Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
G3 (Bethesda). 2021 Jul 14;11(7). doi: 10.1093/g3journal/jkab146.
Advances in genomics techniques are expanding the range of nematode species that are amenable to transgenesis. Due to divergent codon usage biases across species, codon optimization is often a critical step for the successful expression of exogenous transgenes in nematodes. Platforms for generating DNA sequences codon-optimized for the free-living model nematode Caenorhabditis elegans are broadly available. However, until now such tools did not exist for non-Caenorhabditis nematodes. We therefore developed the Wild Worm Codon Adapter, a tool for rapid transgene codon optimization for expression in non-Caenorhabditis nematodes. The app includes built-in optimization for parasitic nematodes in the Strongyloides, Nippostrongylus, and Brugia genera as well as the predatory nematode Pristionchus pacificus. The app also supports custom optimization for any species using user-provided optimization rules. In addition, the app supports automated insertion of synthetic or native introns, as well as the analysis of codon bias in transgene and native sequences. Here, we describe this web-based tool and demonstrate how it may be used to analyze genome-wide codon bias in Strongyloides species.
基因组学技术的进步正在扩大可进行转基因操作的线虫物种范围。由于物种间密码子使用偏好存在差异，因此密码子优化通常是在外源转基因在线虫中成功表达的关键步骤。针对自由生活模式线虫秀丽隐杆线虫的 DNA 序列密码子优化生成平台广泛可用。然而，直到现在，针对非秀丽隐杆线虫的此类工具还不存在。因此，我们开发了“野生蠕虫密码子适配器”，这是一种用于快速进行转基因密码子优化以在非秀丽隐杆线虫中表达的工具。该应用程序包括针对 Strongyloides、Nippostrongylus 和 Brugia 属中的寄生线虫以及捕食性线虫 Pristionchus pacificus 的内置优化。该应用程序还支持使用用户提供的优化规则针对任何物种进行自定义优化。此外，该应用程序还支持合成或天然内含子的自动插入，以及转基因和天然序列中密码子偏好的分析。在这里，我们描述了这个基于网络的工具，并展示了如何使用它来分析 Strongyloides 物种的全基因组密码子偏好。
