title: DNA methylation and gene expression regulation associated with vascularization in Sorghum bicolor.
abstract: Plant secondary cell walls constitute the majority of plant biomass. They are predominantly found in xylem cells, which are derived from vascular initials during vascularization. Little is known about these processes in grass species despite their emerging importance as biomass feedstocks. The targeted biofuel crop Sorghum bicolor has a sequenced and well-annotated genome, making it an ideal monocot model for addressing vascularization and biomass deposition. Here we generated tissue-specific transcriptome and DNA methylome data from sorghum shoots, roots and developing root vascular and nonvascular tissues. Many genes associated with vascular development in other species show enriched expression in developing vasculature. However, several transcription factor families varied in vascular expression in sorghum compared with Arabidopsis and maize. Furthermore, differential expression of genes associated with DNA methylation were identified between vascular and nonvascular tissues, implying that changes in DNA methylation are a feature of sorghum root vascularization, which we confirmed using tissue-specific DNA methylome data. Roots treated with a DNA methylation inhibitor also showed a significant decrease in root length. Tissues and organs can be discriminated based on their genomic methylation patterns and methylation context. Consequently, tissue-specific changes in DNA methylation are part of the normal developmental process.
authors.affiliation: Department of Plant Biology and Genome Center, UC Davis, Davis, CA, 95616, USA.
authors.forename: Gina M
authors.initials: GM
authors.lastname: Turco
authors.affiliation: Department of Plant Biology and Genome Center, UC Davis, Davis, CA, 95616, USA.
authors.forename: Kaisa
authors.initials: K
authors.lastname: Kajala
authors.affiliation: DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
authors.forename: Govindarajan
authors.initials: G
authors.lastname: Kunde-Ramamoorthy
authors.affiliation: DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
authors.forename: Chew-Yee
authors.initials: CY
authors.lastname: Ngan
authors.affiliation: Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Olson
authors.affiliation: DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
authors.forename: Shweta
authors.initials: S
authors.lastname: Deshphande
authors.affiliation: DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
authors.forename: Denis
authors.initials: D
authors.lastname: Tolkunov
authors.affiliation: Department of Plant Biology and Genome Center, UC Davis, Davis, CA, 95616, USA.
authors.forename: Barbara
authors.initials: B
authors.lastname: Waring
authors.affiliation: Department of Agronomy and Great Lakes Bioenergy Research Center, University of Wisconsin, 1575 Linden Drive, Madison, WI, 53706, USA.
authors.forename: Scott
authors.initials: S
authors.lastname: Stelpflug
authors.affiliation: Institute for Plant Genomics and Biotechnology and Department of Horticultural Sciences, Texas A and M University, College Station, TX, 77843, USA.
authors.forename: Patricia
authors.initials: P
authors.lastname: Klein
authors.affiliation: DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.|HudsonAlpha Institute for Biotechnology, 601 Genome Way NW, Huntsville, AL, 35806, USA.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Schmutz
authors.affiliation: Department of Agronomy and Great Lakes Bioenergy Research Center, University of Wisconsin, 1575 Linden Drive, Madison, WI, 53706, USA.
authors.forename: Shawn
authors.initials: S
authors.lastname: Kaeppler
authors.affiliation: Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA.|USDA-ARS, Ithaca, NY, 14853, USA.
authors.forename: Doreen
authors.initials: D
authors.lastname: Ware
authors.affiliation: DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
authors.forename: Chia-Lin
authors.initials: CL
authors.lastname: Wei
authors.affiliation: Department of Plant Biology and Genome Center, UC Davis, Davis, CA, 95616, USA.|School of Biological and Biomedical Sciences, Durham University, South Road, Durham, DH3 1LE, UK.
authors.forename: J Peter
authors.identifier: http://orcid.org/0000-0002-8524-4949
authors.initials: JP
authors.lastname: Etchells
authors.affiliation: Department of Plant Biology and Genome Center, UC Davis, Davis, CA, 95616, USA.
authors.forename: Siobhan M
authors.initials: SM
authors.lastname: Brady
mesh_terms: D002473:Cell Wall / Q000235:genetics; D017124:Conserved Sequence; D019175:DNA Methylation / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018517:Plant Roots / Q000235:genetics; D058526:Plant Vascular Bundle / Q000235:genetics*; D045868:Sorghum / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics
keywords: biofuel; cell type-specific; epigenetics; sorghum (Sorghum bicolor); transcriptome