Martí-Solans Josep, Belyaeva Olga V, Torres-Aguila Nuria P, Kedishvili Natalia Y, Albalat Ricard, Cañestro Cristian
Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.
Department of Biochemistry and Molecular Genetics, University of Alabama-Birmingham.
Mol Biol Evol. 2016 Sep;33(9):2401-16. doi: 10.1093/molbev/msw118. Epub 2016 Jul 12.
The bloom of genomics is revealing gene loss as a pervasive evolutionary force generating genetic diversity that shapes the evolution of species. Outside bacteria and yeast, however, the understanding of the process of gene loss remains elusive, especially in the evolution of animal species. Here, using the dismantling of the retinoic acid metabolic gene network (RA-MGN) in the chordate Oikopleura dioica as a case study, we combine approaches of comparative genomics, phylogenetics, biochemistry, and developmental biology to investigate the mutational robustness associated to biased patterns of gene loss. We demonstrate the absence of alternative pathways for RA-synthesis in O. dioica, which suggests that gene losses of RA-MGN were not compensated by mutational robustness, but occurred in a scenario of regressive evolution. In addition, the lack of drastic phenotypic changes associated to the loss of RA-signaling provides an example of the inverse paradox of Evo-Devo. This work illustrates how the identification of patterns of gene coelimination-in our case five losses (Rdh10, Rdh16, Bco1, Aldh1a, and Cyp26)-is a useful strategy to recognize gene network modules associated to distinct functions. Our work also illustrates how the identification of survival genes helps to recognize neofunctionalization events and ancestral functions. Thus, the survival and extensive duplication of Cco and RdhE2 in O. dioica correlated with the acquisition of complex compartmentalization of expression domains in the digestive system and a process of enzymatic neofunctionalization of the Cco, while the surviving Aldh8 could be related to its ancestral housekeeping role against toxic aldehydes.
基因组学的蓬勃发展揭示了基因丢失是一种普遍存在的进化力量，它产生塑造物种进化的遗传多样性。然而，在细菌和酵母之外，对基因丢失过程的理解仍然难以捉摸，尤其是在动物物种的进化中。在这里，以脊索动物双囊尾海鞘视黄酸代谢基因网络（RA-MGN）的拆解为例，我们结合比较基因组学、系统发育学、生物化学和发育生物学方法，研究与基因丢失偏向模式相关的突变稳健性。我们证明双囊尾海鞘中不存在RA合成的替代途径，这表明RA-MGN的基因丢失没有被突变稳健性所补偿，而是发生在一个退化进化的场景中。此外，与RA信号缺失相关的明显表型变化的缺乏提供了一个进化发育生物学反例的例子。这项工作说明了如何识别基因共消除模式——在我们的例子中有五个基因丢失（Rdh10、Rdh16、Bco1、Aldh1a和Cyp26）——是识别与不同功能相关的基因网络模块的有用策略。我们的工作还说明了如何识别存活基因有助于识别新功能化事件和祖先功能。因此，双囊尾海鞘中Cco和RdhE2的存活和广泛复制与消化系统中表达域复杂区室化的获得以及Cco的酶促新功能化过程相关，而存活的Aldh8可能与其对抗有毒醛类的祖先管家作用有关。
