Transposable elements in individual genotypes of <i>Drosophila simulans</i>

Signor, Sarah

doi:10.1002/ece3.6134

Cited by 10 publications

(10 citation statements)

References 59 publications

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“…These families are likely active in D . simulans as many insertions of these families segregate at low population frequencies (Kofler et al, 2015, Signor, 2020). Finally, we asked if insertions are occurring with younger TE families than deletions.…”

Section: Resultsmentioning

confidence: 99%

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Evolutionary dynamics of piRNA clusters in Drosophila

Wierzbicki¹,

Koer²,

Signor

2021

Molecular Ecology

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Small RNAs produced from transposable element (TE) rich sections of the genome, termed piRNA clusters, are a crucial component in the genomic defense against selfish DNA. In animals it is thought the invasion of a TE is stopped when a copy of the TE inserts into a piRNA cluster, triggering the production of cognate small RNAs that silence the TE. Despite this importance for TE control, little is known about the evolutionary dynamics of piRNA clusters, mostly because these repeat rich regions are difficult to assemble and compare.Here we establish a framework for studying the evolution of piRNA clusters quantitatively. Previously introduced quality metrics and a newly developed software for multiple alignments of repeat annotations (Manna) allow us to estimate the level of polymorphism segregating in piRNA clusters and the divergence among homologous piRNA clusters. By studying 20 conserved piRNA clusters in multiple assemblies of four Drosophila species we show that piRNA clusters are evolving rapidly. While 70-80% of the clusters are conserved within species, the clusters share almost no similarity between species as closely related as D. melanogaster and D. simulans. Furthermore, abundant insertions and deletions are segregating within the Drosophila species. We show that the evolution of clusters is mainly driven by large insertions of recently active TEs, and smaller deletions mostly in older TEs. The effect of these forces is so rapid that homologous clusters often do not contain insertions from the same TE families.

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Section: Resultsmentioning

confidence: 99%

“…The most abundant long insertions were due to the TE families roo and Max-element (two for each family). Both families are likely active in D. simulans [Kofler et al, 2015, Signor, 2020. Finally, we asked if insertions are occurring with younger TE families than deletions.…”

Section: Evolutionary Forces Shaping the Composition Of Pirna Clustersmentioning

confidence: 99%

Evolutionary dynamics of piRNA clusters in Drosophila

Wierzbicki¹,

Koer²,

Signor

2021

Molecular Ecology

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“…Here, we report that a ribosomal protein binds the Doc5 transposon, a non-autonomous TE family enriched in the heterochromatin of D. melanogaster and closely related species [ 48 ], providing in vitro experimental evidence for a functional interaction of Rpl22 with DNA, and possibly to chromosome and chromatin. In Drosophila , the direct binding of protein to TEs, especially involving retrotransposons, has been previously reported [ 49 , 50 , 51 ].…”

Section: Discussionmentioning

confidence: 99%

Evidence of the Physical Interaction between Rpl22 and the Transposable Element Doc5, a Heterochromatic Transposon of Drosophila melanogaster

Berloco

Minervini

Moschetti

et al. 2021

Genes

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Chromatin is a highly dynamic biological entity that allows for both the control of gene expression and the stabilization of chromosomal domains. Given the high degree of plasticity observed in model and non-model organisms, it is not surprising that new chromatin components are frequently described. In this work, we tested the hypothesis that the remnants of the Doc5 transposable element, which retains a heterochromatin insertion pattern in the melanogaster species complex, can be bound by chromatin proteins, and thus be involved in the organization of heterochromatic domains. Using the Yeast One Hybrid approach, we found Rpl22 as a potential interacting protein of Doc5. We further tested in vitro the observed interaction through Electrophoretic Mobility Shift Assay, uncovering that the N-terminal portion of the protein is sufficient to interact with Doc5. However, in situ localization of the native protein failed to detect Rpl22 association with chromatin. The results obtained are discussed in the light of the current knowledge on the extra-ribosomal role of ribosomal protein in eukaryotes, which suggests a possible role of Rpl22 in the determination of the heterochromatin in Drosophila.

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“…The four D. simulans lines SZ232, SZ45, SZ244, and SZ129 were collected in California from the Zuma Organic Orchard in Los Angeles, CA on two consecutive weekends of February 2012 (29)(30)(31)(32)(33). LNP-15-062 was collected in Zambia at the Luwangwa National Park by D. Matute and provided to us by J. Saltz (J. Saltz pers.…”

Section: Fly Strainsmentioning

confidence: 99%

Rapid evolutionary diversification of theflamencolocus across simulans cladeDrosophilaspecies

Signor

Vedanayagam

Wierzbicki³

et al. 2022

Preprint

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Maintaining genomic integrity through suppression of transposable elements (TEs) is paramount to organismal fitness. In D. melanogaster flamenco is the master regulator of TE suppression, preventing TEs from moving from the somatic support cells of the ovary to the germline. It is thought to operate as a trap, suppressing TEs upon their transposition into the locus, with a high representation of recent horizontally transferred TEs. We find that in the simulans clade flamenco has undergone physical and functional diversification. In D. simulans flamenco has duplicated and diverged from its original, maintaining no synteny within the locus but conserving its promotor. In D. simulans and D. mauritiana, flamenco acts as a dual stranded cluster with ping pong signals in some tissues. This expansion in function has been accompanied by an increase in the number of multicopy elements, as expected for regions operating as dual stranded clusters. In addition, we find that in D. simulans presence of a TE in either flamenco or a germline cluster, may be necessary for suppression of a TE but it may not be entirely sufficient. This physical and functional diversity of flamenco in the simulans clade redefines our understanding of this locus.

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Transposable elements in individual genotypes of Drosophila simulans

Cited by 10 publications

References 59 publications

Evolutionary dynamics of piRNA clusters in Drosophila

Evolutionary dynamics of piRNA clusters in Drosophila

Evidence of the Physical Interaction between Rpl22 and the Transposable Element Doc5, a Heterochromatic Transposon of Drosophila melanogaster

Rapid evolutionary diversification of theflamencolocus across simulans cladeDrosophilaspecies

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