A proposal for the reference-based annotation of de novo transposable element insertions

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.

Download Full-text

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

10.1101/814186 ◽

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.

Download Full-text

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

G3 Genes|Genome|Genetics ◽

10.1534/g3.119.400853 ◽

2019 ◽

Vol 10 (2) ◽

pp. 525-537 ◽

Cited By ~ 4

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.

Download Full-text

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

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.91.25.12150 ◽

1994 ◽

Vol 91 (25) ◽

pp. 12150-12154 ◽

Cited By ~ 52

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

Download Full-text

Transposable element annotation in non‐model species: The benefits of species‐specific repeat libraries using semi‐automated EDTA and DeepTE de novo pipelines

Molecular Ecology Resources ◽

10.1111/1755-0998.13489 ◽

2021 ◽

Author(s):

Ellen A. Bell ◽

Christopher L. Butler ◽

Claudio Oliveira ◽

Sarah Marburger ◽

Levi Yant ◽

...

Keyword(s):

Transposable Element ◽

De Novo ◽

Model Species ◽

Species Specific

Download Full-text

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

Mobile DNA ◽

10.1186/s13100-020-00230-y ◽

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.

Download Full-text

Detection of de Novo Insertion of the Medaka Fish Transposable Element Tol2

Genetics ◽

10.1093/genetics/156.3.1243 ◽

2000 ◽

Vol 156 (3) ◽

pp. 1243-1247

Author(s):

Akihiko Koga ◽

Hiroshi Hori

Keyword(s):

Transposable Element ◽

Direct Evidence ◽

De Novo ◽

Tetracycline Resistance ◽

Gene Tagging ◽

Terminal Inverted Repeat ◽

Medaka Fish ◽

Wide Range ◽

Fish Cells ◽

Target Plasmid

Abstract Tol2 is a terminal-inverted-repeat transposable element of the medaka fish Oryzias latipes. It is a member of the hAT (hobo/Activator/Tam3) transposable element family that is distributed in a wide range of organisms. We here document direct evidence for de novo insertion of this element. A Tol2 clone marked with the bacterial tetracycline-resistance gene was microinjected into fertilized eggs together with a target plasmid, and the plasmid was recovered from embryos. The screening of plasmid molecules after transformation into Escherichia coli demonstrated transposition of tet into the plasmid and, by inference, precise insertion of Tol2 in medaka fish cells. De novo excision of Tol2 has previously been demonstrated. The present study provides direct evidence that the Tol2 element has the entire activity necessary for cut-and-paste transposition. Some elements of the mariner/Tc1 family, another widespread group, have already been applied to development of gene tagging systems in vertebrates. The Tol2 element of the hAT family, having different features from mariner/Tc1 family elements, also has potential as an alternative gene tagging tool in vertebrates.

Download Full-text

Genomic re-assessment of the transposable element landscape of the potato genome

10.1101/701888 ◽

2019 ◽

Author(s):

Diego Zavallo ◽

Juan Manuel Crescente ◽

Magdalena Gantuz ◽

Melisa Leone ◽

Leonardo Sebastian Vanzetti ◽

...

Keyword(s):

Stress Response ◽

Transposable Element ◽

Dna Sequences ◽

Scientific Community ◽

De Novo ◽

Distinct Pattern ◽

Ltr Retrotransposon ◽

Potato Genome ◽

Different Types ◽

Clustering Pattern

AbstractTransposable elements (TEs) are DNA sequences with the ability to auto-replicate and move throughout the host genome. TEs are major drivers in stress response and genome evolution. Given their significance, the development of clear and efficient TE annotation pipelines has become essential for many species. The latest de novo TE discovery tools, along with available TEs from Repbase and sRNA-seq data, allowed us to perform a reliable potato TEs detection, classification and annotation through an open-source and freely available pipeline (https://github.com/DiegoZavallo/TE_Discovery). Using a variety of tools, approaches and rules, our pipeline revealed that ca. 16% of the potato genome can be clearly annotated as TEs. Additionally, we described the distribution of the different types of TEs across the genome, where LTRs and MITEs present a clear clustering pattern in pericentromeric and subtelomeric/telomeric regions respectively. Finally, we analyzed the insertion age and distribution of LTR retrotransposon families which display a distinct pattern between the two major superfamilies. While older Gypsy elements concentrated around heterochromatic regions, younger Copia elements located predominantly on euchromatic regions. Overall, we delivered not only a reliable, ready-to-use potato TE annotation files, but also all the necessary steps to perform de novo detection for other species.Key MessageWe provide a comprehensive and reliable potato TE landscape, based on a wide variety of identification tools and integrative approaches, producing clear and ready-to-use outputs for the scientific community.

Download Full-text