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Related Concept Videos

Synteny and Evolution02:31

Synteny and Evolution

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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.
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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.
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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 evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
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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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Related Experiment Video

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Human-specific tandem repeat expansion and differential gene expression during primate evolution.

Arvis Sulovari1, Ruiyang Li1, Peter A Audano1

  • 1Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195.

Proceedings of the National Academy of Sciences of the United States of America
|October 30, 2019
PubMed
Summary
This summary is machine-generated.

We developed a framework to study short tandem repeats (STRs) and variable number tandem repeats (VNTRs) in apes, identifying human-specific expansions and their link to genetic instability and disease.

Keywords:
STRVNTRgenome instabilitytandem repeattandem repeat expansion

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Human Genetics

Background:

  • Short tandem repeats (STRs) and variable number tandem repeats (VNTRs) are key sources of genetic variation but are challenging to analyze in genomes.
  • Understanding their evolution and instability is crucial for human genetics and disease research.

Purpose of the Study:

  • To develop a framework for modeling STR and VNTR evolution and instability in apes.
  • To identify human-specific tandem repeat expansions and their genomic distribution.
  • To investigate the functional impact of VNTRs on gene expression and their association with disease.

Main Methods:

  • Phased and assembled 3 ape genomes (chimpanzee, gorilla, orangutan) using long-read and 10x linked-read sequencing.
  • Analyzed 21,442 human tandem repeats across 6 haplotype-resolved human genome assemblies.
  • Utilized tissue-specific and single-cell expression data from human and chimpanzee brains and cerebral organoids.

Main Results:

  • Identified 1,584 STRs/VNTRs specifically expanded in humans, including those affecting key genes.
  • Short interspersed nuclear element-VNTR-Alu (SVA) retrotransposition drives GC-rich repeat expansion, avoiding genes.
  • Non-retroviral VNTRs cluster near genes, particularly subtelomeres, and influence transcript isoform usage, impacting intermediate progenitor cell profiles.
  • Identified 52 STRs/VNTRs as candidates for genetically unstable regions associated with disease.

Conclusions:

  • The study provides a novel framework for analyzing complex repeat regions in primate genomes.
  • Human-specific repeat expansions, driven by different mechanisms, have significant implications for genome evolution and function.
  • VNTRs represent a potential source of cryptic genetic variation contributing to human diseases.