Kwon Taejoon
Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.
Genesis. 2017 Jan;55(1-2). doi: 10.1002/dvg.23010.
More than five thousand genes annotated in the recently published Xenopus laevis and Xenopus tropicalis genomes do not have a candidate orthologous counterpart in other vertebrate species. To determine whether these sequences represent genuine amphibian-specific genes or annotation errors, it is necessary to analyze them alongside sequences from other amphibian species. However, due to large genome sizes and an abundance of repeat sequences, there are limited numbers of gene sequences available from amphibian species other than Xenopus. AmphiBase is a new genomic resource covering non-model amphibian species, based on public domain transcriptome data and computational methods developed during the X. laevis genome project. Here, I review the current status of AmphiBase, including amphibian species with available transcriptome data or biological samples, and describe the challenges of building a comprehensive amphibian genomic resource in the absence of genomes. This mini-review will be informative for researchers interested in functional genomic experiments using amphibian model organisms, such as Xenopus and axolotl, and will assist in interpretation of results implicating "orphan genes." Additionally, this study highlights an opportunity for researchers working on non-model amphibian species to collaborate in their future efforts and develop amphibian genomic resources as a community.
在最近公布的非洲爪蟾和热带爪蟾基因组中注释的超过五千个基因，在其他脊椎动物物种中没有对应的候选直系同源基因。为了确定这些序列代表的是真正的两栖动物特有的基因还是注释错误，有必要将它们与其他两栖动物物种的序列一起进行分析。然而，由于基因组规模庞大且重复序列丰富，除了爪蟾之外，其他两栖动物物种可获得的基因序列数量有限。两栖动物数据库（AmphiBase）是一种基于公共领域转录组数据以及在非洲爪蟾基因组计划期间开发的计算方法，涵盖非模式两栖动物物种的新基因组资源。在此，我回顾了两栖动物数据库的当前状况，包括具有可用转录组数据或生物样本的两栖动物物种，并描述了在缺乏基因组的情况下构建全面的两栖动物基因组资源所面临的挑战。这篇小型综述对于对使用非洲爪蟾和蝾螈等两栖动物模式生物进行功能基因组实验感兴趣的研究人员将具有参考价值，并将有助于解释涉及“孤儿基因”的结果。此外，这项研究凸显了从事非模式两栖动物物种研究的人员在未来的工作中进行合作并作为一个群体开发两栖动物基因组资源的机会。
