Predicting jumping genes' roles in changing genome size
A genome contains all of the DNA of every living organism, but its contents don't stop there—most of these structures also contain snippets of DNA that can copy and paste themselves to "infect" a genome, expanding its size. Precisely why that happens remains a mystery.
Researchers at The Ohio State University have developed a new computational tool called PrinTE to trace the insertion and deletion dynamics of transposable elements, also known as jumping genes, in the genomes of living organisms. These snippets of DNA can copy and paste themselves within a genome, expanding its size. The tool works from an inferred ancestral point and evolves forward to the modern-day genome, allowing scientists to study the evolutionary history of these jumping genes.
Transposable elements, or transposons or TEs, are known to alter gene functions over time. By using PrinTE, researchers can infer the past activity of these elements based on the current genome. In a case study on fungal genomes, the researchers found that bursts of transposon insertions were followed by deletions, suggesting that the fungus fought back to suppress further insertions. This indicates that the host can eventually purge inserted transposons to control their activity.
The study also highlights the genome size paradox, where plants with major differences in genome size function in the same way. Despite the large size of the genome, the functions of these transposons remain unclear. PrinTE, an enhancement of a previous tool called TEGenomeSimulator, allows researchers to simulate the evolution of a genome over millions of generations, providing a more comprehensive understanding of the role of transposable elements in genome expansion and contraction.
In the case of myrtle rust, a fungal species with an expanded genome due to transposon insertions, the simulations indicated that the insertion rate was four to five times higher than the deletion rate. This led to an excessively large genome, but subsequent declines in insertion rates were consistent with increased host control over TE activity.
The researchers believe that understanding the evolutionary history of transposable elements using PrinTE can lead to potential applications such as genomic rescue to slow TE activity or delete TEs in species struggling to survive.
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