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Overview of Transposition and Recombination02:13

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Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
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DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
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LTR retrotransposons are class I transposable elements with long terminal repeats flanking an internal coding region. These elements are less abundant in mammals compared to other class I transposable elements. About 8 percent of human genomic DNA comprises LTR retrotransposons. Some of the common examples of LTR retrotransposons are Ty elements in yeast and Copia elements in Drosophila.
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As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...
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Excavata is a diverse group of protists that includes both chemoorganotrophic and phototrophic species, with some thriving in anaerobic environments. Among the key groups within Excavata are diplomonads and parabasalids, which are flagellated protists that lack mitochondria and chloroplasts. These microorganisms typically inhabit anoxic environments, such as the intestines of animals, where they exist either symbiotically or as parasites, relying on fermentation for energy production. Some...
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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Updated: Jun 9, 2025

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Transposable Element Diversity and Activity Patterns in Neotropical Salamanders.

Louis Paul Decena-Segarra1, Sean M Rovito1

  • 1Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, km 9.6 Libramiento Norte Carretera Irapuato-León, Irapuato, Guanajuato, Mexico.

Molecular Biology and Evolution
|October 29, 2024
PubMed
Summary
This summary is machine-generated.

Transposable element (TE) diversity negatively correlates with genome size in salamanders. TE activity patterns also differ between large and small genomes, potentially explaining genome size variation.

Keywords:
C-valueBolitoglossinigenomic gigantismlow-coverage sequencingrepeat elements

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Transposable elements (TEs) form a significant part of eukaryotic genomes, especially large ones.
  • A negative correlation between TE diversity and genome size is hypothesized but lacks phylogenetic evidence.
  • Abundance and type of TEs vary across taxa, with unclear patterns related to genome size.

Purpose of the Study:

  • To investigate the relationship between genome size and TE diversity and activity in Neotropical salamanders.
  • To test the hypothesis that TE diversity is negatively correlated with genome size.
  • To explore patterns of TE activity in relation to genome size variation.

Main Methods:

  • Low-coverage sequencing of 16 Neotropical salamander species with a 7-fold range in genome size.
  • Estimation of relative abundance and diversity for each TE superfamily per species.
  • Analysis of TE copy divergence to infer patterns of TE activity.

Main Results:

  • A significant negative relationship was observed between TE diversity and genome size.
  • TE activity patterns differed between species with the largest and smallest genomes.
  • TE diversity and relative abundance showed predictability within the studied taxonomic group.

Conclusions:

  • The findings support the hypothesis of reduced TE diversity in larger eukaryotic genomes.
  • Divergent TE activity histories may contribute to variations in genome size.
  • TE diversity and abundance are potentially predictable factors within specific taxonomic lineages.