title: Functional network analysis of genes differentially expressed during xylogenesis in soc1ful woody Arabidopsis plants.
abstract: Many plant genes are known to be involved in the development of cambium and wood, but how the expression and functional interaction of these genes determine the unique biology of wood remains largely unknown. We used the soc1ful loss of function mutant - the woodiest genotype known in the otherwise herbaceous model plant Arabidopsis - to investigate the expression and interactions of genes involved in secondary growth (wood formation). Detailed anatomical observations of the stem in combination with mRNA sequencing were used to assess transcriptome remodeling during xylogenesis in wild-type and woody soc1ful plants. To interpret the transcriptome changes, we constructed functional gene association networks of differentially expressed genes using the STRING database. This analysis revealed functionally enriched gene association hubs that are differentially expressed in herbaceous and woody tissues. In particular, we observed the differential expression of genes related to mechanical stress and jasmonate biosynthesis/signaling during wood formation in soc1ful plants that may be an effect of greater tension within woody tissues. Our results suggest that habit shifts from herbaceous to woody life forms observed in many angiosperm lineages could have evolved convergently by genetic changes that modulate the gene expression and interaction network, and thereby redeploy the conserved wood developmental program.
authors.affiliation: Naturalis Biodiversity Center, Leiden University, PO Box 9517, 2300 RA Leiden, The Netherlands.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Davin
authors.affiliation: Department of Horticulture, Michigan State University, East Lansing, MI, 48823, USA.
authors.forename: Patrick P
authors.initials: PP
authors.lastname: Edger
authors.affiliation: Department of Botany, University of British Columbia, Department of Botany, 6270 University Blvd, Vancouver BC V6T 1Z4, Canada.|Biotechnology Platform, Agricultural Research Council, Private Bag X5, Onderstepoort, 0110, South Africa.
authors.forename: Charles A
authors.initials: CA
authors.lastname: Hefer
authors.affiliation: Department of Genetics, University of Pretoria, PO Box X20, Pretoria, 0028, South Africa.|Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
authors.forename: Eshchar
authors.initials: E
authors.lastname: Mizrachi
authors.affiliation: Department of Botany, University of British Columbia, Department of Botany, 6270 University Blvd, Vancouver BC V6T 1Z4, Canada.|Michael Smith Laboratories, University of British Columbia, 6270 University boulevard, V6T 1Z4, Vancouver, BC, Canada.
authors.forename: Mathias
authors.initials: M
authors.lastname: Schuetz
authors.affiliation: Naturalis Biodiversity Center, Leiden University, PO Box 9517, 2300 RA Leiden, The Netherlands.|Ecology, Evolution and Biodiversity Conservation Section, Katholieke Universiteit Leuven, Kasteelpark Arenberg 31 box 2435, 3001 Leuven, Belgium.
authors.forename: Erik
authors.initials: E
authors.lastname: Smets
authors.affiliation: Department of Genetics, University of Pretoria, PO Box X20, Pretoria, 0028, South Africa.|Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
authors.forename: Alexander A
authors.initials: AA
authors.lastname: Myburg
authors.affiliation: Department of Botany, University of British Columbia, Department of Botany, 6270 University Blvd, Vancouver BC V6T 1Z4, Canada.
authors.forename: Carl J
authors.initials: CJ
authors.lastname: Douglas
authors.affiliation: Biosystematics Group, Wageningen University, PO Box 16, 6700AP Wageningen, The Netherlands.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Schranz
authors.affiliation: Naturalis Biodiversity Center, Leiden University, PO Box 9517, 2300 RA Leiden, The Netherlands.
authors.forename: Frederic
authors.initials: F
authors.lastname: Lens
mesh_terms: D017360:Arabidopsis / Q000033:anatomy & histology / Q000235:genetics* / Q000254:growth & development; D029681:Arabidopsis Proteins / Q000235:genetics*; D058506:Cambium / Q000033:anatomy & histology / Q000235:genetics / Q000254:growth & development; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D026161:MADS Domain Proteins / Q000235:genetics*; D058977:Molecular Sequence Annotation; D009154:Mutation; D018515:Plant Leaves / Q000033:anatomy & histology / Q000235:genetics / Q000254:growth & development; D018547:Plant Stems / Q000033:anatomy & histology / Q000235:genetics / Q000254:growth & development; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D014934:Wood / Q000032:analysis / Q000235:genetics / Q000254:growth & development
chemical_list: C419046:AGL20 protein, Arabidopsis; C097414:AGL8 protein, Arabidopsis; D029681:Arabidopsis Proteins; D026161:MADS Domain Proteins
keywords: Arabidopsis thaliana; network analysis; secondary woodiness; transcriptome remodeling; wood formation