【摘要】 金鱼(Carassius auratus)是重要的淡水观赏鱼类,部分品种具有罕见的头瘤结构,但金鱼头瘤的遗传调控机制尚不明确。为深入挖掘金鱼头瘤发生相关的重要候选基因,本研究利用转录组测序和生物信息学分析构建了包含脑、眼、鳍、肠、心脏、肾、肝、肌肉、鳞片、皮肤、脾和头瘤在内共计12种金鱼组织或器官的转录组图谱,系统解析了组织间的基因表达差异,在头瘤组织与皮肤的比较分析中共鉴定到3131个差异表达基因,其中上调1376个,下调1755个;进一步将头瘤组织与其他组织比较得到的差异基因进行交集分析筛选,最终获得92个在头瘤与所有其他组织中均呈显著差异表达的基因,其中包括10个新发现的尚未被注释的蛋白编码基因,命名为hrg1～hrg10。功能富集分析显示,这些差异表达基因主要参与透明质酸结合、细胞增殖、细胞外基质重塑等生物学过程。其中,筛选出的关键候选基因tgfbr1b、col7a1、tnfaip6、hapln1a和alpl在其他组织表达水平极低或呈沉默状态,可能在头瘤形成过程中的成纤维细胞过度增生中发挥关键作用。本研究揭示了金鱼多个组织全基因组表达特征,丰富了金鱼的组织转录组学数据,并为金鱼头瘤性状的发育机制研究提供了关键候选基因资源。更多还原

【Abstract】 Goldfish(Carassius auratus) is a globally popular freshwater ornamental fish that has undergone centuries of artificial selection, giving rise to diverse morphological traits. Among these, the development of a fleshy "hood"(also known as a wen or head growth) on the head is one of the most unusual and prized features in fancy goldfish varieties. This benign overgrowth, composed of proliferative epidermal and dermal connective tissues, is extremely rare among fishes and plays a decisive role in determining aesthetic and commercial value. Despite its importance, the genetic and molecular mechanisms underlying hood formation remain poorly understood, and no dedicated transcriptomic analysis has previously addressed this trait. To investigate the molecular basis of hood development, we performed a comprehensive transcriptome analysis of 12 tissues in goldfish, including the hood, using RNA sequencing and integrative bioinformatic approaches. A tissue-wide gene expression atlas was constructed, and differential expression analyses were conducted between the hood and the other tissues. We identified 92 genes that were significantly upregulated in the hood tissue, representing strong candidate genes associated with the hood trait. Functional enrichment analysis revealed that these hood-specific genes are primarily involved in biological processes, such as cell proliferation, extracellular matrix(ECM) organization, and tissue development, aligning with the histological features of the hood, characterized by fibroblast overgrowth and abundant ECM deposition. Among the candidate genes, several well-annotated ones appear to be key regulators of connective tissue growth. For example, tgfbr1b, encoding the type I receptor of Transforming Growth Factor-β(TGF-β), showed hood-exclusive expression and is known to promote fibroblast proliferation and ECM production. col7a1, encoding the α1 chain of type VII collagen, contributes to dermal–epidermal anchoring fibrils and supports the mechanical integrity of connective tissues. tnfaip6 encodes TSG-6, a hyaluronan-binding protein that stabilizes ECM in wound healing and inflammatory responses, while hapln1a encodes a link protein that crosslinks hyaluronic acid and proteoglycans, enhancing matrix elasticity. Furthermore, alpl, a marker of osteogenesis and tissue regeneration, was significantly upregulated in the hood, suggesting an activation of regenerative pathways. In addition, we identified 10 novel hood-specific genes that showed no homology to known genes in current databases. These were provisionally named hood-related gene 1 through hood-related gene 10(hrg1–hrg10) and may represent goldfish-specific genetic components involved in this unique morphological trait. Together, these findings suggest that goldfish hood formation results from the overactivation or prolonged activity of skin growth and regeneration pathways, leading to benign hyperplasia of dermal and epidermal tissues. The hood thus offers a valuable model for studying genetic regulation of non-malignant tissue overgrowth and regeneration in vertebrates. Beyond its biological insights, this study provides the first comprehensive multi-organ transcriptomic resource in goldfish, filling a critical gap in cyprinid genomics. The identified candidate genes and the novel hrg family lay a solid foundation for future functional investigations, such as expression validation and knockout or overexpression studies, to further elucidate the molecular control of hood development. These findings also offer practical implications for ornamental fish breeding, enabling molecular marker-assisted selection to enhance hood traits in commercial lines. In summary, our results contribute to the understanding of a distinctive vertebrate phenotype and broaden our knowledge of tissue growth and morphological regulation driven by genetic and transcriptomic mechanisms.更多还原