Curation Guidelines for de novo Generated Transposable Element Families

2021 ◽  
Vol 1 (6) ◽  
Author(s):  
Jessica M. Storer ◽  
Robert Hubley ◽  
Jeb Rosen ◽  
Arian F. A. Smit
Keyword(s):  
Transposable Element ◽  
De Novo

De novo activation of the transposable element Tam2 of Antirrhinum majus

1987 ◽  
Vol 207 (1) ◽  
pp. 54-59 ◽  
Author(s):  
Andrew Hudson ◽  
Rosemary Carpenter ◽  
Enrico S. Coen
Keyword(s):  
Transposable Element ◽  
De Novo ◽  
Antirrhinum Majus

scholarly journals Contingency in the convergent evolution of a regulatory network: Dosage compensation in Drosophila

2018 ◽  
Author(s):  
Doris Bachtrog ◽  
Chris Ellison
Keyword(s):  
Transposable Element ◽  
Dosage Compensation ◽  
Sex Chromosomes ◽  
Binding Sites ◽  
Evolutionary Biology ◽  
De Novo ◽  
Binding Motif ◽  
Sequence Motif ◽  
X Chromosomes ◽  
Msl Complex

The repeatability or predictability of evolution is a central question in evolutionary biology, and most often addressed in experimental evolution studies. Here, we infer how genetically heterogeneous natural systems acquire the same molecular changes, to address how genomic background affects adaptation in natural populations. In particular, we take advantage of independently formed neo-sex chromosomes in Drosophila species that have evolved dosage compensation by co-opting the dosage compensation (MSL) complex, to study the mutational paths that have led to the acquisition of 100s of novel binding sites for the MSL complex in different species. This complex recognizes a conserved 21-bp GA-rich sequence motif that is enriched on the X chromosome, and newly formed X chromosomes recruit the MSL complex by de novo acquisition of this binding motif. We identify recently formed sex chromosomes in the Drosophila repleta and robusta species groups by genome sequencing, and generate genomic occupancy maps of the MSL complex to infer the location of novel binding sites. We find that diverse mutational paths were utilized in each species to evolve 100s of de novo binding motifs along the neo-X, including expansions of microsatellites and transposable element insertions. However, the propensity to utilize a particular mutational path differs between independently formed X chromosomes, and appears to be contingent on genomic properties of that species, such as simple repeat or transposable element density. This establishes the “genomic environment” as an important determinant in predicting the outcome of evolutionary adaptations.

scholarly journals Synaptonemal complex-deficient Drosophila melanogaster females exhibit rare DSB repair events, recurrent copy number variation, and an increased rate of de novo transposable element movement

2019 ◽  
Author(s):  
Danny E. Miller
Keyword(s):  
Drosophila Melanogaster ◽  
Copy Number Variation ◽  
Transposable Element ◽  
Synaptonemal Complex ◽  
Copy Number ◽  
De Novo ◽  
Wild Type ◽  
Dsb Repair ◽  
Number Variation ◽  
Element Movement

ABSTRACTGenetic stability depends on the maintenance of a variety of chromosome structures and the precise repair of DNA breaks. During meiosis, programmed double-strand breaks (DSBs) made in prophase I are normally repaired as gene conversions or crossovers. Additionally, DSBs are made by the movement of transposable elements (TEs), which must also be resolved. Incorrect repair of these DNA lesions can lead to mutations, copy number variations, translocations, and/or aneuploid gametes. In Drosophila melanogaster, as in most organisms, meiotic DSB repair occurs in the presence of a rapidly evolving multiprotein structure called the synaptonemal complex (SC). Here, whole-genome sequencing is used to investigate the fate of meiotic DSBs in D. melanogaster mutant females lacking functional SC, to assay for de novo CNV formation, and to examine the role of the SC in transposable element movement in flies. The data indicate that, in the absence of SC, copy number variation still occurs but meiotic DSB repair by gene conversion may occur only rarely. Remarkably, an 856-kilobase de novo CNV was observed in two unrelated individuals of different genetic backgrounds and was identical to a CNV recovered in a previous wild-type study, suggesting that recurrent formation of large CNVs occurs in Drosophila. In addition, the rate of novel TE insertion was markedly higher than wild type in one of two SC mutants tested, suggesting that SC proteins may contribute to the regulation of TE movement and insertion in the genome. Overall, this study provides novel insight into the role that the SC plays in genome stability and provides clues as to why SC proteins are among the most rapidly evolving in any organism.

scholarly journals Synaptonemal Complex-Deficient Drosophila melanogaster Females Exhibit Rare DSB Repair Events, Recurrent Copy-Number Variation, and an Increased Rate of de Novo Transposable Element Movement

2019 ◽  
Vol 10 (2) ◽  
pp. 525-537 ◽  
Author(s):  
Danny E. Miller
Keyword(s):  
Drosophila Melanogaster ◽  
Copy Number Variation ◽  
Transposable Element ◽  
Synaptonemal Complex ◽  
Copy Number ◽  
De Novo ◽  
Wild Type ◽  
Dsb Repair ◽  
Number Variation ◽  
Element Movement

Genetic stability depends on the maintenance of a variety of chromosome structures and the precise repair of DNA breaks. During meiosis, programmed double-strand breaks (DSBs) made in prophase I are normally repaired as gene conversions or crossovers. DSBs can also be made by other mechanisms, such as the movement of transposable elements (TEs), which must also be resolved. Incorrect repair of these DNA lesions can lead to mutations, copy-number changes, translocations, and/or aneuploid gametes. In Drosophila melanogaster, as in most organisms, meiotic DSB repair occurs in the presence of a rapidly evolving multiprotein structure called the synaptonemal complex (SC). Here, whole-genome sequencing is used to investigate the fate of meiotic DSBs in D. melanogaster mutant females lacking functional SC, to assay for de novo CNV formation, and to examine the role of the SC in transposable element movement in flies. The data indicate that, in the absence of SC, copy-number variation still occurs and meiotic DSB repair by gene conversion occurs infrequently. Remarkably, an 856-kilobase de novo CNV was observed in two unrelated individuals of different genetic backgrounds and was identical to a CNV recovered in a previous wild-type study, suggesting that recurrent formation of large CNVs occurs in Drosophila. In addition, the rate of novel TE insertion was markedly higher than wild type in one of two SC mutants tested, suggesting that SC proteins may contribute to the regulation of TE movement and insertion in the genome. Overall, this study provides novel insight into the role that the SC plays in genome stability and provides clues as to why the sequence, but not structure, of SC proteins is rapidly evolving.

scholarly journals The Dfam Community Resource of Transposable Element Families, Sequence Models, and Genome Annotations

2020 ◽  
Author(s):  
Jessica Storer ◽  
Robert Hubley ◽  
Jeb Rosen ◽  
Travis Wheeler ◽  
Arian F.A. Smit
Keyword(s):  
Transposable Element ◽  
De Novo ◽  
Consensus Sequence ◽  
Model Organisms ◽  
Community Resource ◽  
Genome Annotations ◽  
Protein Alignments ◽  
Insight Into ◽  
Proof Of Principle

Abstract The 3.0-3.2 releases of Dfam (https://dfam.org) represent an evolution from a proof-of-principle collection of transposable element families in model organisms into a community resource for a broad range of species and for both curated and uncurated datasets. In addition, releases since Dfam 3.0 provide auxiliary consensus sequence models, transposable element protein alignments, and a formalized classification system to support the growing diversity of organisms represented in the resource. The latest release includes 266,740 new de novo generated transposable element families from 336 species contributed by the EBI. This expansion demonstrates the utility of many of Dfam’s new features and provides insight into the long term challenges ahead for improving de novo generated transposable element datasets.

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 De novo synthesis of an intron by the maize transposable element Dissociation.

1994 ◽  
Vol 91 (25) ◽  
pp. 12150-12154 ◽  
Author(s):  
M. J. Giroux ◽  
M. Clancy ◽  
J. Baier ◽  
L. Ingham ◽  
D. McCarty ◽  
...  
Keyword(s):  
Transposable Element ◽  
De Novo ◽  
De Novo Synthesis ◽  
Maize Transposable Element

scholarly journals The Dfam community resource of transposable element families, sequence models, and genome annotations

Mobile DNA ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jessica Storer ◽  
Robert Hubley ◽  
Jeb Rosen ◽  
Travis J. Wheeler ◽  
Arian F. Smit
Keyword(s):  
Transposable Element ◽  
De Novo ◽  
Consensus Sequence ◽  
Model Organisms ◽  
Community Resource ◽  
Open Access Database ◽  
Genome Annotations ◽  
Protein Alignments ◽  
Insight Into

AbstractDfam is an open access database of repetitive DNA families, sequence models, and genome annotations. The 3.0–3.3 releases of Dfam (https://dfam.org) represent an evolution from a proof-of-principle collection of transposable element families in model organisms into a community resource for a broad range of species, and for both curated and uncurated datasets. In addition, releases since Dfam 3.0 provide auxiliary consensus sequence models, transposable element protein alignments, and a formalized classification system to support the growing diversity of organisms represented in the resource. The latest release includes 266,740 new de novo generated transposable element families from 336 species contributed by the EBI. This expansion demonstrates the utility of many of Dfam’s new features and provides insight into the long term challenges ahead for improving de novo generated transposable element datasets.

Sign in / Sign up

Export Citation Format

Share Document