Department of Biology, University of Turku, 20014, Turku, Finland.
Mol Ecol. 2013 Jun;22(12):3216-41. doi: 10.1111/mec.12309.
Recent advances in molecular technologies have opened up unprecedented opportunities for molecular ecologists to better understand the molecular basis of traits of ecological and evolutionary importance in almost any organism. Nevertheless, reliable and systematic inference of functionally relevant information from these masses of data remains challenging. The aim of this review is to highlight how the Gene Ontology (GO) database can be of use in resolving this challenge. The GO provides a largely species-neutral source of information on the molecular function, biological role and cellular location of tens of thousands of gene products. As it is designed to be species-neutral, the GO is well suited for cross-species use, meaning that, functional annotation derived from model organisms can be transferred to inferred orthologues in newly sequenced species. In other words, the GO can provide gene annotation information for species with nonannotated genomes. In this review, we describe the GO database, how functional information is linked with genes/gene products in model organisms, and how molecular ecologists can utilize this information to annotate their own data. Then, we outline various applications of GO for enhancing the understanding of molecular basis of traits in ecologically relevant species. We also highlight potential pitfalls, provide step-by-step recommendations for conducting a sound study in nonmodel organisms, suggest avenues for future research and outline a strategy for maximizing the benefits of a more ecological and evolutionary genomics-oriented ontology by ensuring its compatibility with the GO.
近年来，分子技术的进步为分子生态学家提供了前所未有的机会，使他们能够更好地理解几乎任何生物体中具有生态和进化重要性的特征的分子基础。然而，从这些大量数据中可靠而系统地推断出与功能相关的信息仍然具有挑战性。本文旨在强调基因本体论（GO）数据库如何有助于解决这一挑战。GO 为成千上万的基因产物的分子功能、生物作用和细胞位置提供了一个在很大程度上与物种无关的信息来源。由于它被设计为与物种无关，GO 非常适合跨物种使用，这意味着，从模式生物中得出的功能注释可以转移到新测序物种中的推断直系同源物上。换句话说，GO 可以为没有基因组注释的物种提供基因注释信息。在本文中，我们描述了 GO 数据库、在模式生物中如何将功能信息与基因/基因产物联系起来，以及分子生态学家如何利用这些信息来注释他们自己的数据。然后，我们概述了 GO 在增强对生态相关物种特征的分子基础的理解方面的各种应用。我们还强调了潜在的陷阱，为非模式生物中的合理研究提供了逐步建议，提出了未来研究的途径，并概述了通过确保与 GO 的兼容性来最大化更具生态和进化基因组学导向的本体的优势的策略。
