Background Unravelling the genetic basis of polymorphic characters is central to our understanding of the origins and diversification of living organisms. Recently, supergenes have been implicated in a wide range of complex polymorphisms, from adaptive colouration in butterflies and fish to reproductive strategies in birds and plants. The concept of a supergene is now a hot topic in biology, and identification of its functional elements is needed to shed light on the evolution of highly divergent adaptive traits. Here, we apply different gene expression analyses to study the supergene P that controls polymorphism of mimetic wing colour patterns in the neotropical butterfly Heliconius numata. Results We performed de novo transcriptome assembly and differential expression analyses using high-throughput Illumina RNA sequencing on developing wing discs of different H. numata morphs. Within the P interval, 30 and 17 of the 191 transcripts were expressed differentially in prepupae and day-1 pupae, respectively. Among these is the gene cortex, known to play a role in wing pattern formation in Heliconius and other Lepidoptera. Our in situ hybridization experiments confirmed the relationship between cortex expression and adult wing patterns. Conclusions This study found the majority of genes in the P interval to be expressed in the developing wing discs during the critical stages of colour pattern formation, and detect drastic changes in expression patterns in multiple genes associated with structural variants. The patterns of expression of cortex only partially recapitulate the variation in adult phenotype, suggesting that the remaining phenotypic variation could be controlled by other genes within the P interval. Although functional studies on cortex are now needed to determine its exact developmental role, our results are in accordance with the classical supergene hypothesis, whereby several genes inherited together due to tight linkage control a major developmental switch.

中文翻译：

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解开多态蝴蝶 Heliconius numata 中形成翼型超基因的基因。

背景 揭示多态性特征的遗传基础对于我们理解生物体的起源和多样化至关重要。最近，超基因与广泛的复杂多态性有关，从蝴蝶和鱼类的适应性着色到鸟类和植物的繁殖策略。超基因的概念现在是生物学中的热门话题，需要鉴定其功能元件以阐明高度分化的适应性特征的进化。在这里，我们应用不同的基因表达分析来研究控制新热带蝴蝶 Heliconius numata 中模拟翅膀颜色模式多态性的超基因 P。结果 我们使用高通量 Illumina RNA 测序对发育中的不同 H. numata 变形的翼盘进行了从头转录组组装和差异表达分析。在 P 间隔内，191 个转录本中的 30 个和 17 个分别在预蛹和第 1 天的蛹中表达差异。其中包括基因皮层，已知它在 Heliconius 和其他鳞翅目的翅膀图案形成中发挥作用。我们的原位杂交实验证实了皮层表达与成人翼型之间的关系。结论 本研究发现 P 区间的大部分基因在颜色模式形成的关键阶段在发育中的翼盘中表达，并检测到与结构变异相关的多个基因中表达模式的剧烈变化。皮质的表达模式仅部分概括了成人表型的变异，表明剩余的表型变异可以由 P 区间内的其他基因控制。尽管现在需要对皮层进行功能研究以确定其确切的发育作用，但我们的结果与经典的超基因假说一致，即由于紧密连锁控制一个主要发育开关，几个基因一起遗传。