A two-level model for the role of complex and young genes in the formation of organism complexity and new insights into the relationship between evolution and development.
A two-level model for the role of complex and young genes in the formation of organism complexity and new insights into the relationship between evolution and development.
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作者：
Yang D;Xu A;Shen P;Gao C;Zang J;Qiu C;Ouyang H;Jiang Y;He F
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，缺乏回答这个问题的通用模型。在这里，我们引入了一个“两级”模型，用于在表型水平上实现基因组复杂性。本研究涉及原口目和后口目的五个代表性物种。影响基因组复杂性的内在基因特性被分为两类：蛋白质编码基因和非编码基因的复杂性和年龄。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出最高比例的高复杂性。复杂基因往往在胚胎发育的每个阶段被优先利用，在器官发生的后期具有最大的代表性。这种趋势主要归因于中年复杂的基因。相反，年轻的基因往往在特定的时空状态下表达。观察到过度代表和不足代表变化的时间点与基因年龄顺序之间存在明显的相关性，这支持了发育保护模式的漏斗状模型。此外，我们还发现了看似矛盾的“漏斗状”或“沙漏”模型的一些可能原因。这些结果表明，复杂基因和年轻基因在两个不同的层面上对生物体的复杂性做出贡献：复杂基因在某些状态下对个体蛋白质组的复杂性做出贡献，而年轻基因在不同时空状态下对蛋白质组的多样性做出贡献。这一结论在所调查的五个物种中都是有效的，表明它是原口目和后口目中的保守模型。这项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。本文的在线版本 (10.1186/s13227-018-0111-4) 包含补充材料，可供授权用户使用。
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. The online version of this article (10.1186/s13227-018-0111-4) contains supplementary material, which is available to authorized users.
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影响因子：
14.9
作者：
Imrichová H;Hulselmans G;Atak ZK;Potier D;Aerts S
通讯作者：
Aerts S
DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
4.6
作者：
Alhindi T;Zhang Z;Ruelens P;Coenen H;Degroote H;Iraci N;Geuten K
通讯作者：
Geuten K
影响因子：
56.9
作者：
Bailey, JA;Gu, ZP;Eichler, EE
通讯作者：
Eichler, EE
影响因子：
5.8
作者：
Hubbell, E;Liu, WM;Mei, R
通讯作者：
Mei, R