ORCID Profile
0000-0002-6134-1488
Current Organisations
University of Western Australia
,
Danmarks Tekniske Universitet The Novo Nordisk Foundation Center for Biosustainability
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Publisher: Oxford University Press (OUP)
Date: 2021
Abstract: Genes involved in coordinated biological pathways, including metabolism, drug resistance and virulence, are often collocalized as gene clusters. Identifying homologous gene clusters aids in the study of their function and evolution, however, existing tools are limited to searching local sequence databases. Tools for remotely searching public databases are necessary to keep pace with the rapid growth of online genomic data. Here, we present cblaster, a Python-based tool to rapidly detect collocated genes in local and remote databases. cblaster is easy to use, offering both a command line and a user-friendly graphical user interface. It generates outputs that enable intuitive visualizations of large datasets and can be readily incorporated into larger bioinformatic pipelines. cblaster is a significant update to the comparative genomics toolbox. cblaster source code and documentation is freely available from GitHub under the MIT license (amcil/cblaster). Supplementary data are available at Bioinformatics Advances online.
Publisher: Royal Society of Chemistry (RSC)
Date: 2020
DOI: 10.1039/D0SC01712D
Abstract: Using a combination of biomimetic chemistry and molecular genetics we demonstrate that formicamycin biosynthesis proceeds via reductive Favorskii-like reaction.
Publisher: Royal Society of Chemistry (RSC)
Date: 2016
DOI: 10.1039/C6CC01930G
Abstract: Two spontaneous intramolecular cycloadditions lead to the biosynthetic congeners heronamide A and B.
Publisher: Cold Spring Harbor Laboratory
Date: 13-10-2023
Publisher: Elsevier BV
Date: 11-2013
Publisher: Royal Society of Chemistry (RSC)
Date: 2021
DOI: 10.1039/D1OB00600B
Abstract: Biosynthetic mosaics and superclusters provide rare insights into the evolution of microbial chemical ersity.
Publisher: Society of Conservatoire at Jardin Botaniques de la Ville de Geneve
Date: 02-08-2016
DOI: 10.15553/C2016V712A8
Publisher: Magnolia Press
Date: 19-06-2013
DOI: 10.11646/PHYTOTAXA.112.2.4
Abstract: The paleotropical monocot Pandanaceae family comprises c. 700 species distributed into five genera: Benstonea (c. 60 spp.), Freycinetia (c. 250 spp.), Martellidendron (6 spp.), Pandanus (c. 450 spp.) and Sararanga (2 spp.). Benstonea was circumscribed to include species previously placed in Pandanus section Acrostigma (one of the four sections of Pandanus subgenus Acrostigma). New phylogenetic data show that the six species of the remaining three sections of subgenus Acrostigma (sections Epiphytica, Fusiforma and Platystigma) and a seventh species doubtfully placed in section Acrostigma (Pandanus microglottis) also belonged to Benstonea. This genus is therefore characterized by a suite of morphological characters, viz. stigmatic groove on the adaxial side of the stigma and a staminate flower reduced to 1 to 3 free stamens (sometimes joined at base). We therefore make here the necessary seven new combinations accompanied by one lectotypification in Benstonea, a genus that now reflects the view of the visionary Benjamin Stone who had already grouped these species in Pandanus subgenus Acrostigma based solely on morphology.
Publisher: Cold Spring Harbor Laboratory
Date: 23-06-2021
DOI: 10.1101/2021.06.23.449585
Abstract: Reprogramming biosynthetic assembly-lines is a topic of intense interest. This is unsurprising as the scaffolds of most antibiotics in current clinical use are produced by such pathways. The modular nature of assembly-lines provides a direct relationship between the sequence of enzymatic domains and the chemical structure of the product, but rational reprogramming efforts have been met with limited success. To gain greater insight into the design process, we wanted to examine how Nature creates assembly-lines and searched for biosynthetic pathways that might represent evolutionary transitions. By examining the biosynthesis of the anti-tubercular wollamides, we show how whole gene duplication and neofunctionalization can result in pathway bifurcation. Importantly, we show that neofunctionalization occurs primarily through intragenomic recombination. This pathway bifurcation leads to redundancy, providing the genetic robustness required to enable large structural changes during the evolution of antibiotic structures. Should the new product be none-functional, gene loss can restore the original genotype. However, if the new product confers an advantage, depreciation and eventual loss of the original gene creates a new linear pathway. This provides the blind watchmaker equivalent to the ‘design, build, test’ cycle of synthetic biology.
Publisher: Springer Science and Business Media LLC
Date: 17-06-2020
Publisher: Cold Spring Harbor Laboratory
Date: 29-07-2023
DOI: 10.1101/2023.07.26.550493
Abstract: Phylogenetic trees are the primary tool for visualising evolutionary relationships. Traditionally, phylogenies are inferred from manually curated sets of marker genes. As available genomic data increases, there is increasing demand for tools to automatically build phylogenies from assembled genomes. Existing tools rely on reference databases of preselected marker genes, limiting their taxonomic scope. We sought to develop a tool that could quickly build phylogeny from input genomes alone. We developed getphylo , a tool to automatically generate multi-locus phylogenetic trees from GenBank files. It has a low barrier to entry with minimal dependencies. getphylo uses a parallelised, heuristic workflow to keep runtime and system requirements as low as possible. getphylo consistently produces trees with topologies comparable to other tools in less time. Furthermore, as getphylo does not rely on reference databases, it has a virtually unlimited scope in terms of taxonomy (e.g., not limited to bacteria) and genetic scale (e.g., can analyse plasmids, prophage, and gene clusters). This combination of speed and flexibility makes getphylo a valuable addition to the phylogenetics toolkit. getphylo is freely available and is downloadable through the Python Package Index ( pip install getphylo roject/getphylo/ ) and GitHub ( rboothtj/getphylo ).
Publisher: Elsevier
Date: 2020
Publisher: Oxford University Press (OUP)
Date: 18-11-2022
DOI: 10.1093/NAR/GKAC1049
Abstract: With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for erse natural products. MIBiG 3.0 is accessible online at
Publisher: Royal Society of Chemistry (RSC)
Date: 2020
DOI: 10.1039/D0SC01928C
Abstract: Reactivation of quiescent polyketide production in a domesticated lab strain.
Publisher: Elsevier BV
Date: 09-2021
Publisher: Royal Society of Chemistry (RSC)
Date: 2023
DOI: 10.1039/D2OB02332F
Abstract: The discovery of the resoruclins, new 3,5-dihydroxybenzoic acid containing macrolides for Steptomyces sp. MST-91080, and their putative biosynthetic pathway.
Publisher: Cold Spring Harbor Laboratory
Date: 10-02-2023
DOI: 10.1101/2023.02.08.527634
Abstract: Co-localized sets of genes that encode specialized functions are common across microbial genomes and occur in genomes of larger eukaryotes as well. Important ex les include Biosynthetic Gene Clusters (BGCs) that produce specialized metabolites with medicinal, agricultural, and industrial value (e.g. antimicrobials). Comparative analysis of BGCs can aid in the discovery of novel metabolites by highlighting distribution and identifying variants in public genomes. Unfortunately, gene-cluster-level homology detection remains inaccessible, time-consuming and difficult to interpret. The comparative gene cluster analysis toolbox (CAGECAT) is a rapid and user-friendly platform to mitigate difficulties in comparative analysis of whole gene clusters. The software provides homology searches and downstream analyses without the need for command-line or programming expertise. By leveraging remote BLAST databases, which always provide up-to-date results, CAGECAT can yield relevant matches that aid in the comparison, taxonomic distribution, or evolution of an unknown query. The service is extensible and interoperable and implements the cblaster and clinker pipelines to perform homology search, filtering, gene neighbourhood estimation, and dynamic visualisation of resulting variant BGCs. With the visualisation module, publication-quality figures can be customized directly from a web-browser, which greatly accelerates their interpretation via informative overlays to identify conserved genes in a BGC query. Overall, CAGECAT is an extensible software that can be interfaced via a standard web-browser for whole region homology searches and comparison on continually updated genomes from NCBI. The public web server and installable docker image are open source and freely available without registration at: cagecat.bioinformatics.nl
Location: Denmark
No related grants have been discovered for Thomas James Booth.