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Related Concept Videos

Gene Duplication and Divergence02:37

Gene Duplication and Divergence

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The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
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Phylogeny01:23

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Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.
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Centrosome Duplication02:25

Centrosome Duplication

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The primary microtubule organizing center (MTOC) in animal cells is the centrosome. A centrosome has two cylindrical centrioles at its core. Each centriole consists of nine sets of three microtubules held together by proteins. The centrioles are positioned at right angles to each other and surrounded by a shapeless protein cloud called the pericentriolar matrix, or pericentriolar material (PCM).
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Duplication of Chromatin Structure02:05

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The process of chromosome duplication during cell division requires genome-wide disruption and re-assembly of chromatin. The chromatin structure must be accurately inherited, reassembled, and maintained in the daughter cells to ensure lineage propagation.
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Analysis of Population Pharmacokinetic Data01:12

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Analysis of population pharmacokinetic data involves studying the behavior of drugs within diverse populations to understand their pharmacokinetic parameters. Traditional pharmacokinetic methods typically involve collecting samples from a few individuals and estimating these parameters. While these methods are commonly used, they have limitations in capturing the variability in drug response among individuals or heterogeneous populations. Population pharmacokinetics is employed to address these...
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Gene Families01:57

Gene Families

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Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
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Related Experiment Video

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Sample Preparation and Analysis of RNASeq-based Gene Expression Data from Zebrafish
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Phylogeny analysis from gene-order data with massive duplications.

Lingxi Zhou1, Yu Lin2, Bing Feng1

  • 1Department of Computer Science and Engineering, University of South Carolina, Columbia, 29208, South Carolina, USA.

BMC Genomics
|March 8, 2018
PubMed
Summary
This summary is machine-generated.

New maximum-likelihood methods accurately reconstruct gene-order phylogenies, even with large genomes and gene duplications. These phylogenetic approaches offer improved accuracy for evolutionary studies.

Keywords:
Maximum likelihoodPhylogeny reconstructionVariable length binary encodingWhole genome duplication

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Area of Science:

  • Genomics
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Gene order changes (rearrangements, insertions, deletions, duplications) offer a unique data source for phylogenetic reconstruction.
  • These rare events allow inference of deeper evolutionary relationships compared to sequence mutations.
  • Existing methods like maximum parsimony and maximum likelihood struggle with large genomes and gene duplications, especially whole genome duplication.

Purpose of the Study:

  • To present novel maximum-likelihood (ML) based methods for phylogenetic reconstruction.
  • To encode gene adjacency and gene content multiplicity information within an ML framework.

Main Methods:

  • Developed three new methods based on maximum-likelihood (ML) approaches.
  • Incorporated multiplicity of gene adjacency and gene content information.

Main Results:

  • New methods demonstrated superior accuracy in reconstructing phylogenies on simulated data compared to existing approaches.
  • Evaluated the method's performance on real whole-genome data from eleven mammals.
  • The developed software package is publicly available.

Conclusions:

  • The new encoding schemes effectively integrate gene adjacency and content multiplicity into an ML framework.
  • These methods show significant promise for reconstructing phylogenies from whole-genome data, particularly in the presence of extensive gene duplications.