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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: Transposable elements drive the evolution of metazoan zinc finger genes
- Jonathan N. Wells,
- Ni-Chen Chang,
- John McCormick,
- Caitlyn Coleman,
- Nathalie Ramos,
- Bozhou Jin,
- and Cédric Feschotte
Genome Res. August 2023 33: 1325-1339; Published in Advance September 15, 2023, doi:10.1101/gr.277966.123
...by LTR elements (odds ratio = 6.56, P-value = 1.2 × 10−8, Fisher's exact test) (Supplemental Fig. 10A). Because LTRs include many of the youngest TE families in the zebrafish (Chang et al. 2022), we reasoned that their enrichment among up-regulated genes and TE families may reflect a tendency for young...
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Method: MCHelper automatically curates transposable element libraries across eukaryotic species
- Simon Orozco-Arias,
- Pío Sierra,
- Richard Durbin,
- and Josefa González
Genome Res. December 2024 34: 2256-2268; Published in Advance December 9, 2024, doi:10.1101/gr.278821.123
....View larger version: In this window In a new window Figure 4. Genome-wide number and type of TE annotations for each of the three libraries analyzed in the six species. The BDGP, EDTA, MClibrary, Dfam-zebrafish, MTEC, and Dfam-Human libraries were used as reference for D. melanogaster, O. sativa, C. cornix, D...
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Resource: Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish
- Hyung Joo Lee,
- Yiran Hou,
- Ju Heon Maeng,
- Nakul M. Shah,
- Yujie Chen,
- Heather A. Lawson,
- Hongbo Yang,
- Feng Yue,
- and Ting Wang
Genome Res. July 2022 32: 1424-1436; Published in Advance June 1, 2022, doi:10.1101/gr.276052.121
...with surrounding genomic regions. We provide insights into the evolutionarily conserved phenomenon of TEs as a powerful source of regulatory function in host s.ResultsEpigenomic annotation of zebrafish transposable elementsTo profile the epigenetic landscape of TEs in zebrafish, we used the epigenetic states...
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Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
- Shahmir Naseer,
- Thomas C Clark,
- Bertrand Collet,
- Pooran Dewari,
- Damir Baranasic,
- Daniel J Macqueen,
- Pierre Boudinot,
- and Samuel A.M. Martin
Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
...stimulation. We identified a set of 197 ISGs with regulatory elements showing increased 23 chromatin accessibility and H3K27ac signal in concert with increased gene expression in 24 response to poly I:C. Fifty-four of these genes were conserved ISGs in rainbow trout, 25 zebrafish, and human. Our analysis...
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Research: Widespread roles of enhancer-like transposable elements in cell identity and long-range genomic interactions
- Yaqiang Cao,
- Guoyu Chen,
- Gang Wu,
- Xiaoli Zhang,
- Joseph McDermott,
- Xingwei Chen,
- Chi Xu,
- Quanlong Jiang,
- Zhaoxiong Chen,
- Yingying Zeng,
- Daosheng Ai,
- Yi Huang,
- and Jing-Dong J. Han
Genome Res. January 2019 29: 40-52; Published in Advance November 19, 2018, doi:10.1101/gr.235747.118
...as the evolutionary distances increase. Generally, the mapping ratios are above 60% in primates, with up to 100% in chimpanzee and gorilla, while less than 1% in chicken, frog, and zebrafish (Fig. 3F). Moreover, different from the UCSC phylogenetic tree or the annotated evolutionary-separation years by Time...
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Research: Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles
- Jianbin Wang,
- Benjamin Czech,
- Amanda Crunk,
- Adam Wallace,
- Makedonka Mitreva,
- Gregory J. Hannon,
- and Richard E. Davis
Genome Res. September 2011 21: 1462-1477; Published in Advance June 17, 2011, doi:10.1101/gr.121426.111
...Horvitz 2010; Brenner et al. 2010; Shaw et al. 2010) as they do in mice, Xenopus, and flies (Bernstein et al. 2003; Leaman et al. 2005; Martello et al. 2007; Tang et al. 2007). miRNAs are also known to contribute to the maternal to zygotic transition in zebrafish and flies, although the miRNAs involved...
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Research: KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution
- Kai Otsuka,
- Akihiko Sakashita,
- So Maezawa,
- Richard M. Schultz,
- and Satoshi H. Namekawa
Genome Res. March 2025 35: 417-431; Published in Advance March 12, 2025, doi:10.1101/gr.279924.124
...Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan; 5Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA Corresponding author: snamekawa@ucdavis.eduAbstractAs transposable elements (TEs) coevolved with the host , the host exploited...
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Research: Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary
- Satyam P. Srivastav,
- Cédric Feschotte,
- and Andrew G. Clark
Genome Res. May 2024 34: 711-724; Published in Advance May 15, 2024, doi:10.1101/gr.278062.123
...transposable element (TE) activity in the animal germline via a specialized class of small RNAs called piwi-interacting RNAs (piRNAs). piRNAs are produced from discrete genomic regions called piRNA clusters (piCs). Although the molecular processes by which piCs function are relatively well understood...
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Research: High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis
- Yuan Lu,
- Edward Rice,
- Kang Du,
- Susanne Kneitz,
- Magali Naville,
- Corentin Dechaud,
- Jean-Nicolas Volff,
- Mikki Boswell,
- William Boswell,
- LaDeana Hillier,
- Chad Tomlinson,
- Kremitzki Milin,
- Ronald B. Walter,
- Manfred Schartl,
- and Wesley C. Warren
Genome Res. April 2023 33: 557-571; Published in Advance May 5, 2023, doi:10.1101/gr.277434.122
...epidermal growth factor receptor (EGFR) named Xiphophorus melanoma receptor kinase (xmrk) (Wittbrodt et al. 1989). The xmrk gene harbors two mutations that lead to constitutive proliferation-promoting function of the receptor. In fact, ectopic expression of xmrk in medaka, zebrafish, and murine cells led...

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