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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
...different preferences. Transposable elements are a source of genetic novelty between populations and species, driving rapid adaptive evolution. However, the extent of TEs’ contribution to host shift remains unexplored. Here, we perform genomic and transcriptomic analyses in six s of cactophilic species...
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Research: Differences in activity and stability drive transposable element variation in tropical and temperate maize
- Shujun Ou,
- Armin Scheben,
- Tyler Collins,
- Yinjie Qiu,
- Arun S. Seetharam,
- Claire C. Menard,
- Nancy Manchanda,
- Jonathan I. Gent,
- Michael C. Schatz,
- Sarah N. Anderson,
- Matthew B. Hufford,
- and Candice N. Hirsch
Genome Res. August 2024 34: 1140-1153; Published in Advance September 9, 2024, doi:10.1101/gr.278131.123
..., as a result, can have functional consequences by altering transcript structure or regulation (Della Coletta et al. 2021). For example, the maize bz locus varies in length from 50 kb to 160 kb across genotypes owing to TE insertion/deletion polymorphism (Wang and Dooner 2006). TEs alter transcript abundance...
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Research: Analyses of 600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges
- John S. Sproul,
- Scott Hotaling,
- Jacqueline Heckenhauer,
- Ashlyn Powell,
- Dez Marshall,
- Amanda M. Larracuente,
- Joanna L. Kelley,
- Steffen U. Pauls,
- and Paul B. Frandsen
Genome Res. October 2023 33: 1708-1717; Published in Advance September 22, 2023, doi:10.1101/gr.277387.122
...highlight the tremendous opportunity and need for the biodiversity genomics field to embrace REs and suggest collective steps for making progress toward this goal.Repetitive elements (REs) comprise large proportions of eukaryotic s and are fundamental to the evolutionary process (Bourque et al. 2018...
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Research: Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis
- Alexandra Dallaire,
- Bethan F. Manley,
- Maya Wilkens,
- Iliana Bista,
- Clement Quan,
- Edouard Evangelisti,
- Charles R. Bradshaw,
- Navin B. Ramakrishna,
- Sebastian Schornack,
- Falk Butter,
- Uta Paszkowski,
- and Eric A. Miska
Genome Res. December 2021 31: 2290-2302; Published in Advance November 12, 2021, doi:10.1101/gr.275752.121
...; Maeda et al. 2018). Genomic analyses of AMF have revealed contents of repetitive sequences ranging from 23% to 43% (Chen et al. 2018a; Morin et al. 2019). These repeats consist of transposable elements (TEs) and expanded gene families that occasionally form tandemly repeated arrays of duplicate genes...
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Research: Genome-wide mapping reveals R-loops associated with centromeric repeats in maize
- Yang Liu,
- Qian Liu,
- Handong Su,
- Kunpeng Liu,
- Xue Xiao,
- Wei Li,
- Qianwen Sun,
- James A. Birchler,
- and Fangpu Han
Genome Res. August 2021 31: 1409-1418; Published in Advance July 9, 2021, doi:10.1101/gr.275270.121
...for investigating the association between repetitive elements and R-loop formation.In this study, we present -wide R-loop maps of maize leaf generated by ssDRIP-seq (single-strand DNA ligation-based library construction from DNA:RNA hybrid immunoprecipitation, followed by sequencing) and determine the general...
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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...into DNA elements and retroelements. Colors represent the TE-subfamily age proxy calculated as mean divergence between genomic insertions and their consensus TE sequence. (Post-WGD) <7 Kimura distance, (WGD) 7–10 Kimura distance, (pre-WGD) >10 Kimura distance. (C) Number of TE-CREs from TEs...
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Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
- Ni-Chen Chang,
- Quirze Rovira,
- Jonathan Wells,
- Cédric Feschotte,
- and Juan M. Vaquerizas
Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
...remains a challenge in genomic analyses owing to their repetitive nature, intricate transcriptional relationship with host gene expression, and the general complexity of the transcriptome (Lanciano and Cristofari 2020). Short reads mapping to TE sequences cannot easily distinguish whether they derive from...
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Research: Accumulation and ineffective silencing of transposable elements on an avian W Chromosome
- Vera M. Warmuth,
- Matthias H. Weissensteiner,
- and Jochen B.W. Wolf
Genome Res. April 2022 32: 671-681; Published in Advance February 11, 2022, doi:10.1101/gr.275465.121
...newly assembled W chromosomal sequence to quantify the genomic abundance and transcription of TEs in 15 Eurasian crows raised under common garden conditions.ResultsW Chromosomal sequenceTo identify W Chromosome–linked sequences in the hooded crow , we generated a de novo assembly for a female individual...
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Research: Evolution of genome structure in the Drosophila simulans species complex
- Mahul Chakraborty,
- Ching-Ho Chang,
- Danielle E. Khost,
- Jeffrey Vedanayagam,
- Jeffrey R. Adrion,
- Yi Liao,
- Kristi L. Montooth,
- Colin D. Meiklejohn,
- Amanda M. Larracuente,
- and J.J. Emerson
Genome Res. March 2021 31: 380-396; Published in Advance February 9, 2021, doi:10.1101/gr.263442.120
...Present address: Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA Corresponding authors: alarracu@ur.rochester.edu, jje@uci.eduAbstractThe rapid evolution of repetitive DNA sequences, including satellite DNA, tandem duplications, and transposable elements...
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Method: Double insertion of transposable elements provides a substrate for the evolution of satellite DNA
- Michael P. McGurk and
- Daniel A. Barbash
Genome Res. May 2018 28: 714-725; Published in Advance March 27, 2018, doi:10.1101/gr.231472.117
...individual repeats to unique genomic locations. Here we develop a new pipeline called ConTExt that demonstrates that paired-end Illumina data can be successfully leveraged to identify a wide range of structural variation within repetitive sequence, including tandem elements. By analyzing 85 s from five...

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