TraDIS-Vault: an interactive searchable genome browser and repository for TraDIS data
Aim
To create a web browser for community access and easy visualisation and comparison of hundreds of TraDIS datasets.
Brief project outline
Professor Henderson's research group studies bacteria and their interaction with humans and animals. Their approach to identifying genes encoding essential functions is Transposon-directed insertion-site sequencing (TraDIS), which couples transposon mutagenesis with DNA sequencing to identify essential regions of a bacterial genome. The current TraDIS library has a median distance between mutations of 2 bp and is the densest mutant library described for any organism; this resource positions the Henderson group uniquely within the global community.
Together with the QCIF Facility for Advanced Bioinformatics (QFAB) and UQ’s Genome Innovation Hub (GIH), the project will develop TraDIS-Vault, a flexible and user-friendly web-based interface ideal for storing and visualizing microbial genome datasets. We will populate this database with our TraDIS datasets. This will be accompanied by a simple interface to allow users to upload their own datasets for analysis and visualisation.
Genomics-based innovative aspect of proposal
TraDIS-Vault will provide a stable public resource that can be used to store, visualise, and compare multiple TraDIS datasets. We propose to expand this to assimilate relevant microbial RNAseq and ChIPseq datasets into the database providing a comprehensive tool for analysing and integrating genetic information.
Broad applicability of the technique
TraDIS-Vault will be a crucial resource for those studying the fundamentals of bacterial viability and biochemistry, infection, vaccine development and antibiotic development. A web based interaction tool for low resolution genetic interactions based on single gene knockouts libraries was published 8 years ago in Cell and has been cited 450 times; this is the “go-to” resource for all teams studying the fundamental biology of E. coli (https://ecoliwiki.org/tools/chemgen/). TraDIS-Vault will replace this resource with a much higher level of resolution and expand it to integrate additional pathogens and genomic datasets.
At the technical level, TraDIS-Vault will be based on Web Apollo, a platform for genome annotation that is widely adopted by the genomics community. For example, it is one of the platforms that the Australian BioCommons is deploying to support large initiatives such as the Oz Mammals Genomics initiative. The availability of PacBio Sequel II at UQ will dramatically increase the number of draft genomes being assembled. UQ researchers and collaborators in the fields of agriculture, environmental biology, microbiology as well as human and animal health will require a collaborative platform to share, annotate and curate those draft genomes. This project will enable GIH staff to have exposure to this tool.
Developments arising from this project
TraDIS-Vault can be access from the following link https://tradis-vault.qfab.org/apollo/jbrowse/
Publications referencing the web browser
Cain, A.K., Barquist, L., Goodman, A.L. et al. A decade of advances in transposon-insertion sequencing. Nat Rev Genet 21, 526–540 (2020). https://doi.org/10.1038/s41576-020-0244-x
DpaA detaches Braun’s lipoprotein from peptidoglycan
Matthias Winkle, Víctor M. Hernández-Rocamora, Karthik Pullela, Emily C. A. Goodall, Alessandra M. Martorana, Joe Gray, Ian R. Henderson, Alessandra Polissi, Waldemar Vollmer
bioRxiv 2021.02.21.432140; doi: https://doi.org/10.1101/2021.02.21.432140
News and media releases
UQ and QCIF develop portal for microbial genome data sets, QCIF news, 27 November 2020.
