ArticleBioinformatics (Oxford, England)2015
An event-driven approach for studying gene block evolution in bacteria.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed, 16 citations in OpenAlex.
- Exploring the enzymatic repertoires of Bacteria and Archaea and their associations with metabolic maps.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2024Article
- Finding orthologous gene blocks in bacteria: the computational hardness of the problem and novel methods to address it.Bioinformatics (Oxford, England) · 2020Article
- Unraveling a Tangled Skein: Evolutionary Analysis of the Bacterial Gibberellin Biosynthetic Operon.mSphere · 2020Article
- A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries.PLoS computational biology · 2020Article
- Emerging evolutionary paradigms in antibiotic discovery.Journal of industrial microbiology & biotechnology · 2019Review
- Interpreting Microbial Biosynthesis in the Genomic Age: Biological and Practical Considerations.Marine drugs · 2017Review
- Functional Annotations of Paralogs: A Blessing and a Curse.Life (Basel, Switzerland) · 2016Article
- Investigating Evolutionary Dynamics of RHA1 Operons.Evolutionary bioinformatics online · 2016Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationGene blocks are genes co-located on the chromosome. In many cases, gene blocks are conserved between bacterial species, sometimes as operons, when genes are co-transcribed. The conservation is rarely absolute: gene loss, gain, duplication, block splitting and block fusion are frequently observed. An open question in bacterial molecular evolution is that of the formation and breakup of gene blocks, for which several models have been proposed. These models, however, are not generally applicable to all types of gene blocks, and consequently cannot be used to broadly compare and study gene block evolution. To address this problem, we introduce an event-based method for tracking gene block evolution in bacteria.
resultsWe show here that the evolution of gene blocks in proteobacteria can be described by a small set of events. Those include the insertion of genes into, or the splitting of genes out of a gene block, gene loss, and gene duplication. We show how the event-based method of gene block evolution allows us to determine the evolutionary rateand may be used to trace the ancestral states of their formation. We conclude that the event-based method can be used to help us understand the formation of these important bacterial genomic structures. AVAILABILITY AND IMPLEMENTATION: The software is available under GPLv3 license on http://github.com/reamdc1/gene_block_evolution.git. Supplementary online material: http://iddo-friedberg.net/operon-evolution
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.