Key message
The core set of biosynthetic genes potentially involved in developmental lignification was identified in the model C4 grass Setaria viridis.
Abstract
Lignin has been recognized as a major recalcitrant factor negatively affecting the processing of plant biomass into bioproducts. However, the efficient manipulation of lignin deposition in order to generate optimized crops for the biorefinery requires a fundamental knowledge of several aspects of lignin metabolism, including regulation, biosynthesis and polymerization. The current availability of an annotated genome for the model grass Setaria viridis allows the genome-wide characterization of genes involved in the metabolic pathway leading to the production of monolignols, the main building blocks of lignin. Here we performed a comprehensive study of monolignol biosynthetic genes as an initial step into the characterization of lignin metabolism in S. viridis. A total of 56 genes encoding bona fide enzymes catalyzing the consecutive ten steps of the monolignol biosynthetic pathway were identified in the S. viridis genome. A combination of comparative phylogenetic studies, high-throughput expression analysis and quantitative RT-PCR analysis was further employed to identify the family members potentially involved in developmental lignification. Accordingly, 14 genes clustered with genes from closely related species with a known function in lignification and showed an expression pattern that correlates with lignin deposition. These genes were considered the “core lignin toolbox” responsible for the constitutive, developmental lignification in S. viridis. These results provide the basis for further understanding lignin deposition in C4 grasses and will ultimately allow the validation of biotechnological strategies to produce crops with enhanced processing properties.
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Acknowledgements
This work was supported by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) via the BIOEN Young Investigators Awards research grant (Processo FAPESP no. 2015/02527-1). This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) - Finance Code 001. IC thanks FAPESP for the SPRINT Project grant number 2016/50189-0. IC is indebted to Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) for the research fellowship 302927/2018-2. SSF was funded by FAPESP for a postdoctoral fellowship (Processo FAPESP no. 2016/06917-1). MSS was funded by CAPES for a predoctoral fellowship. RMAS was funded by CNPq for a Master’s fellowship. GGC was funded by CNPq-PIBIC for a scientific initiation fellowship.
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SSF conducted most of the experiments, analyzed data and complemented the writing. MSS, GGC, LGAL and RMAS performed experiments and analyzed data. IC conceived and designed the experiments and wrote the article. All authors read and approved the final manuscript.
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11103_2019_897_MOESM2_ESM.xlsx
Supplementary material 2 Table S1. Distribution of SNBEs, SMREs and AC elements in the promoter region of the 56 phenylpropanoid and monolignol biosynthetic genes in S. viridis. (XLSX 92 kb)
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Supplementary material 3 Table S2. List of bona fide genes involved in the phenylpropanoid and monolignol biosynthetic pathways in Arabidopsis and some grasses. (XLSX 63 kb)
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Supplementary material 4 Table S3. Protein sequence identity matrixes of all phenylpropanoid and monolignol gene families. (XLSX 60 kb)
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Supplementary material 5 Table S4. RNAseq expression data (FPKM) of all phenylpropanoid and monolignol biosynthetic genes in S. viridis retrieved from the work of Martin et al. (2016). (XLSX 61 kb)
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Ferreira, S.S., Simões, M.S., Carvalho, G.G. et al. The lignin toolbox of the model grass Setaria viridis. Plant Mol Biol 101, 235–255 (2019). https://doi.org/10.1007/s11103-019-00897-9
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DOI: https://doi.org/10.1007/s11103-019-00897-9