Background How genome complexity affects organismal phenotypic complexity is a fundamental question in evolutionary developmental biology. Previous studies proposed various contributing factors of genome complexity and tried to find the connection between genomic complexity and organism complexity. However, a general model to answer this question is lacking. Here, we introduce a 'two-level' model for the realization of genome complexity at phenotypic level. Results Five representative species across Protostomia and Deuterostomia were involved in this study. The intrinsic gene properties contributing to genome complexity were classified into two generalized groups: the complexity and age degree of both protein-coding and noncoding genes. We found that young genes tend to be simpler; however, the mid-age genes, rather than the oldest genes, show the highest proportion of high complexity. Complex genes tend to be utilized preferentially in each stage of embryonic development, with maximum representation during the late stage of organogenesis. This trend is mainly attributed to mid-age complex genes. In contrast, young genes tend to be expressed in specific spatiotemporal states. An obvious correlation between the time point of the change in over- and under-representation and the order of gene age was observed, which supports the funnel-like model of the conservation pattern of development. In addition, we found some probable causes for the seemingly contradictory 'funnel-like' or 'hourglass' model. Conclusions These results indicate that complex and young genes contribute to organismal complexity at two different levels: Complex genes contribute to the complexity of individual proteomes in certain states, whereas young genes contribute to the diversity of proteomes in different spatiotemporal states. This conclusion is valid across the five species investigated, indicating it is a conserved model across Protostomia and Deuterostomia. The results in this study also support 'funnel-like model' from a new viewpoint and explain why there are different evo-devo relation models.

中文翻译：

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复杂和年轻基因在有机体复杂性形成中的作用的两级模型以及对进化与发展之间关系的新见解。

背景 基因组复杂性如何影响有机体表型复杂性是进化发育生物学中的一个基本问题。以前的研究提出了基因组复杂性的各种影响因素，并试图找到基因组复杂性和生物复杂性之间的联系。然而，缺乏回答这个问题的通用模型。在这里，我们介绍了在表型水平上实现基因组复杂性的“两级”模型。结果本研究涉及原生口和氘代口的五个代表性物种。导致基因组复杂性的内在基因特性被分为两大类：蛋白质编码和非编码基因的复杂性和年龄程度。我们发现年轻的基因往往更简单。然而，中年基因，而不是最古老的基因，显示高复杂度的比例最高。复杂基因倾向于优先用于胚胎发育的每个阶段，在器官形成的后期具有最大的代表性。这种趋势主要归因于中年复杂基因。相反，年轻基因倾向于在特定的时空状态下表达。观察到表达过度和表达不足变化的时间点与基因年龄顺序之间存在明显的相关性，这支持了发展保护模式的漏斗状模型。此外，我们发现了看似矛盾的“漏斗状”或“沙漏”模型的一些可能原因。结论 这些结果表明，复杂和年轻的基因在两个不同的水平上对有机体的复杂性有贡献：复杂基因有助于特定状态下单个蛋白质组的复杂性，而年轻基因有助于不同时空状态下蛋白质组的多样性。这一结论在所调查的五个物种中都是有效的，表明它是一个跨原口动物和氘代口动物的保守模型。本研究的结果也从一个新的角度支持了“漏斗状模型”，并解释了为什么存在不同的 evo-devo 关系模型。