scholarly journals Evolutionary dynamics of piRNA clusters in Drosophila

2021 ◽  
Author(s):  
Filip Wierzbicki ◽  
Robert Kofler ◽  
Sarah Signor
Keyword(s):  
Transposable Element ◽  
Small Rnas ◽  
Evolutionary Dynamics ◽  
Quality Metrics ◽  
Selfish Dna ◽  
Insertions And Deletions ◽  
Multiple Alignments ◽  
Pirna Cluster ◽  
Crucial Component

AbstractSmall 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.x

scholarly journals Rapid evolution of piRNA-mediated silencing of an invading transposable element was driven by abundant de novo mutations

2019 ◽  
Author(s):  
Shuo Zhang ◽  
Erin S. Kelleher
Keyword(s):  
Transposable Element ◽  
Small Rnas ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
Rapid Evolution ◽  
De Novo Mutations ◽  
Element Insertion ◽  
Pirna Cluster ◽  
Genomic Regions ◽  
First Time

ABSTRACTThe regulation of transposable element (TE) activity by small RNAs is a ubiquitous feature of germlines. However, despite the obvious benefits to the host in terms of ensuring the production of viable gametes and maintaining the integrity of the genomes they carry, it remains controversial whether TE regulation evolves adaptively. We examined the emergence and evolutionary dynamics of repressor alleles after P-elements invaded the Drosophila melanogaster genome in the mid 20th century. In many animals including Drosophila, repressor alleles are produced by transpositional insertions into piRNA clusters, genomic regions encoding the Piwi-interacting RNAs (piRNAs) that regulate TEs. We discovered that ∼94% of recently collected isofemale lines in the Drosophila Genetic Reference Panel (DGRP) contain at least one P-element insertion in a piRNA cluster, indicating that repressor alleles are produced by de novo insertion at an exceptional rate. Furthermore, in our sample of ∼200 genomes, we uncovered no fewer than 80 unique P-element insertion alleles in at least 15 different piRNA clusters. Finally, we observe no footprint of positive selection on P-element insertions in piRNA clusters, suggesting that the rapid evolution of piRNA-mediated repression in D. melanogaster was driven primarily by mutation. Our results reveal for the first time how the unique genetic architecture of piRNA production, in which numerous piRNA clusters can encode regulatory small RNAs upon transpositional insertion, facilitates the non-adaptive rapid evolution of repression.

scholarly journals tRNA-derived small RNAs target transposable element transcripts

2017 ◽  
Vol 45 (9) ◽  
pp. 5142-5152 ◽  
Author(s):  
German Martinez ◽  
Sarah G. Choudury ◽  
R. Keith Slotkin
Keyword(s):  
Transposable Element ◽  
Small Rnas

scholarly journals Do human transposable element small RNAs serve primarily as genome defenders or genome regulators?

2012 ◽  
Vol 2 (1) ◽  
pp. 19-25 ◽  
Author(s):  
Kevin J. Lee ◽  
Andrew B. Conley ◽  
Victoria V. Lunyak ◽  
I. King Jordan
Keyword(s):  
Transposable Element ◽  
Small Rnas

scholarly journals Evolutionary dynamics of selfish DNA explains the abundance distribution of genomic subsequences

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Michael Sheinman ◽  
Anna Ramisch ◽  
Florian Massip ◽  
Peter F. Arndt
Keyword(s):  
Evolutionary Dynamics ◽  
Abundance Distribution ◽  
Selfish Dna

scholarly journals Birth, School, Work, Death, and Resurrection: The Life Stages and Dynamics of Transposable Element Proliferation

Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 336 ◽  
Author(s):  
Justin P. Blumenstiel
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Horizontal Transfer ◽  
Evolutionary Dynamics ◽  
Evolutionary Strategies ◽  
Species Boundaries ◽  
Life Stages ◽  
School Work

Transposable elements (TEs) can be maintained in sexually reproducing species even if they are harmful. However, the evolutionary strategies that TEs employ during proliferation can modulate their impact. In this review, I outline the different life stages of a TE lineage, from birth to proliferation to extinction. Through their interactions with the host, TEs can exploit diverse strategies that range from long-term coexistence to recurrent movement across species boundaries by horizontal transfer. TEs can also engage in a poorly understood phenomenon of TE resurrection, where TE lineages can apparently go extinct, only to proliferate again. By determining how this is possible, we may obtain new insights into the evolutionary dynamics of TEs and how they shape the genomes of their hosts.

scholarly journals Transposable Element Bm1645 is a Source of BmAGO2-associated Small RNAs that affect its expression in Bombyx mori

BMC Genomics ◽  
2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Hongqiang Si ◽  
Yunjie Cao ◽  
Honglin Zhu ◽  
Dan Li ◽  
Zhengbing Lv ◽  
...  
Keyword(s):  
Transposable Element ◽  
Bombyx Mori ◽  
Small Rnas

scholarly journals Contribution of insertions and deletions to the variability of hepatitis C virus populations

2007 ◽  
Vol 88 (8) ◽  
pp. 2198-2203 ◽  
Author(s):  
Manuela Torres-Puente ◽  
José M. Cuevas ◽  
Nuria Jiménez-Hernández ◽  
María A. Bracho ◽  
Inmaculada García-Robles ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Evolutionary Dynamics ◽  
Antiviral Treatment ◽  
Serum Samples ◽  
Frequency Distributions ◽  
Sequencing Project ◽  
Biologically Relevant ◽  
Insertions And Deletions ◽  
Hypervariable Regions

Little is known about the potential effects of insertions and deletions (indels) on the evolutionary dynamics of hepatitis C virus (HCV). In fact, the consequences of indels on antiviral treatment response are a field of investigation completely unexplored. Here, an extensive sequencing project was undertaken by cloning and sequencing serum samples from 25 patients infected with HCV subtype 1a and 48 patients with subtype 1b. For 23 patients, samples obtained after treatment with alpha interferon plus ribavirin were also available. Two genome fragments containing the hypervariable regions in the envelope 2 glycoprotein and the PKR-BD domain in NS5A were sequenced, yielding almost 16 000 sequences. Our results show that insertions are quite rare, but they are often present in biologically relevant domains of the HCV genome. Moreover, their frequency distributions between different time samples reflect the quasispecies dynamics of HCV populations. Deletions seem to be subject to negative selection.

Transposable element small RNAs as regulators of gene expression

2012 ◽  
Vol 28 (12) ◽  
pp. 616-623 ◽  
Author(s):  
Andrea D. McCue ◽  
R. Keith Slotkin
Keyword(s):  
Gene Expression ◽  
Transposable Element ◽  
Small Rnas

scholarly journals Evolutionary Dynamics of Small RNAs in 27 Escherichia coli and Shigella Genomes

2012 ◽  
Vol 4 (3) ◽  
pp. 330-345 ◽  
Author(s):  
Elizabeth Skippington ◽  
Mark A. Ragan
Keyword(s):  
Escherichia Coli ◽  
Small Rnas ◽  
Evolutionary Dynamics

scholarly journals Indels in SARS-CoV-2 occur at template-switching hotspots

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Brianna Sierra Chrisman ◽  
Kelley Paskov ◽  
Nate. Stockham ◽  
Kevin Tabatabaei ◽  
Jae-Yoon Jung ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Rna Polymerase ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
Template Switching ◽  
Nucleotide Polymorphisms ◽  
Rna Dependent Rna Polymerase ◽  
Consensus Sequences ◽  
Insertions And Deletions

AbstractThe evolutionary dynamics of SARS-CoV-2 have been carefully monitored since the COVID-19 pandemic began in December 2019. However, analysis has focused primarily on single nucleotide polymorphisms and largely ignored the role of insertions and deletions (indels) as well as recombination in SARS-CoV-2 evolution. Using sequences from the GISAID database, we catalogue over 100 insertions and deletions in the SARS-CoV-2 consensus sequences. We hypothesize that these indels are artifacts of recombination events between SARS-CoV-2 replicates whereby RNA-dependent RNA polymerase (RdRp) re-associates with a homologous template at a different loci (“imperfect homologous recombination”). We provide several independent pieces of evidence that suggest this. (1) The indels from the GISAID consensus sequences are clustered at specific regions of the genome. (2) These regions are also enriched for 5’ and 3’ breakpoints in the transcription regulatory site (TRS) independent transcriptome, presumably sites of RNA-dependent RNA polymerase (RdRp) template-switching. (3) Within raw reads, these indel hotspots have cases of both high intra-host heterogeneity and intra-host homogeneity, suggesting that these indels are both consequences of de novo recombination events within a host and artifacts of previous recombination. We briefly analyze the indels in the context of RNA secondary structure, noting that indels preferentially occur in “arms” and loop structures of the predicted folded RNA, suggesting that secondary structure may be a mechanism for TRS-independent template-switching in SARS-CoV-2 or other coronaviruses. These insights into the relationship between structural variation and recombination in SARS-CoV-2 can improve our reconstructions of the SARS-CoV-2 evolutionary history as well as our understanding of the process of RdRp template-switching in RNA viruses.

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