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Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

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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Convergent Evolution

Evolution shapes the features of organisms over time, ensuring that they are suited for the environments in which they live. Sometimes, selection pressure leads to the rise of similar but unrelated adaptations in organisms with no recent common ancestors, a process known as convergent evolution.
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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 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...
Synteny and Evolution02:31

Synteny and Evolution

John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral chromosome underwent...

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An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

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Published on: July 12, 2022

Testing the ortholog conjecture with comparative functional genomic data from mammals.

Nathan L Nehrt1, Wyatt T Clark, Predrag Radivojac

  • 1School of Informatics and Computing, Indiana University, Bloomington, Indiana, USA.

Plos Computational Biology
|June 23, 2011
PubMed
Summary

The ortholog conjecture, assuming orthologs are more functionally similar than paralogs, is largely untested. Our study reveals paralogs often predict protein function better than orthologs, challenging this common assumption in comparative genomics.

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Area of Science:

  • Comparative genomics
  • Molecular biology
  • Bioinformatics

Background:

  • The "ortholog conjecture" posits that orthologous genes exhibit greater functional similarity than paralogous genes.
  • This assumption underpins many computational protein function prediction methods but remains largely unverified.
  • A large-scale empirical test is needed to validate this fundamental concept.

Purpose of the Study:

  • To conduct the first comprehensive, large-scale investigation of the ortholog conjecture.
  • To compare the functional similarity predictive power of orthologs versus paralogs using real-world data.
  • To explore factors influencing functional divergence between gene families.

Main Methods:

  • Utilized comparative functional genomic data from human and mouse.
  • Analyzed experimentally derived functions for over 8,900 genes.
  • Employed an independent microarray dataset to assess functional prediction accuracy.

Main Results:

  • Both datasets demonstrated that paralogs frequently outperform orthologs in predicting protein function, even at lower sequence identities.
  • Intraspecific paralogs (within the same species) showed higher functional similarity than interspecific paralogs.
  • Paralogous pairs on the same chromosome exhibited greater functional similarity than those on different chromosomes, suggesting interlocus gene conversion.

Conclusions:

  • The ortholog conjecture is not universally supported; paralogs can be superior functional predictors.
  • Protein function evolution is more influenced by cellular context than by amino acid sequence alone.
  • Findings have significant implications for computational protein function prediction and understanding gene evolution.