Genome-wide characterization of the lignification toolbox in Arabidopsis.

Abstract

Lignin, one of the most abundant terrestrial biopolymers, is indispensable for plant structure and defense. With the availability of the full genome sequence, large collections of insertion mutants, and functional genomics tools, Arabidopsis constitutes an excellent model system to profoundly unravel the monolignol biosynthetic pathway. In a genome-wide bioinformatics survey of the Arabidopsis genome, 34 candidate genes were annotated that encode genes homologous to the 10 presently known enzymes of the monolignol biosynthesis pathway, nine of which have not been described before. By combining evolutionary analysis of these 10 gene families with in silico promoter analysis and expression data (from a reverse transcription-polymerase chain reaction analysis on an extensive tissue panel, mining of expressed sequence tags from publicly available resources, and assembling expression data from literature), 12 genes could be pinpointed as the most likely candidates for a role in vascular lignification. Furthermore, a possible novel link was detected between the presence of the AC regulatory promoter element and the biosynthesis of G lignin during vascular development. Together, these data describe the full complement of monolignol biosynthesis genes in Arabidopsis, provide a unified nomenclature, and serve as a basis for further functional studies.

Supplementary Data

• List of monolignol pathway genes in Arabidopsis thaliana
• Position of genes on genome and correlation with large-scale duplications (not described in paper)
• List of primers used for gene-specific amplification
• AC element matrix used for promoter analysis
• Supplementary tables summarising known and new expression data of each gene family
• EST analysis details:
  1. Complete list of ESTs found for each gene
  2. EST classification details (zipped Microsoft Excell file)