Protist.guru: gene expression, co-expression network and comparative transcriptomics database for protists

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, major gaps in our understanding of the microbial world remain, and one example is that microbial eukaryotes, or protists, are still neglected. To address this gap, we used gene expression data from 15 distinct protist species to create protist.guru - an online database equipped with tools for identifying functional co-expression networks, gene families, and enriched gene clusters. Here, we show how our database can be used to reveal genes involved in important 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.

在过去的几十年间，微生物生态学的研究得益于分子和基因组数据的推动。DNA测序技术揭示了微生物多样性的惊人广度以及微生物过程在全球生态系统中的运行机制。然而，我们对微生物世界的理解仍存在重大空白，其中一个例子便是微生物真核生物，或称原生生物，仍然被忽视。为了填补这一空白，我们利用来自15种不同原生生物物种的基因表达数据，创建了protist.guru——一个配备有识别功能共表达网络、基因家族和富集基因簇工具的在线数据库。在此，我们展示了如何利用我们的数据库揭示参与重要途径（如淡水螺旋藻中次生类胡萝卜素的合成）的基因。我们期望protist.guru将成为原生生物学家宝贵的资源，同时也是推动对微生物真核生物生物学过程发现和新见解的催化剂。