BCCM/IHEM, Mycology and Aerobiology, Sciensano, 1050, Brussels, Belgium.
InBioS, Physiology and Bacterial Genetics, University of Liège, 4000, Liège, Belgium.
Gigascience. 2022 Dec 28;12. doi: 10.1093/gigascience/giad022. Epub 2023 Apr 10.
Microbial culture collections play a key role in taxonomy by studying the diversity of their strains and providing well-characterized biological material to the scientific community for fundamental and applied research. These microbial resource centers thus need to implement new standards in species delineation, including whole-genome sequencing and phylogenomics. In this context, the genomic needs of the Belgian Coordinated Collections of Microorganisms were studied, resulting in the GEN-ERA toolbox. The latter is a unified cluster of bioinformatic workflows dedicated to both bacteria and small eukaryotes (e.g., yeasts).
This public toolbox allows researchers without a specific training in bioinformatics to perform robust phylogenomic analyses. Hence, it facilitates all steps from genome downloading and quality assessment, including genomic contamination estimation, to tree reconstruction. It also offers workflows for average nucleotide identity comparisons and metabolic modeling.
Nextflow workflows are launched by a single command and are available on the GEN-ERA GitHub repository (https://github.com/Lcornet/GENERA). All the workflows are based on Singularity containers to increase reproducibility.
The toolbox was developed for a diversity of microorganisms, including bacteria and fungi. It was further tested on an empirical dataset of 18 (meta)genomes of early branching Cyanobacteria, providing the most up-to-date phylogenomic analysis of the Gloeobacterales order, the first group to diverge in the evolutionary tree of Cyanobacteria.
The GEN-ERA toolbox can be used to infer completely reproducible comparative genomic and metabolic analyses on prokaryotes and small eukaryotes. Although designed for routine bioinformatics of culture collections, it can also be used by all researchers interested in microbial taxonomy, as exemplified by our case study on Gloeobacterales.
微生物培养物收藏通过研究其菌株的多样性并为科学界提供经过良好表征的生物材料，在分类学中发挥着关键作用，用于基础和应用研究。因此，这些微生物资源中心需要在物种划分方面实施新标准，包括全基因组测序和系统发育基因组学。在此背景下，研究了比利时协调微生物收藏的基因组需求，从而产生了 GEN-ERA 工具箱。后者是一个统一的生物信息学工作流程簇，专门用于细菌和小型真核生物（例如酵母）。
这个公共工具箱允许没有生物信息学专业培训的研究人员进行稳健的系统发育基因组分析。因此，它简化了从基因组下载和质量评估到树重建的所有步骤。它还提供了平均核苷酸同一性比较和代谢建模的工作流程。
通过单个命令启动 Nextflow 工作流程，并可在 GEN-ERA GitHub 存储库（https://github.com/Lcornet/GENERA）上使用。所有工作流程都基于 Singularity 容器，以提高可重复性。
该工具箱针对包括细菌和真菌在内的各种微生物进行了开发。进一步在 18 个早期分支蓝细菌的（宏）基因组的实证数据集上进行了测试，提供了 Gloeobacterales 目（蓝细菌进化树中第一个分支的第一个群体）的最新系统发育基因组分析。
GEN-ERA 工具箱可用于对原核生物和小型真核生物进行完全可重现的比较基因组和代谢分析。尽管专为培养物收藏的常规生物信息学设计，但对所有对微生物分类学感兴趣的研究人员也可以使用，例如我们对 Gloeobacterales 的案例研究。
