant Pathology, and Nematology (T.L., M.S.), University of Tennessee, Knoxville, Tennessee 37996 thewezi@utk.edu.
authors.forename: Tarek
authors.initials: T
authors.lastname: Hewezi
mesh_terms: D000818:Animals; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D015870:Gene Expression; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D006790:Host-Parasite Interactions; D010935:Plant Diseases / Q000469:parasitology*; D018517:Plant Roots / Q000235:genetics / Q000469:parasitology; D013025:Glycine max / Q000235:genetics* / Q000469:parasitology; D014431:Tylenchoidea / Q000502:physiology*