Related Experiment Video
Updated: May 22, 2026
10:24
Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons
Published on: August 29, 2014
Phylogenetic footprinting: a boost for microbial regulatory genomics
Pramod Katara1, Atul Grover, Vinay Sharma
1Department of Bioscience and Biotechnology, Banasthali University, Banasthali, 304022, India. pmkatara@gmail.com
Protoplasma
|November 25, 2011
Summary
Phylogenetic footprinting identifies conserved regulatory elements across species. This review critically assesses methods and resources for prokaryotes, highlighting factors influencing discovery success.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Phylogenetic footprinting is a key method for discovering regulatory elements by identifying conserved motifs in homologous genomic regions across species.
- Current approaches primarily use alignment-based or motif-based methods, with a notable lack of dedicated tools for phylogenetic footprinting.
- Existing software offers variable success, often influenced by the availability of knowledge, techniques, and resources.
Purpose of the Study:
- To critically review various phylogenetic footprinting approaches relevant to prokaryotes.
- To outline available resources and discuss factors impacting the effectiveness of phylogenetic footprinting in prokaryotic genomes.
- To provide a clear understanding for the proper application of phylogenetic footprinting in prokaryotes.
Main Methods:
- Comparative genomics analysis of homologous regulatory regions.
- Review and critical apprehension of existing alignment-based and motif-based phylogenetic methods.
- Assessment of factors influencing the success of computational tools in regulatory element discovery.
Main Results:
- Identified a gap in specialized phylogenetic footprinting tools, despite the utility of existing general bioinformatics software.
- Highlighted the variability in success rates of current tools due to knowledge, techniques, and resource limitations.
- Detailed the critical factors affecting phylogenetic footprinting efficacy in prokaryotic systems.
Conclusions:
- Phylogenetic footprinting is a valuable technique for prokaryotic regulatory element discovery, but requires careful consideration of methodology and resources.
- Further development of dedicated tools and standardized approaches is needed to improve the reliability and success of phylogenetic footprinting in prokaryotes.
- A comprehensive understanding of influencing factors is crucial for optimizing the application of phylogenetic footprinting in prokaryotic genomics.
Related Concept Videos
02:16Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes
The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
01:29Modern Molecular Taxonomy
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
01:20Applications of Molecular Taxonomy
Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
01:08Evolution of Microbial Genome
Microbial genome evolution is a highly dynamic process shaped by continual gene gain and loss across species and strains. This genomic flexibility allows microorganisms to adapt rapidly to environmental pressures and interactions with other organisms. Central to understanding this diversity is the distinction between the core and pan genomes.The core genome comprises the genes shared by all sampled strains of a species, representing essential functions needed for fundamental cellular processes.
01:28Microbial Phylogeny
Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
01:22Phylogenetic Species Concept in Microbiology
The phylogenetic species concept (PSC) is a framework used to delineate species based on evolutionary relationships, emphasizing shared ancestry and diagnosable genetic traits. Unlike morphological or biological species concepts, the PSC is particularly advantageous for microbial taxonomy, where traditional reproductive or phenotypic criteria often fall short due to the prevalence of asexual reproduction, minimal morphological differentiation, and widespread horizontal gene transfer among...