Expression atlas and comparative coexpression network analyses reveal important genes involved in the formation of lignified cell wall in Brachypodium distachyon

New Phytol. 2017 Aug;215(3):1009-1025. doi: 10.1111/nph.14635. Epub 2017 Jun 15.


While Brachypodium distachyon (Brachypodium) is an emerging model for grasses, no expression atlas or gene coexpression network is available. Such tools are of high importance to provide insights into the function of Brachypodium genes. We present a detailed Brachypodium expression atlas, capturing gene expression in its major organs at different developmental stages. The data were integrated into a large-scale coexpression database (, enabling identification of duplicated pathways and conserved processes across 10 plant species, thus allowing genome-wide inference of gene function. We highlight the importance of the atlas and the platform through the identification of duplicated cell wall modules, and show that a lignin biosynthesis module is conserved across angiosperms. We identified and functionally characterised a putative ferulate 5-hydroxylase gene through overexpression of it in Brachypodium, which resulted in an increase in lignin syringyl units and reduced lignin content of mature stems, and led to improved saccharification of the stem biomass. Our Brachypodium expression atlas thus provides a powerful resource to reveal functionally related genes, which may advance our understanding of important biological processes in grasses.

Keywords: Brachypodium distachyon; coexpression; comparative coexpression; expression atlas; functional modules; gene function; lignin.

MeSH terms

  • Arabidopsis / genetics
  • Brachypodium / cytology*
  • Brachypodium / genetics*
  • Cell Wall / genetics*
  • Databases, Genetic
  • Gene Expression Regulation, Plant*
  • Gene Regulatory Networks*
  • Genes, Plant*
  • Lignin / metabolism*
  • Oryza / genetics
  • Plant Stems / metabolism
  • Plants, Genetically Modified
  • Transcriptome / genetics


  • Lignin