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Background <p>Sugarcane (<i>Saccharum</i> spp. hybrid) is a globally important crop, and its bagasse can be converted into bioethanol and other industrial products. Lignin, a core component of sugarcane cell walls, plays a crucial role in bagasse quality and lodging resistance. Shikimic acid hydroxycinnamyl transferase (HCT) is the key enzyme in lignin biosynthesis. However, the <i>HCT</i> gene family in sugarcane and its regulatory roles in sugarcane remain poorly understood.</p> Results <p>A total of 663 <i>HCT</i> genes (including alleles) were identified in the <i>Saccharum</i> hybrid R570 genome, which were classified into six groups (I-VI) and were unevenly distributed across 77 chromosomes. Bioinformatics analysis revealed that the subgroups of <i>R570HCTs</i> had similar gene structures, suggesting conserved functions. Moreover, the different subgroups presented unique putative cis‑element distribution patterns. Transcriptome data indicated that some <i>R570HCTs</i> exhibited significant spatiotemporal and tissue‑specific expression patterns. Further Pearson correlation analysis between putative cis‑element distribution and normalized expression values at the subgroup level revealed that light-responsive elements (L‑box and GA‑motif) were positively correlated with <i>R570HCT</i> expression, and different subgroups formed a complex regulatory network by integrating hormone response and stress elements. Importantly, this subgroup-level correlation was cross-validated by comparing the cis‑element clustering heatmap with the expression heatmap, revealing consistent enrichment patterns.</p> Conclusions <p>The study’s findings provide novel insights into the correlation among motifs, putative cis‑elements, and gene expression, and propose a cross-validated framework for understanding regulatory divergence among <i>HCT</i> subfamilies in polyploid sugarcane, serving as a hypothesis generating resource for future research on <i>R570HCT</i> expression.</p>

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Genome-wide identification of HCT gene family in sugarcane (Saccharum spp. hybrid) and characterization of putative cis-elements in gene regulation

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年6月22日

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  • Yanrong Tao,
  • Meiyan Chen,
  • Shanrui Tang,
  • Xiping Yang

摘要

Background

Sugarcane (Saccharum spp. hybrid) is a globally important crop, and its bagasse can be converted into bioethanol and other industrial products. Lignin, a core component of sugarcane cell walls, plays a crucial role in bagasse quality and lodging resistance. Shikimic acid hydroxycinnamyl transferase (HCT) is the key enzyme in lignin biosynthesis. However, the HCT gene family in sugarcane and its regulatory roles in sugarcane remain poorly understood.

Results

A total of 663 HCT genes (including alleles) were identified in the Saccharum hybrid R570 genome, which were classified into six groups (I-VI) and were unevenly distributed across 77 chromosomes. Bioinformatics analysis revealed that the subgroups of R570HCTs had similar gene structures, suggesting conserved functions. Moreover, the different subgroups presented unique putative cis‑element distribution patterns. Transcriptome data indicated that some R570HCTs exhibited significant spatiotemporal and tissue‑specific expression patterns. Further Pearson correlation analysis between putative cis‑element distribution and normalized expression values at the subgroup level revealed that light-responsive elements (L‑box and GA‑motif) were positively correlated with R570HCT expression, and different subgroups formed a complex regulatory network by integrating hormone response and stress elements. Importantly, this subgroup-level correlation was cross-validated by comparing the cis‑element clustering heatmap with the expression heatmap, revealing consistent enrichment patterns.

Conclusions

The study’s findings provide novel insights into the correlation among motifs, putative cis‑elements, and gene expression, and propose a cross-validated framework for understanding regulatory divergence among HCT subfamilies in polyploid sugarcane, serving as a hypothesis generating resource for future research on R570HCT expression.