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Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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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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Gene Evolution - Fast or Slow?02:05

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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
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Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

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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...
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Applications of Molecular Taxonomy01:20

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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...
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Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

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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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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Analyzing microbial evolution through gene and genome phylogenies.

Sarah Teichman1, Michael D Lee2,3, Amy D Willis4

  • 1University of Washington Department of Statistics, Box 354322, Seattle, WA 98195-4322, USA.

Biostatistics (Oxford, England)
|October 28, 2023
PubMed
Summary
This summary is machine-generated.

Scientists developed a new R package to visualize and analyze microbial gene evolution. This tool helps explore distinct gene histories within microbial genomes, aiding evolutionary studies.

Keywords:
Dimension reductionMicrobiomeNon-EuclideanStatistical geneticsVisualization

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Area of Science:

  • Microbial evolution
  • Bioinformatics
  • Phylogenetics

Background:

  • Microbiome research requires advanced tools for analyzing microbial evolution.
  • Studying whole microbial genomes can obscure distinct evolutionary histories of individual genes.
  • Existing methods for gene-level phylogenetic analysis have practical limitations.

Purpose of the Study:

  • To present an interactive method for analyzing collections of gene phylogenies.
  • To treat estimated gene-level phylogenies as data objects for analysis.
  • To provide an intuitive visualization of complex phylogenetic data.

Main Methods:

  • Utilized a local linear approximation of phylogenetic tree space.
  • Visualized estimated gene trees as points in low-dimensional Euclidean space.
  • Developed an open-source R package for phylogenetic analysis.

Main Results:

  • Demonstrated utility through microbial data analyses.
  • Successfully identified outlying gene histories in Prevotella strains.
  • Contrasted Streptococcus phylogenies estimated using different gene sets.

Conclusions:

  • The proposed method offers an intuitive visualization of gene-level evolutionary histories.
  • The R package assists in estimating, visualizing, and interacting with bacterial gene phylogenies.
  • This approach addresses practical limitations in analyzing collections of gene trees.