BSGatlas: a unified Bacillus subtilis genome and transcriptome annotation atlas with enhanced information access

Geissler, Adrian Sven; Anthon, Christian; Alkan, Ferhat; Gonzalez Tortuero, E; Poulsen, Line Dahl; Kallehauge, Thomas Beuchert; Breüner, Anne; Seemann, Stefan Ernst; Vinther, Jeppe; Gorodkin, Jan

Abstract

A large part of our current understanding of gene regulation in Gram-positive bacteria is based on Bacillus subtilis , as it is one of the most well studied bacterial model systems. The rapid growth in data concerning its molecular and genomic biology is distributed across multiple annotation resources. Consequently, the interpretation of data from further B. subtilis experiments becomes increasingly challenging in both low- and large-scale analyses. Additionally, B. subtilis annotation of structured RNA and non-coding RNA (ncRNA), as well as the operon structure, is still lagging behind the annotation of the coding sequences. To address these challenges, we created the B. subtilis genome atlas, BSGatlas, which integrates and unifies multiple existing annotation resources. Compared to any of the individual resources, the BSGatlas contains twice as many ncRNAs, while improving the positional annotation for 70 % of the ncRNAs. Furthermore, we combined known transcription start and termination sites with lists of known co-transcribed gene sets to create a comprehensive transcript map. The combination with transcription start/termination site annotations resulted in 717 new sets of co-transcribed genes and 5335 untranslated regions (UTRs). In comparison to existing resources, the number of 5′ and 3′ UTRs increased nearly fivefold, and the number of internal UTRs doubled. The transcript map is organized in 2266 operons, which provides transcriptional annotation for 92 % of all genes in the genome compared to the at most 82 % by previous resources. We predicted an off-target-aware genome-wide library of CRISPR–Cas9 guide RNAs, which we also linked to polycistronic operons. We provide the BSGatlas in multiple forms: as a website (https://rth.dk/resources/bsgatlas/), an annotation hub for display in the UCSC genome browser, supplementary tables and standardized GFF3 format, which can be used in large scale -omics studies. By complementing existing resources, the BSGatlas supports analyses of the B. subtilis genome and its molecular biology with respect to not only non-coding genes but also genome-wide transcriptional relationships of all genes.

Citation

Geissler, A. S., Anthon, C., Alkan, F., Gonzalez Tortuero, E., Poulsen, L. D., Kallehauge, T. B., …Gorodkin, J. (2021). BSGatlas: a unified Bacillus subtilis genome and transcriptome annotation atlas with enhanced information access. Microbial Genomics, 7(2), 000524. https://doi.org/10.1099/mgen.0.000524

• Journal Article Type: Article
• Acceptance Date: Jan 11, 2021
• Publication Date: Feb 1, 2021
• Deposit Date: Feb 16, 2021
• Publicly Available Date: Feb 16, 2021
• Journal: Microbial Genomics
• Publisher: Microbiology Society
• Volume: 7
• Issue: 2
• Pages: 000524
• DOI: https://doi.org/10.1099/mgen.0.000524
• Keywords: General Medicine
• Publisher URL: https://doi.org/10.1099/mgen.0.000524
• Related Public URLs: https://www.microbiologyresearch.org/content/journal/mgen
• Additional Information: Additional Information : ** From Crossref journal articles via Jisc Publications Router **Journal IDs: eissn 2057-5858 **History: issued 04-02-2021; published 04-02-2021; Access Information : The original pre-print version of this article (published in 2019) can be accessed using the following link: https://www.biorxiv.org/content/10.1101/807263v1; Funders : Innovation Fund Denmark (Innovationsfonden);Innovationsfonden; Projects : 5163-00010B; Grant Number: 5163-00010B