The small subunit ribosomal RNA (SSU rRNA) gene is a widely used molecular marker to study the diversity of life. Sequencing of SSU rRNA gene amplicons has become a standard approach for the investigation of the ecology and diversity of microbes. However, a well-curated database is necessary for correct classification of these data. While available for many groups of Bacteria and Archaea, such reference databases are absent for most eukaryotes. The primary goal of the EukRef project (eukref.org) is to close this gap and generate well-curated reference databases for major groups of eukaryotes, especially protists. Here we present a set of EukRef-curated databases for the excavate protists—a large assemblage that includes numerous taxa with divergent SSU rRNA gene sequences, which are prone to misclassification. We identified 6121 sequences, 625 of which were obtained from cultures, 3053 from cell isolations or enrichments and 2419 from environmental samples. We have corrected the classification for the majority of these curated sequences. The resulting publicly available databases will provide phylogenetically based standards for the improved identification of excavates in ecological and microbiome studies, as well as resources to classify new discoveries in excavate diversity.

中文翻译：

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EukRef 挖掘：七个精选的 SSU 核糖体 RNA 基因数据库

小亚基核糖体 RNA (SSU rRNA) 基因是一种广泛用于研究生命多样性的分子标记。SSU rRNA 基因扩增子的测序已成为研究微生物生态学和多样性的标准方法。然而，一个精心策划的数据库对于正确分类这些数据是必要的。虽然可用于许多细菌和古细菌群，但大多数真核生物不存在此类参考数据库。EukRef 项目 (eukref.org) 的主要目标是缩小这一差距，并为真核生物的主要群体，尤其是原生生物生成精心策划的参考数据库。在这里，我们为挖掘的原生生物提供了一组 EukRef 策划的数据库——一个大型集合，其中包括许多具有不同 SSU rRNA 基因序列的分类群，这些分类群很容易被错误分类。我们确定了 6121 个序列，其中 625 个来自培养物，3053 个来自细胞分离或富集，2419 个来自环境样本。我们已经更正了大多数这些精选序列的分类。由此产生的公开可用数据库将为改进生态和微生物组研究中的挖掘物识别提供基于系统发育的标准，以及对挖掘物多样性中的新发现进行分类的资源。