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

A thorough understanding of fungal pathogen adaptations is essential for treating fungal infections. Recent studies have suggested that the role of small RNAs expressed in fungal microsporidia genomes are important for elucidating the mechanisms of fungal infections.

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Germ line transformation of the silkworm, Bombyx mori, using the transposable element Minos

Molecular Genetics and Genomics ◽

10.1007/s00438-006-0176-y ◽

2007 ◽

Vol 277 (3) ◽

pp. 213-220 ◽

Cited By ~ 28

Author(s):

K. Uchino ◽

M. Imamura ◽

K. Shimizu ◽

T. Kanda ◽

T. Tamura

Keyword(s):

Transposable Element ◽

Bombyx Mori ◽

Germ Line ◽

Germ Line Transformation ◽

Silkworm Bombyx Mori

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A miniature inverted-repeat transposable element, AddIn-MITE, located inside a WD40 gene is conserved in Andropogoneae grasses

PeerJ ◽

10.7717/peerj.6080 ◽

2019 ◽

Vol 7 ◽

pp. e6080

Author(s):

Clicia Grativol ◽

Flavia Thiebaut ◽

Sara Sangi ◽

Patricia Montessoro ◽

Walaci da Silva Santos ◽

...

Keyword(s):

Transposable Elements ◽

Transposable Element ◽

Small Rna ◽

Genome Assembly ◽

Inverted Repeat ◽

Small Rnas ◽

Distribution Patterns ◽

Plant Genomes ◽

Sugarcane Genome

Miniature inverted-repeat transposable elements (MITEs) have been associated with genic regions in plant genomes and may play important roles in the regulation of nearby genes via recruitment of small RNAs (sRNA) to the MITEs loci. We identified eight families of MITEs in the sugarcane genome assembly with MITE-Hunter pipeline. These sequences were found to be upstream, downstream or inserted into 67 genic regions in the genome. The position of the most abundant MITE (Stowaway-like) in genic regions, which we call AddIn-MITE, was confirmed in a WD40 gene. The analysis of four monocot species showed conservation of the AddIn-MITE sequence, with a large number of copies in their genomes. We also investigated the conservation of the AddIn-MITE’ position in the WD40 genes from sorghum, maize and, in sugarcane cultivars and wild Saccharum species. In all analyzed plants, AddIn-MITE has located in WD40 intronic region. Furthermore, the role of AddIn-MITE-related sRNA in WD40 genic region was investigated. We found sRNAs preferentially mapped to the AddIn-MITE than to other regions in the WD40 gene in sugarcane. In addition, the analysis of the small RNA distribution patterns in the WD40 gene and the structure of AddIn-MITE, suggests that the MITE region is a proto-miRNA locus in sugarcane. Together, these data provide insights into the AddIn-MITE role in Andropogoneae grasses.

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Evolutionary dynamics of piRNA clusters in Drosophila

10.1101/2021.08.20.457083 ◽

2021 ◽

Cited By ~ 1

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

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

10.1101/611350 ◽

2019 ◽

Cited By ~ 1

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.

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