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Related Concept Videos

Microbial Phylogeny01:28

Microbial 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,...
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Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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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...
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The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
Genomic Diversity in Bacteria
Although bacterial genomes are much...

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Related Experiment Video

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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

Reconstructing genome trees of prokaryotes using overlapping genes.

Chih-Hsien Cheng1, Chung-Han Yang, Hsien-Tai Chiu

  • 1Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan.

BMC Bioinformatics
|February 26, 2010
PubMed
Summary
This summary is machine-generated.

The new OGtree2 web server improves prokaryotic genome tree reconstruction by using a refined overlapping gene (OG) distance metric. This enhanced method accounts for complex genomic rearrangements and regulatory regions, outperforming previous tools.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Phylogenetics

Background:

  • Overlapping genes (OGs) are conserved in microbial genomes and useful for phylogenetic analysis.
  • Previous OGtree server used OG content and breakpoint distances, limiting multi-chromosomal genome analysis and distant species comparisons.
  • Breakpoint-based distances struggle with limited OGs in distantly related prokaryotes.

Purpose of the Study:

  • To develop an improved method for reconstructing prokaryotic genome trees using overlapping genes.
  • To address limitations of previous methods, including applicability to multi-chromosomal genomes and analysis of distantly related species.
  • To introduce the OGtree2 web server for more accurate phylogenetic analysis.

Main Methods:

  • Defined a new OG order distance incorporating biologically accurate rearrangements (reversals, transpositions, translocations).
  • Expanded the definition of overlapping genes to include regulatory regions alongside coding sequences.
  • Reimplemented the OGtree server as OGtree2, a web server for genome tree reconstruction.
  • Evaluated OGtree2 accuracy using 21 Proteobacteria genomes.

Main Results:

  • The new OG order distance is applicable to both uni-chromosomal and multi-chromosomal genomes.
  • OGtree2 demonstrated significantly improved genome tree reconstruction quality compared to OGtree and BPhyOG.
  • Phylogenetic trees generated by OGtree2 showed high congruence with accepted Proteobacteria taxonomy.

Conclusions:

  • OGtree2 provides a more precise and robust tool for prokaryotic genome tree reconstruction.
  • The enhanced OG distance metric and expanded gene definition improve phylogenetic accuracy.
  • The OGtree2 web server is available at http://bioalgorithm.life.nctu.edu.tw/OGtree2.0/.