Janssen Axel B, Gibson Paddy S, Bravo Afonso M, de Bakker Vincent, Slager Jelle, Veening Jan-Willem
Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland.
Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, the Netherlands.
Nucleic Acids Res. 2025 Jan 6;53(D1):D839-D851. doi: 10.1093/nar/gkae923.
Streptococcus pneumoniae is an opportunistic human pathogen responsible for high morbidity and mortality rates. Extensive genome sequencing revealed its large pangenome, serotype diversity, and provided insight into genome dynamics. However, functional genome analysis has lagged behind, as that requires detailed and time-consuming manual curation of genome annotations and integration of genomic and phenotypic data. To remedy this, PneumoBrowse was presented in 2018, a user-friendly interactive online platform, which provided the detailed annotation of the S. pneumoniae D39V genome, alongside transcriptomic data. Since 2018, many new studies on S. pneumoniae genome biology and protein functioning have been performed. Here, we present PneumoBrowse 2 (https://veeninglab.com/pneumobrowse), fully rebuilt in JBrowse 2. We updated annotations for transcribed and transcriptional regulatory features in the D39V genome. We added genome-wide data tracks for high-resolution chromosome conformation capture (Hi-C) data, chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq), ribosome profiling, CRISPRi-seq gene essentiality data and more. Additionally, we included 18 phylogenetically diverse S. pneumoniae genomes and their annotations. By providing easy access to diverse high-quality genome annotations and links to other databases (including UniProt and AlphaFold), PneumoBrowse 2 will further accelerate research and development into preventive and treatment strategies, through increased understanding of the pneumococcal genome.
肺炎链球菌是一种机会性人类病原体，可导致高发病率和死亡率。广泛的基因组测序揭示了其庞大的泛基因组、血清型多样性，并为基因组动态变化提供了见解。然而，功能基因组分析却滞后了，因为这需要对基因组注释进行详细且耗时的人工整理，以及整合基因组和表型数据。为了弥补这一不足，2018年推出了PneumoBrowse，这是一个用户友好的交互式在线平台，它提供了肺炎链球菌D39V基因组的详细注释以及转录组数据。自2018年以来，已经开展了许多关于肺炎链球菌基因组生物学和蛋白质功能的新研究。在此，我们展示了在JBrowse 2中完全重建的PneumoBrowse 2（https://veeninglab.com/pneumobrowse）。我们更新了D39V基因组中转录和转录调控特征的注释。我们添加了全基因组数据轨道，用于高分辨率染色体构象捕获（Hi-C）数据、与高通量测序相结合的染色质免疫沉淀（ChIP-Seq）、核糖体分析、CRISPRi-seq基因必需性数据等。此外，我们纳入了18个系统发育上不同的肺炎链球菌基因组及其注释。通过提供对各种高质量基因组注释的便捷访问以及与其他数据库（包括UniProt和AlphaFold）的链接，PneumoBrowse 2将通过增进对肺炎球菌基因组的了解，进一步加速预防和治疗策略的研发。
