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Clade classification of monolignol biosynthesis gene family members reveals target genes to decrease lignin in Lolium perenne

(2015) PLANT BIOLOGY. 17(4). p.877-892
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Biotechnology for a sustainable economy (Bio-Economy)
Abstract
In monocots, lignin content has a strong impact on the digestibility of the cell wall fraction. Engineering lignin biosynthesis requires a profound knowledge of the role of paralogues in the multigene families that constitute the monolignol biosynthesis pathway. We applied a bioinformatics approach for genome-wide identification of candidate genes in Lolium perenne that are likely to be involved in the biosynthesis of monolignols. More specifically, we performed functional subtyping of phylogenetic clades in four multigene families: 4CL, COMT, CAD and CCR. Essential residues were considered for functional clade delineation within these families. This classification was complemented with previously published experimental evidence on gene expression, gene function and enzymatic activity in closely related crops and model species. This allowed us to assign functions to novel identified L.perenne genes, and to assess functional redundancy among paralogues. We found that two 4CL paralogues, two COMT paralogues, three CCR paralogues and one CAD gene are prime targets for genetic studies to engineer developmentally regulated lignin in this species. Based on the delineation of sequence conservation between paralogues and a first analysis of allelic diversity, we discuss possibilities to further study the roles of these paralogues in lignin biosynthesis, including expression analysis, reverse genetics and forward genetics, such as association mapping. We propose criteria to prioritise paralogues within multigene families and certain SNPs within these genes for developing genotyping assays or increasing power in association mapping studies. Although L.perenne was the target of the analyses presented here, this functional subtyping of phylogenetic clades represents a valuable tool for studies investigating monolignol biosynthesis genes in other monocot species.
Keywords
CAD (cinnamyl alcohol dehydrogenase), 4CL (4-coumarate:CoA ligase), CCR (cinnamoyl CoA reductase), COMT (caffeic acid 3-O-methyltransferase), lignin, monocots, monolignol biosynthesis genes, Lolium perenne, CINNAMYL-ALCOHOL-DEHYDROGENASE, ACID-O-METHYLTRANSFERASE, FESCUE FESTUCA-ARUNDINACEA, BIOETHANOL PRODUCTION, TRANSGENIC DOWN-REGULATION, COA-REDUCTASE, CRYSTAL-STRUCTURES, POPULUS-TRICHOCARPA, WALL DEGRADABILITY, SYSTEMS BIOLOGY

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Citation

Please use this url to cite or link to this publication:

Chicago
van Parijs, Frederik, Tom Ruttink, Wout Boerjan, Geert Haesaert, SL Byrne, T Asp, Isabel Roldàn-Ruiz, and H Muylle. 2015. “Clade Classification of Monolignol Biosynthesis Gene Family Members Reveals Target Genes to Decrease Lignin in Lolium Perenne.” Plant Biology 17 (4): 877–892.
APA
van Parijs, Frederik, Ruttink, T., Boerjan, W., Haesaert, G., Byrne, S., Asp, T., Roldàn-Ruiz, I., et al. (2015). Clade classification of monolignol biosynthesis gene family members reveals target genes to decrease lignin in Lolium perenne. PLANT BIOLOGY, 17(4), 877–892.
Vancouver
1.
van Parijs F, Ruttink T, Boerjan W, Haesaert G, Byrne S, Asp T, et al. Clade classification of monolignol biosynthesis gene family members reveals target genes to decrease lignin in Lolium perenne. PLANT BIOLOGY. 2015;17(4):877–92.
MLA
van Parijs, Frederik, Tom Ruttink, Wout Boerjan, et al. “Clade Classification of Monolignol Biosynthesis Gene Family Members Reveals Target Genes to Decrease Lignin in Lolium Perenne.” PLANT BIOLOGY 17.4 (2015): 877–892. Print.
@article{6929851,
  abstract     = {In monocots, lignin content has a strong impact on the digestibility of the cell wall fraction. Engineering lignin biosynthesis requires a profound knowledge of the role of paralogues in the multigene families that constitute the monolignol biosynthesis pathway. We applied a bioinformatics approach for genome-wide identification of candidate genes in Lolium perenne that are likely to be involved in the biosynthesis of monolignols. More specifically, we performed functional subtyping of phylogenetic clades in four multigene families: 4CL, COMT, CAD and CCR. Essential residues were considered for functional clade delineation within these families. This classification was complemented with previously published experimental evidence on gene expression, gene function and enzymatic activity in closely related crops and model species. This allowed us to assign functions to novel identified L.perenne genes, and to assess functional redundancy among paralogues. We found that two 4CL paralogues, two COMT paralogues, three CCR paralogues and one CAD gene are prime targets for genetic studies to engineer developmentally regulated lignin in this species. Based on the delineation of sequence conservation between paralogues and a first analysis of allelic diversity, we discuss possibilities to further study the roles of these paralogues in lignin biosynthesis, including expression analysis, reverse genetics and forward genetics, such as association mapping. We propose criteria to prioritise paralogues within multigene families and certain SNPs within these genes for developing genotyping assays or increasing power in association mapping studies. Although L.perenne was the target of the analyses presented here, this functional subtyping of phylogenetic clades represents a valuable tool for studies investigating monolignol biosynthesis genes in other monocot species.},
  author       = {van Parijs, Frederik and Ruttink, Tom and Boerjan, Wout and Haesaert, Geert and Byrne, SL and Asp, T and Rold{\`a}n-Ruiz, Isabel and Muylle, H},
  issn         = {1435-8603},
  journal      = {PLANT BIOLOGY},
  keyword      = {CAD (cinnamyl alcohol dehydrogenase),4CL (4-coumarate:CoA ligase),CCR (cinnamoyl CoA reductase),COMT (caffeic acid 3-O-methyltransferase),lignin,monocots,monolignol biosynthesis genes,Lolium perenne,CINNAMYL-ALCOHOL-DEHYDROGENASE,ACID-O-METHYLTRANSFERASE,FESCUE FESTUCA-ARUNDINACEA,BIOETHANOL PRODUCTION,TRANSGENIC DOWN-REGULATION,COA-REDUCTASE,CRYSTAL-STRUCTURES,POPULUS-TRICHOCARPA,WALL DEGRADABILITY,SYSTEMS BIOLOGY},
  language     = {eng},
  number       = {4},
  pages        = {877--892},
  title        = {Clade classification of monolignol biosynthesis gene family members reveals target genes to decrease lignin in Lolium perenne},
  url          = {http://dx.doi.org/10.1111/plb.12316},
  volume       = {17},
  year         = {2015},
}

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