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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
Summary
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.
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.
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