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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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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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Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
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Multi-species Conserved Sequences02:51

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Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
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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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Consensus properties and their large-scale applications for the gene duplication problem.

Jucheol Moon1, Harris T Lin1, Oliver Eulenstein1

  • 11 Department of Computer Science, Iowa State University, 226 Atanasoff Hall, Ames, Iowa 50010, USA.

Journal of Bioinformatics and Computational Biology
|April 29, 2016
PubMed
Summary
This summary is machine-generated.

The gene duplication problem in species tree inference has a key conjecture disproven. However, a weaker Pareto property was found, enabling a new efficient algorithm for analyzing gene duplication events.

Keywords:
Phylogenticsconsensus propertygene duplicationlarge-scale application

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Area of Science:

  • Phylogenetics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Species tree inference is crucial for understanding evolutionary relationships.
  • Gene trees are often confounded by gene duplications, complicating species tree reconstruction.
  • The gene duplication problem aims to find a species tree minimizing gene duplications.

Purpose of the Study:

  • To investigate the Pareto property for clusters in the gene duplication problem.
  • To determine if all commonly present clusters in input gene trees are present in all solutions.
  • To develop an efficient algorithm for species tree inference based on gene duplication.

Main Methods:

  • Disproving a conjecture regarding the Pareto property for clusters in the gene duplication problem.
  • Demonstrating a weaker Pareto property where strict consensus is found in at least one solution.
  • Designing and implementing a scalable algorithm for the gene duplication problem.

Main Results:

  • The conjecture that all strict consensus clusters are in every solution is disproven.
  • A weaker Pareto property, where strict consensus is in at least one solution, is established.
  • An efficient and scalable algorithm for the gene duplication problem was developed.

Conclusions:

  • The gene duplication problem does not generally satisfy the strong Pareto property for clusters.
  • A weaker Pareto property supports the development of efficient species tree inference algorithms.
  • The new algorithm performs well on large datasets and can evaluate heuristic accuracy.