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1. The impact of insertion bias into piRNA clusters on the invasion of transposable elements

   https://doi.org/10.1186/s12915-025-02370-0  

   Pritam, Shashank; Scarpa, Almorò; Kofler, Robert; Signor, Sarah (December 2025, BMC Biology)

   Abstract BackgroundIn our current understanding of transposable element (TE) invasions, TEs move freely until they accidentally insert into a piRNA cluster, where they are silenced by the production of piRNA cognate to the TE. Under this model, one would expect that selection might favor TEs that avoid piRNA clusters. However, empirical observations show that some TEs, such as theP-element, insert into piRNA clusters preferentially. We were thus wondering if such a bias, by minimizing harm to the host, could facilitate the spread of TEs throughout a population. ResultsWe performed extensive forward simulations of TE invasions with different insertion biases into piRNA clusters to determine if there was ever a situation in which the insertion bias was beneficial to the TE. We found that insertion bias significantly altered the invasion dynamics of TEs, primarily by changing the number of TE copies in individuals before silencing. Insertion into a piRNA cluster reduced the deleterious effects of TEs to the host population, but we found that TEs avoiding piRNA clusters out-compete TEs with a bias toward cluster insertions. Insertion bias was only beneficial to the TE when there was negative selection against TEs and a lack of recombination. ConclusionsDifferent TEs show different insertion biases into piRNA clusters suggesting they are an attribute of the TE not the host, yet scenarios in which this is beneficial for TE propagation are quite limited. This opens up an interesting area for future research into the dynamics of insertion bias during TE invasions. 

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2. Structural Variants Contribute to Phenotypic Variation in Maize

   https://doi.org/10.1111/mec.17662  

   Catlin, Nathan S; Agha, Husain I; Platts, Adrian E; Munasinghe, Manisha; Hirsch, Candice N; Josephs, Emily B (December 2025, Molecular Ecology)

   ABSTRACT Comprehensively identifying the loci shaping trait variation has been challenging, in part because standard approaches often miss many types of genetic variants. Structural variants (SVs), especially transposable elements (TEs), are likely to affect phenotypic variation but we lack methods that can detect polymorphic SVs and TEs using short‐read sequencing data. Here, we used a whole genome alignment between two maize genotypes to identify polymorphic SVs and then genotyped a large maize diversity panel for these variants using short‐read sequencing data. After characterising SV variation in the panel, we identified SV polymorphisms that are associated with life history traits and genotype‐by‐environment (GxE) interactions. While most of the SVs associated with traits contained TEs, only two of the SVs had boundaries that clearly matched TE breakpoints indicative of a TE insertion, while the other polymorphisms were likely caused by deletions. One of the SVs that appeared to be caused by a TE insertion had the most associations with gene expression compared to other trait‐associated SVs. All of the SVs associated with traits were in linkage disequilibrium with nearby single nucleotide polymorphisms (SNPs), suggesting that the approach used here did not identify unique associations that would have been missed in a SNP association study. Overall, we have (1) created a technique to genotype SV polymorphisms across a large diversity panel using support from genomic short‐read sequencing alignments and (2) connected this presence/absence SV variation to diverse traits and GxE interactions. 

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3. The PIWI/piRNA response is relaxed in a rodent that lacks mobilizing transposable elements

   https://doi.org/10.1261/rna.078862.121  

   Vandewege, Michael W.; Patt, Roy N.; Merriman, Dana K.; Ray, David A.; Hoffmann, Federico G. (March 2022, RNA)

   Transposable elements (TEs) are genomic parasites that can propagate throughout host genomes. Mammalian genomes are typically dominated by LINE retrotransposons and their associated SINEs, and germline mobilization is a challenge to genome integrity. There are defenses against TE proliferation and the PIWI/piRNA defense is among the most well understood. However, the PIWI/piRNA system has been investigated largely in animals with actively mobilizing TEs and it is unclear how the PIWI/piRNA system functions in the absence of mobilizing TEs. The 13-lined ground squirrel provides the opportunity to examine PIWI/piRNA and TE dynamics within the context of minimal, and possibly nonexistent, TE accumulation. To do so, we compared the PIWI/piRNA dynamics in squirrels to observations from the rabbit and mouse. Despite a lack of young insertions in squirrels, TEs were still actively transcribed at higher levels compared to mouse and rabbit. All three Piwi genes were not expressed, prior to P8 in squirrel testis, and there was little TE expression change with the onset of Piwi expression. We also demonstrated there was not a major expression change in the young squirrel LINE families in the transition from juvenile to adult testis in contrast to young mouse and rabbit LINE families. These observations lead us to conclude that PIWI suppression, was weaker for squirrel LINEs and SINEs and did not strongly reduce their transcription. We speculate that, although the PIWI/piRNA system is adaptable to novel TE threats, transcripts from TEs that are no longer threatening receive less attention from PIWI proteins. 

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4. A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility

   https://doi.org/10.1101/gr.276839.122  

   Ruggieri, Angelo A.; Livraghi, Luca; Lewis, James J.; Evans, Elizabeth; Cicconardi, Francesco; Hebberecht, Laura; Ortiz-Ruiz, Yadira; Montgomery, Stephen H.; Ghezzi, Alfredo; Rodriguez-Martinez, José Arcadio; et al (October 2022, Genome Research)

   Despite insertions and deletions being the most common structural variants (SVs) found across genomes, not much is known about how much these SVs vary within populations and between closely related species, nor their significance in evolution. To address these questions, we characterized the evolution of indel SVs using genome assemblies of three closely related Heliconius butterfly species. Over the relatively short evolutionary timescales investigated, up to 18.0% of the genome was composed of indels between two haplotypes of an individual Heliconius charithonia butterfly and up to 62.7% included lineage-specific SVs between the genomes of the most distant species (11 Mya). Lineage-specific sequences were mostly characterized as transposable elements (TEs) inserted at random throughout the genome and their overall distribution was similarly affected by linked selection as single nucleotide substitutions. Using chromatin accessibility profiles (i.e., ATAC-seq) of head tissue in caterpillars to identify sequences with potential cis -regulatory function, we found that out of the 31,066 identified differences in chromatin accessibility between species, 30.4% were within lineage-specific SVs and 9.4% were characterized as TE insertions. These TE insertions were localized closer to gene transcription start sites than expected at random and were enriched for sites with significant resemblance to several transcription factor binding sites with known function in neuron development in Drosophila . We also identified 24 TE insertions with head-specific chromatin accessibility. Our results show high rates of structural genome evolution that were previously overlooked in comparative genomic studies and suggest a high potential for structural variation to serve as raw material for adaptive evolution. 

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5. A butterfly pan-genome reveals a large amount of structural variation underlies the evolution of chromatin accessibility

   https://doi.org/10.1101/2022.04.14.488334  

   Ruggieri, Angelo A.; Livraghi, Luca; Lewis, James J.; Cicconardi, Francesco; Hebberecht, Laura; Montgomery, Stephen H.; Ghezzi, Alfredo; Rodriguez-Martinez, José Arcadio; Jiggins, Chris D.; McMillan, W. Owen; et al (April 2022, bioRxiv)

   Despite insertions and deletions being the most common structural variants (SVs) found across genomes, not much is known about how much these SVs vary within populations and between closely related species, nor their significance in evolution. To address these questions, we characterized the evolution of indel SVs using genome assemblies of three closely related Heliconius butterfly species. Over the relatively short evolutionary timescales investigated, up to 18.0% of the genome was composed of indels between two haplotypes of an individual H. charithonia butterfly and up to 62.7% included lineage-specific SVs between the genomes of the most distant species (11 Mya). Lineage-specific sequences were mostly characterized as transposable elements (TEs) inserted at random throughout the genome and their overall distribution was similarly affected by linked selection as single nucleotide substitutions. Using chromatin accessibility profiles (i.e., ATAC-seq) of head tissue in caterpillars to identify sequences with potential cis-regulatory function, we found that out of the 31,066 identified differences in chromatin accessibility between species, 30.4% were within lineage-specific SVs and 9.4% were characterized as TE insertions. These TE insertions were localized closer to gene transcription start sites than expected at random and were enriched for several transcription factor binding site candidates with known function in neuron development in Drosophila. We also identified 24 TE insertions with head-specific chromatin accessibility. Our results show high rates of structural genome evolution that were previously overlooked in comparative genomic studies and suggest a high potential for structural variation to serve as raw material for adaptive evolution. 

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