Abstract
Lignin is the main component of secondary cell walls and is essential for plant development and defense. However, lignin is recognized as a major recalcitrant factor for efficiency of industrial biomass processing. Genes involved in general phenylpropanoid and monolignol-specific metabolism in sugarcane have been previously analyzed at the transcriptomic level. Nevertheless, the number of genes identified in this species is still very low. The recently released sugarcane genome sequence has allowed the genome-wide characterization of the 11 gene families involved in the monolignol biosynthesis branch of the phenylpropanoid pathway. After an exhaustive analysis of sugarcane genomes, 438 haplotypes derived from 175 candidate genes from Saccharum spontaneum and 144 from Saccharum hybrid R570 were identified as associated with this biosynthetic route. The phylogenetic analyses, combined with the search for protein conserved residues involved in the catalytic activity of the encoded enzymes, were employed to identify the family members potentially involved in developmental lignification. Accordingly, 15 candidates were identified as bona fide lignin biosynthesis genes: PTAL1, PAL2, C4H4, 4CL1, HCT1, HCT2, C3’H1, C3’H2, CCoAOMT1, COMT1, F5H1, CCR1, CCR2, CAD2, and CAD7. For this core set of lignin biosynthetic genes, we searched for the chromosomal location, the gene expression pattern, the promoter cis-acting elements, and microRNA targets. Altogether, our results present a comprehensive characterization of sugarcane general phenylpropanoid and monolignol-specific genes, providing the basis for further functional studies focusing on lignin biosynthesis manipulation and biotechnological strategies to improve sugarcane biomass utilization.
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Acknowledgments
This work is part of the PhD thesis of Thais Felix-Cordeiro. DJM was supported by Post-doctoral fellowship CAPES-PNPD. TFC was supported by CAPES PhD fellowship. YSV, VG, GVA, and YRAA were recipient of CNPq PIBIC fellowship.
Funding
This work was supported by grants from the Conselho Nacional de Desenvolvimento Científico e Tecnológico – CNPq (grant number 474911/2012-8); Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES (PNPD N ° 02691/09-4 - linha MEC / CAPES); Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro – FAPERJ (E26/111.234/2014); and Petrobras (grant number ANP 01070 0050.0076123.12.9) to GSM.
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DJM and GSM conceived and designed the experiments.
DJM, TFC, LB, YSV, VG, GAB, GVA, YRAA, AFR, RLC, and GSM performed the experiments.
DJM, LB, RLC, and GSM analyzed the data.
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Jardim-Messeder, D., Felix-Cordeiro, T., Barzilai, L. et al. Genome-wide analysis of general phenylpropanoid and monolignol-specific metabolism genes in sugarcane. Funct Integr Genomics 21, 73–99 (2021). https://doi.org/10.1007/s10142-020-00762-9
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DOI: https://doi.org/10.1007/s10142-020-00762-9