Molecular Genetics and Genomics

, Volume 276, Issue 6, pp 517–531

Global comparative transcriptome analysis identifies gene network regulating secondary xylem development in Arabidopsis thaliana

Original Paper


Our knowledge of the genetic control of wood formation (i.e., secondary growth) is limited. Here, we present a novel approach to unraveling the gene network regulating secondary xylem development in Arabidopsis, which incorporates complementary platforms of comparative-transcriptome analyses such as “digital northern” and “digital in situ” analysis. This approach effectively eliminated any genes that are expressed in either non-stem tissues/organs (“digital northern”) or phloem and non-vascular regions (“digital in situ”), thereby identifying 52 genes that are upregulated only in the xylem cells of secondary growth tissues as “core xylem gene set”. The proteins encoded by this gene set participate in signal transduction, transcriptional regulation, cell wall metabolism, and unknown functions. Five of the seven signal transduction-related genes represented in the core xylem gene set encode the essential components of ROP (Rho-related GTPase from plants) signaling cascade. Furthermore, the analysis of promoter sequences of the core xylem gene set identified a novel cis-regulatory element, ACAAAGAA. The functional significances of this gene set were verified by several independent experimental and bioinformatics methods.


Arabidopsis Comparative transcriptome analysis Genechip Secondary cell wall Secondary xylem Wood formation 

Supplementary material

Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  1. 1.Department of ForestryMichigan State UniversityEast LansingUSA
  2. 2.Department of HorticultureVirginia Polytechnic Institute and State UniversityBlacksburgUSA

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