Functional network analysis of genes differentially expressed during xylogenesis insoc1fulwoody Arabidopsis plants

• DOI: 10.1111/tpj.13157
• Publication Date: 2016-03-08T07:24:49Z
• Authors: Nicolas Davin; Patrick P. Edger; Charles A. Hefer; Eshchar Mizrachi; Mathias Schuetz; Erik Smets; Alexander A. Myburg; Carl J. Douglas; Michael E. Schranz; Frederic Lens
• Keywords: 0301 basic medicine; Arabidopsis thaliana; Arabidopsis; MADS Domain Proteins; Transcriptome remodeling; Secondary woodiness; 03 medical and health sciences; Gene Expression Regulation, Plant; Gene Regulatory Networks; network analysis; transcriptome remodeling; 580; Wood formation; secondary woodiness; 0303 health sciences; Cambium; Plant Stems; Arabidopsis Proteins; Sequence Analysis, RNA; Molecular Sequence Annotation; 15. Life on land; Wood; Plant Leaves; Mutation; wood formation; Network analysis; Transcriptome

SummaryMany 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 thesoc1fulloss 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 withmRNAsequencing were used to assess transcriptome remodeling during xylogenesis in wild‐type and woodysoc1fulplants. To interpret the transcriptome changes, we constructed functional gene association networks of differentially expressed genes using theSTRINGdatabase. 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 insoc1fulplants 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.