旱金莲（Tropaeolum majus）是一种具有重要观赏与经济价值的植物，其花朵色彩绚丽，形态独特，从明艳的橙红色到柔和的杏黄色均有分布，加之攀援生长的习性，使其成为庭院装饰与垂直绿化的理想选择。除观赏价值外，旱金莲种子中芥酸（erucic acid, C22:1）含量高达总脂肪酸的66%，是已知芥酸含量最高的植物资源之一。芥酸作为工业润滑剂和医药中间体的重要原料，其生物合成途径在十字花科作物中已有较深入研究，涉及质体内脂肪酸从头合成和内质网KCS酶介导的碳链延长两个关键阶段。然而，旱金莲这一兼具高观赏性与高芥酸含量的特殊物种，其芥酸合成的分子机制却长期未被阐明，尤其缺乏对关键KCS基因的系统鉴定与功能解析，这主要受限于该物种基因组资源的缺失和多组学研究的不足。

针对这一科学问题，本研究通过整合二代Illumina短读长、三代Nanopore长读长测序和Hi-C染色质构象捕获技术，首次完成了旱金莲染色体级别的高质量基因组组装，其contig N50达到12.3 Mb，BUSCO评估完整度为98.50%。基于精确的基因组注释（BUSCO 92.20%），我们系统分析了KCS基因家族的结构特征，并结合多组织及发育时期的转录组数据，通过表达模式分析、共表达网络构建和进化保守性评估，筛选出两个与芥酸合成密切相关的候选基因TM-KCS2和TM-KCS11。进一步的异源功能验证实验显示，在35S组成型启动子驱动下，这两个基因在拟南芥中的过表达均能显著提升种子芥酸含量；而在种子特异性Napin启动子调控下，仅TM-KCS11表现出显著的芥酸合成促进作用，这一结果揭示了KCS基因家族成员在表达调控和功能上的分化现象。通过构建涵盖藻类至被子植物的21个物种KCS系统发育树，我们发现芥酸合成能力在不同进化谱系中独立出现，表明KCS基因家族存在平行演化现象，这一发现为理解植物代谢途径的适应性进化提供了新视角。

本研究的创新性不仅在于揭示了旱金莲高芥酸含量形成的分子基础，更重要的是建立了一套整合多组学数据、进化分析与异源验证的研究范式。该范式特别适用于解析次生代谢产物合成途径中未知功能基因的鉴定与演化溯源问题，为其他高价值植物代谢物的研究与开发利用提供了方法论参考。未来可基于此策略深入探究KCS基因家族的功能分化机制，并利用旱金莲的观赏与代谢双重特性，开展兼具观赏价值与工业应用潜力的分子设计育种。

Tropaeolum majus (nasturtium) is a plant species of significant ornamental and economic value, renowned for its vibrant flowers ranging from bright orange-red to soft apricot-yellow, and its unique morphology. Its climbing growth habit makes it ideal for garden decoration and vertical landscaping. Beyond its aesthetic appeal, T. majus seeds contain exceptionally high levels of erucic acid (C22:1), reaching up to 66% of total fatty acids, ranking among the highest known plant sources of this industrially important compound. While the biosynthetic pathway of erucic acid—involving plastidial de novo fatty acid synthesis followed by endoplasmic reticulum-based chain elongation catalyzed by β-ketoacyl-CoA synthase (KCS)—has been well characterized in Brassicaceae oil crops, the molecular mechanisms underlying its high erucic acid content remain unexplored in this dual-purpose species. The lack of genomic resources and multi-omics studies has particularly hindered systematic identification and functional characterization of key KCS genes.

To address this knowledge gap, we performed the first chromosome-level genome assembly of T. majus by integrating Illumina short-read, Nanopore long-read, and Hi-C chromatin conformation capture technologies. The assembled genome achieved a contig N50 of 12.3 Mb with 98.50% BUSCO completeness. Through comprehensive genome annotation (92.20% BUSCO completeness), we systematically analyzed the KCS gene family and identified two candidate genes (TM-KCS2 and TM-KCS11) strongly associated with erucic acid biosynthesis, using a combination of expression profiling across tissues and developmental stages, co-expression network analysis, and evolutionary conservation assessment. Heterologous functional validation in Arabidopsis demonstrated that both genes significantly increased seed erucic acid content when driven by the 35S constitutive promoter. However, under the seed-specific Napin promoter, only TM-KCS11 exhibited significant erucic acid enhancement, revealing functional divergence within the KCS family. Phylogenetic reconstruction across 21 species from algae to angiosperms revealed independent emergence of erucic acid biosynthesis capacity in distinct evolutionary lineages, providing evidence for parallel evolution within the KCS gene family and new insights into the adaptive evolution of plant metabolic pathways.

This study not only elucidates the molecular basis of high erucic acid accumulation in T. majus, but also establishes an integrative research framework combining multi-omics, evolutionary analysis, and cross-species validation. This paradigm is particularly valuable for characterizing unknown functional genes in secondary metabolite biosynthesis and tracing their evolutionary origins. The strategy paves the way for investigating other high-value plant metabolites and enables molecular breeding approaches that simultaneously enhance ornamental traits and industrial compound production in dual-purpose species like T. majus.

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