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.

木质素是次生细胞壁的主要成分，对植物发育和防御至关重要。然而，木质素被认为是工业生物质加工效率的主要顽固因素。先前已在转录组水平上分析了甘蔗中涉及一般苯丙烷和单木酚特异性代谢的基因。尽管如此，在该物种中鉴定的基因数量仍然很少。最近发布的甘蔗基因组序列允许对涉及苯丙烷途径的单木质醇生物合成分支的 11 个基因家族进行全基因组表征。在对甘蔗基因组进行详尽分析后，438 个单倍型来自 175 个来自自发甘蔗的候选基因和 144 个来自甘蔗的候选基因杂种 R570 被鉴定为与这种生物合成路线有关。系统发育分析结合寻找参与编码酶催化活性的蛋白质保守残基，用于鉴定可能参与发育木质化的家族成员。因此，15点的候选被确定为真正的木质素生物合成基因：PTAL1，PAL2，C4H4，4CL1，HCT1，HCT2，C3'H1，C3'H2，CCoAOMT1，COMT1，F5H1，CCR1，CCR2，CAD2和CAD7。对于这组核心木质素生物合成基因，我们搜索了染色体位置、基因表达模式、启动子顺式作用元件和 microRNA 靶标。总而言之，我们的结果展示了甘蔗一般苯丙烷和单木素醇特异性基因的综合特征，为进一步的功能研究提供了基础，重点是木质素生物合成操作和生物技术策略，以提高甘蔗生物质利用率。