Studying the dark matter of the genome 09.05.2022

Transposable elements (TE) largely represent what is commonly referred to as the dark matter of the genome, a non-coding portion of the genome that has so far been considered only as “selfish”” or “junk” DNA.
First discovered in maize plants by Barbara McClintock, TEs are repetitive DNA sequences with the ability to mobilize within a host genome directly by a cut-and-paste mechanism (Class II of DNA transposons) or indirectly through an RNA intermediate and a copy-and-paste mechanism (Class I of Retrotransposons).
TEs can impact host genome architecture and evolution in numerous ways: they can lead to large structural genomic variation, such as deletions, inversions, duplications, and translocations; they can insert in gene regions disrupting open reading frames and regulatory regions; they can alter chromosome structure and promote genomic rearrangements through ectopic recombination between transposon copies. On the other hand, TEs represent an important source of genomic novelty and potentially adaptive variation as they can be co-opted and “domesticated” by the host genome to perform new functions.
TE diversity and abundance are highly variable among different organisms and among vertebrate lineages because of their impact on the host genomes, which could be negative or positive, and because different strategies evolved in the host to repress TE mobilization.
Interestingly, transposable elements can be the driver of genome expansion, thus playing a major role in genome size variation. In particular, a positive correlation was detected between the accumulation of specific TE families and very large genomes in species belonging to the Plethodontidae, the largest family of salamanders, which show a much larger amount of long terminal repeat (LTR) retrotransposons, in the caecilian Ichthyophis bannanicus whose genome is dominated by DIRS elements, or in the lungfish, the closest living relative of tetrapods. For example, the Australian lungfish Neoceratodus forsteri has a genome size of 43 Gb, represented mostly by huge intergenic regions and introns with ~90% of repetitive elements still active, maybe due to poor TE silencing and deletion.
The investigation of transposable elements dynamics is an important task in the ENDEMIXIT species with the largest genome, which is the Apennine yellow-bellied toad (estimated size of 10Gb). We aim to characterize the landscape of transposable elements in this big genome to unveil the history of TE-host evolutionary dynamics, to study the impact of TEs on the structural genomic variation, and to understand the impact of selection on TE dynamics by comparing two different populations of toad characterized by different recent evolutionary histories.

Genome size and TE content in different vertebrate genomes
(Figure from Almojil et al., Genes, 2021)

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