title: Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA.
authors.forename: Zhanyou
authors.initials: Z
authors.lastname: Xu
authors.forename: Dandan
authors.initials: D
authors.lastname: Zhang
authors.forename: Jun
authors.initials: J
authors.lastname: Hu
authors.forename: Xin
authors.initials: X
authors.lastname: Zhou
authors.forename: Xia
authors.initials: X
authors.lastname: Ye
authors.forename: Kristen L
authors.initials: KL
authors.lastname: Reichel
authors.forename: Nathan R
authors.initials: NR
authors.lastname: Stewart
authors.forename: Ryan D
authors.initials: RD
authors.lastname: Syrenne
authors.forename: Xiaohan
authors.initials: X
authors.lastname: Yang
authors.forename: Peng
authors.initials: P
authors.lastname: Gao
authors.forename: Weibing
authors.initials: W
authors.lastname: Shi
authors.forename: Crissa
authors.initials: C
authors.lastname: Doeppke
authors.forename: Robert W
authors.initials: RW
authors.lastname: Sykes
authors.forename: Jason N
authors.initials: JN
authors.lastname: Burris
authors.forename: Joseph J
authors.initials: JJ
authors.lastname: Bozell
authors.forename: Max Zong-Ming
authors.initials: MZ
authors.lastname: Cheng
authors.forename: Douglas G
authors.initials: DG
authors.lastname: Hayes
authors.forename: Nicole
authors.initials: N
authors.lastname: Labbe
authors.forename: Mark
authors.initials: M
authors.lastname: Davis
authors.forename: C Neal
authors.initials: CN
authors.lastname: Stewart
authors.forename: Joshua S
authors.initials: JS
authors.lastname: Yuan
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D008031:Lignin / Q000096:biosynthesis*; D012275:Oryza / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D010944:Plants / Q000235:genetics*; D006109:Poaceae / Q000235:genetics
chemical_list: D010940:Plant Proteins; D008031:Lignin