Ruprecht Colin, Mendrinna Amelie, Tohge Takayuki, Sampathkumar Arun, Klie Sebastian, Fernie Alisdair R, Nikoloski Zoran, Persson Staffan, Mutwil Marek
Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (C.R., T.T, S.K., A.R.F., Z.N., M.M.), School of Biosciences and Australian Research Council Centre of Excellence in Plant Cell Walls, University of Melbourne, Parkville, Victoria 3010, Australia (A.M., S.P.); andDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 (A.S.).
Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (C.R., T.T, S.K., A.R.F., Z.N., M.M.), School of Biosciences and Australian Research Council Centre of Excellence in Plant Cell Walls, University of Melbourne, Parkville, Victoria 3010, Australia (A.M., S.P.); andDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 (A.S.)
Plant Physiol. 2016 Mar;170(3):1878-94. doi: 10.1104/pp.15.01281. Epub 2016 Jan 11.
Gene duplications generate new genes that can acquire similar but often diversified functions. Recent studies of gene coexpression networks have indicated that, not only genes, but also pathways can be multiplied and diversified to perform related functions in different parts of an organism. Identification of such diversified pathways, or modules, is needed to expand our knowledge of biological processes in plants and to understand how biological functions evolve. However, systematic explorations of modules remain scarce, and no user-friendly platform to identify them exists. We have established a statistical framework to identify modules and show that approximately one-third of the genes of a plant's genome participate in hundreds of multiplied modules. Using this framework as a basis, we implemented a platform that can explore and visualize multiplied modules in coexpression networks of eight plant species. To validate the usefulness of the platform, we identified and functionally characterized pollen- and root-specific cell wall modules that multiplied to confer tip growth in pollen tubes and root hairs, respectively. Furthermore, we identified multiplied modules involved in secondary metabolite synthesis and corroborated them by metabolite profiling of tobacco (Nicotiana tabacum) tissues. The interactive platform, referred to as FamNet, is available at http://www.gene2function.de/famnet.html.
基因复制产生新的基因，这些新基因能够获得相似但往往又多样化的功能。最近对基因共表达网络的研究表明，不仅基因，而且途径也能够成倍增加并多样化，以便在生物体的不同部位执行相关功能。需要识别这些多样化的途径或模块，以扩展我们对植物生物学过程的认识，并了解生物学功能是如何进化的。然而，对模块的系统探索仍然很少，而且不存在一个便于用户识别它们的平台。我们建立了一个统计框架来识别模块，并表明植物基因组中约三分之一的基因参与了数百个成倍增加的模块。以这个框架为基础，我们实现了一个平台，该平台能够探索和可视化八种植物物种共表达网络中的成倍增加的模块。为了验证该平台的实用性，我们识别了花粉和根特异性细胞壁模块，并对其进行了功能表征，这些模块成倍增加，分别赋予花粉管和根毛顶端生长的能力。此外，我们识别了参与次生代谢物合成的成倍增加的模块，并通过烟草组织的代谢物谱分析对其进行了确证。这个交互式平台称为FamNet，可在http://www.gene2function.de/famnet.html上获取。
