Yang Dong, Xu Aishi, Shen Pan, Gao Chao, Zang Jiayin, Qiu Chen, Ouyang Hongsheng, Jiang Ying, He Fuchu
State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206 The People's Republic of China.
2Animal Sciences College of Jilin University, Changchun, 130062 The People's Republic of China.
Evodevo. 2018 Nov 12;9:22. doi: 10.1186/s13227-018-0111-4. eCollection 2018.
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.
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.
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.
基因组复杂性如何影响生物体表型复杂性是进化发育生物学中的一个基本问题。先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与生物体复杂性之间的联系。然而，目前仍缺乏一个通用模型来回答这个问题。在此，我们引入一个在表型水平实现基因组复杂性的“两级”模型。
本研究涉及原口动物和后口动物中的五个代表性物种。导致基因组复杂性的内在基因特性被分为两个广义类别：蛋白质编码基因和非编码基因的复杂性和年龄程度。我们发现年轻基因往往更简单；然而，中年基因而非最古老的基因显示出最高比例的高复杂性。复杂基因在胚胎发育的每个阶段往往被优先利用，在器官发生后期占比最大。这一趋势主要归因于中年复杂基因。相比之下，年轻基因倾向于在特定的时空状态下表达。观察到基因表达丰度过高和过低变化的时间点与基因年龄顺序之间存在明显相关性，这支持了发育保守模式的漏斗状模型。此外，我们发现了一些可能导致看似矛盾的“漏斗状”或“沙漏状”模型的原因。
这些结果表明，复杂基因和年轻基因在两个不同层面上对生物体复杂性有贡献：复杂基因在特定状态下有助于个体蛋白质组的复杂性，而年轻基因在不同时空状态下有助于蛋白质组的多样性。这一结论在所研究的五个物种中均成立，表明它是原口动物和后口动物中一个保守的模型。本研究结果也从一个新的角度支持了“漏斗状模型”，并解释了为何存在不同的进化发育关系模型。
