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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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Single Nucleotide Polymorphisms-SNPs01:05

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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...
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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.
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The Tree of Life - Bacteria, Archaea, Eukaryotes02:40

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The “tree of life” describes the evolution of life and the evolutionary relationships between organisms. The root of the tree is the common ancestor to all life on Earth. All other species radiate from this point, much like the branches of a tree. The numerous tips of these branches on the tree of life represent every living, or extant, species. Extinct species, which are species that no longer exist, can be found towards the center of the tree. Currently, these organisms, both...
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Phylogenetic Trees03:21

Phylogenetic Trees

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Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
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Updated: Jun 26, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.

Martin Hunt1,2,3,4, Angie S Hinrichs5, Daniel Anderson1

  • 1European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK.

Biorxiv : the Preprint Server for Biology
|May 15, 2024
PubMed
Summary
This summary is machine-generated.

Researchers reprocessed SARS-CoV-2 sequencing data using a novel amplicon-aware tool, Viridian, to create a cleaner global phylogeny. This new resource improves SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) genomic analysis for science and public health.

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Area of Science:

  • Genomics and Bioinformatics
  • Virology and Infectious Diseases
  • Computational Biology

Background:

  • The SARS-CoV-2 genome is the most highly sequenced globally, offering rich phylogenetic data for public health.
  • Existing SARS-CoV-2 genome assemblies contain systematic errors due to variable amplicon schemes and inconsistent quality control.
  • These errors significantly impact phylogenetic accuracy, necessitating extensive manual curation of viral trees.

Purpose of the Study:

  • To reprocess all available public SARS-CoV-2 raw sequence data using a rigorous, amplicon-aware methodology.
  • To construct a cleaner, more accurate global phylogeny of SARS-CoV-2.
  • To provide a valuable, high-quality resource for researchers studying viral evolution and epidemiology.

Main Methods:

  • Developed and utilized a novel assembly tool, Viridian, specifically designed for amplicon sequence data.
  • Processed the complete set of public SARS-CoV-2 raw sequence data, assembling high-quality consensus sequences.
  • Implemented rigorous quality control and amplicon-aware processing to eliminate artefactual errors and mask low-quality positions.

Main Results:

  • Generated a global phylogenetic tree comprising 4,471,579 SARS-CoV-2 samples, representing all available public data as of June 2024.
  • The Viridian tool successfully eliminated artefactual errors common in previous SARS-CoV-2 genome assemblies.
  • Validated the methodology through simulation and empirical data, quantifying significant improvements in phylogenetic accuracy.

Conclusions:

  • The reprocessing of SARS-CoV-2 data with Viridian provides a substantially improved and reliable global phylogeny.
  • The Viridian tool and the resulting high-quality consensus sequences offer a valuable resource for the scientific community.
  • This cleaner phylogenetic resource will enhance research in SARS-CoV-2 evolution, transmission dynamics, and public health interventions.