This article is part of the supplement: Proceedings of the Sixth Annual MCBIOS Conference. Transformational Bioinformatics: Delivering Value from Genomes

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Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom

Zhanyou Xu12, Dandan Zhang3, Jun Hu123, Xin Zhou2, Xia Ye3, Kristen L Reichel4, Nathan R Stewart3, Ryan D Syrenne1, Xiaohan Yang5, Peng Gao12, Weibing Shi12, Crissa Doeppke4, Robert W Sykes4, Jason N Burris3, Joseph J Bozell6, (Max) Zong-Ming Cheng3, Douglas G Hayes6, Nicole Labbe6, Mark Davis4, C Neal Stewart3 and Joshua S Yuan12*

  • * Corresponding author: Joshua S Yuan

  • † Equal contributors

Author Affiliations

1 Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA

2 Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA

3 Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA

4 National Renewable Energy Laboratory, Golden, CO, USA

5 Oak Ridge National Laboratory, Oak Ridge, TN, USA

6 Department of Biosystems Engineering and Soil Sciences, University of Tennessee, Knoxville, TN, USA

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BMC Bioinformatics 2009, 10(Suppl 11):S3  doi:10.1186/1471-2105-10-S11-S3

Published: 8 October 2009



As a major component of plant cell wall, lignin plays important roles in mechanical support, water transport, and stress responses. As the main cause for the recalcitrance of plant cell wall, lignin modification has been a major task for bioenergy feedstock improvement. The study of the evolution and function of lignin biosynthesis genes thus has two-fold implications. First, the lignin biosynthesis pathway provides an excellent model to study the coordinative evolution of a biochemical pathway in plants. Second, understanding the function and evolution of lignin biosynthesis genes will guide us to develop better strategies for bioenergy feedstock improvement.


We analyzed lignin biosynthesis genes from fourteen plant species and one symbiotic fungal species. Comprehensive comparative genome analysis was carried out to study the distribution, relatedness, and family expansion of the lignin biosynthesis genes across the plant kingdom. In addition, we also analyzed the comparative synteny map between rice and sorghum to study the evolution of lignin biosynthesis genes within the Poaceae family and the chromosome evolution between the two species. Comprehensive lignin biosynthesis gene expression analysis was performed in rice, poplar and Arabidopsis. The representative data from rice indicates that different fates of gene duplications exist for lignin biosynthesis genes. In addition, we also carried out the biomass composition analysis of nine Arabidopsis mutants with both MBMS analysis and traditional wet chemistry methods. The results were analyzed together with the genomics analysis.


The research revealed that, among the species analyzed, the complete lignin biosynthesis pathway first appeared in moss; the pathway is absent in green algae. The expansion of lignin biosynthesis gene families correlates with substrate diversity. In addition, we found that the expansion of the gene families mostly occurred after the divergence of monocots and dicots, with the exception of the C4H gene family. Gene expression analysis revealed different fates of gene duplications, largely confirming plants are tolerant to gene dosage effects. The rapid expansion of lignin biosynthesis genes indicated that the translation of transgenic lignin modification strategies from model species to bioenergy feedstock might only be successful between the closely relevant species within the same family.