School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
Asian School of the Environment, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
J Mol Biol. 2022 Jun 15;434(11):167502. doi: 10.1016/j.jmb.2022.167502. Epub 2022 Feb 18.
During the last few decades, the study of microbial ecology has been enabled by molecular and genomic data. DNA sequencing has revealed the surprising extent of microbial diversity and how microbial processes run global ecosystems. However, significant gaps in our understanding of the microbial world remain, and one example is that microbial eukaryotes, or protists, are still largely neglected. To address this gap, we used gene expression data from 17 protist species to create protist.guru: an online database equipped with tools for identifying co-expressed genes, gene families, and co-expression clusters enriched for specific biological functions. Here, we show how our database can be used to reveal genes involved in essential pathways, such as the synthesis of secondary carotenoids in Haematococcus lacustris. We expect protist.guru to serve as a valuable resource for protistologists, as well as a catalyst for discoveries and new insights into the biological processes of microbial eukaryotes. AVAILABILITY: The database and co-expression networks are freely available from http://protist.guru/. The expression matrices and sample annotations are found in the supplementary data.
在过去的几十年中，分子和基因组数据使微生物生态学的研究成为可能。DNA 测序揭示了微生物多样性的惊人程度，以及微生物过程如何运行全球生态系统。然而，我们对微生物世界的理解仍然存在重大差距，其中一个例子是，微生物真核生物，或原生生物，仍然在很大程度上被忽视。为了解决这一差距，我们使用了来自 17 个原生生物物种的基因表达数据来创建 protist.guru：一个配备了用于识别共表达基因、基因家族和富含特定生物学功能的共表达簇的在线数据库。在这里，我们展示了如何使用我们的数据库来揭示参与必需途径的基因，例如在 Haematococcus lacustris 中合成次生类胡萝卜素。我们预计 protist.guru 将成为原生生物学家的宝贵资源，以及发现和深入了解微生物真核生物的生物学过程的催化剂。可用性：该数据库和共表达网络可从 http://protist.guru/ 免费获得。表达矩阵和样本注释可在补充数据中找到。
