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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
...Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species Daniel Siqueira de Oliveira1,2,3, Anaïs Larue2, William Vilas Boas Nunes2, Francois Sabot4, Alejandra Bodelón5, María Pilar García Guerreiro5, Cristina Vieira2 and Claudia Marcia...
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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
...are therefore likely to impact evolution of gene regulation. Yet, the role of TEs in regulatory evolution after WGDs is not well understood. Here we used Atlantic salmon as a model system to explore how TE activity after the salmonid WGD ∼100 MYA shaped CRE evolution. We identified 55,080 putative TE-CREs using...
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Research: Long-range promoter–enhancer contacts are conserved during evolution and contribute to gene expression robustness
- Alexandre Laverré,
- Eric Tannier,
- and Anamaria Necsulea
Genome Res. February 2022 32: 280-296; Published in Advance December 20, 2021, doi:10.1101/gr.275901.121
...the structure of regulatory landscapes constrains large-scale evolution. We show that the evolution of cis-regulatory landscapes, measured in terms of distal element sequences, synteny, or contacts with target genes, is significantly associated with gene expression evolution.The evolution of gene expression...
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Research: Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks
- Marta Farré,
- Jaebum Kim,
- Anastasia A. Proskuryakova,
- Yang Zhang,
- Anastasia I. Kulemzina,
- Qiye Li,
- Yang Zhou,
- Yingqi Xiong,
- Jennifer L. Johnson,
- Polina L. Perelman,
- Warren E. Johnson,
- Wesley C. Warren,
- Anna V. Kukekova,
- Guojie Zhang,
- Stephen J. O'Brien,
- Oliver A. Ryder,
- Alexander S. Graphodatsky,
- Jian Ma,
- Harris A. Lewin,
- and Denis M. Larkin
Genome Res. April 2019 29: 576-589; Published in Advance February 13, 2019, doi:10.1101/gr.239863.118
...rearrangements in driving evolution has been a long-standing question of evolutionary biology. Here we focused on ruminants as a model to assess how rearrangements may have contributed to the evolution of gene regulation. Using reconstructed ancestral karyotypes of Cetartiodactyls, Ruminants, Pecorans...
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ARTICLE: ATG deserts define a novel core promoter subclass
- Maxwell P. Lee,
- Kevin Howcroft,
- Aparna Kotekar,
- Howard H. Yang,
- Kenneth H. Buetow,
- and Dinah S. Singer
Genome Res. September 2005 15: 1189-1197; Published in Advance August 18, 2005, doi:10.1101/gr.3873705
...ATG codons within ∼460 bp upstream of the translation initiation codon of the class I gene. The presence of this “ATG desert” ensures that only a single protein product is made, regardless of the TSS selected. Importantly, we identify a subclass of promoters in the human, mouse, and rat s that contain...
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Research: Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
- David Thybert,
- Maša Roller,
- Fábio C.P. Navarro,
- Ian Fiddes,
- Ian Streeter,
- Christine Feig,
- David Martin-Galvez,
- Mikhail Kolmogorov,
- Václav Janoušek,
- Wasiu Akanni,
- Bronwen Aken,
- Sarah Aldridge,
- Varshith Chakrapani,
- William Chow,
- Laura Clarke,
- Carla Cummins,
- Anthony Doran,
- Matthew Dunn,
- Leo Goodstadt,
- Kerstin Howe,
- Matthew Howell,
- Ambre-Aurore Josselin,
- Robert C. Karn,
- Christina M. Laukaitis,
- Lilue Jingtao,
- Fergal Martin,
- Matthieu Muffato,
- Stefanie Nachtweide,
- Michael A. Quail,
- Cristina Sisu,
- Mario Stanke,
- Klara Stefflova,
- Cock Van Oosterhout,
- Frederic Veyrunes,
- Ben Ward,
- Fengtang Yang,
- Golbahar Yazdanifar,
- Amonida Zadissa,
- David J. Adams,
- Alvis Brazma,
- Mark Gerstein,
- Benedict Paten,
- Son Pham,
- Thomas M. Keane,
- Duncan T. Odom,
- and Paul Flicek
Genome Res. April 2018 28: 448-459; Published in Advance March 21, 2018, doi:10.1101/gr.234096.117
...resulted in the birth of several hundred megabases of novel genomic sequence (69–374 Mb) in each assayed rodent .Accelerated LINE retrotransposon activity has shaped coding gene evolution in rodentsWe next asked how retrotransposon activity has changed during the evolutionary history of both clades. We...
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LETTER: A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts
- Elisa de la Calle-Mustienes,
- Cármen Gloria Feijóo,
- Miguel Manzanares,
- Juan J. Tena,
- Elisa Rodríguez-Seguel,
- Annalisa Letizia,
- Miguel L. Allende,
- and José Luis Gómez-Skarmeta
Genome Res. August 2005 15: 1061-1072; Published in Advance July 15, 2005, doi:10.1101/gr.4004805
...organized in large genomic complexes that show patterns of expression highly conserved during evolution. We performed a detailed search for conserved sequences present in the two gene deserts spanning the intergenic regions between the Irx3–Irx5 (GD3–5) and Irx5–Irx6 (GD5–6) genes in the IrxB cluster. Our...
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Research: Drought responsive gene expression regulatory divergence between upland and lowland ecotypes of a perennial C₄ grass
- John T. Lovell,
- Scott Schwartz,
- David B. Lowry,
- Eugene V. Shakirov,
- Jason E. Bonnette,
- Xiaoyu Weng,
- Mei Wang,
- Jenifer Johnson,
- Avinash Sreedasyam,
- Christopher Plott,
- Jerry Jenkins,
- Jeremy Schmutz,
- and Thomas E. Juenger
Genome Res. April 2016 26: 510-518; Published in Advance March 7, 2016, doi:10.1101/gr.198135.115
...of genes exhibiting G×E and trans regulation, indicating that expression G×E and heterosis may result from the evolution of transcription factors or their binding sites. P. hallii serves as the genomic model for its close relative and emerging biofuel crop, switchgrass ( Panicum virgatum ). Accordingly...
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Review: Recent advances in methods to characterize archaic introgression in modern humans
- David Peede,
- Mayra M. Bañuelos,
- Jazeps Medina Tretmanis,
- Miriam Miyagi,
- and Emilia Huerta-Sánchez
Genome Res. February 2026 36: 239-256; Published in Advance January 16, 2026, doi:10.1101/gr.278993.124
...and Akey 2025). This work also uncovered genomic regions devoid of any archaic ancestry (“introgression deserts”), which commonly reside in regions of high gene density or low recombination (Sankararaman et al. 2014; Vernot and Akey 2014; Sankararaman et al. 2016; Vernot et al. 2016; Schumer et al. 2018...
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Research: Continuous infiltration and evolutionary trajectory of nuclear organelle DNA in Oryza
- Chenbo Gong,
- Yicheng Huang,
- Mengmeng Liu,
- Yong Zhou,
- Yinwei Xu,
- Nahed Mohammed,
- Xintong Qiao,
- Andrea Zuccolo,
- Weibo Xie,
- Rod A. Wing,
- Jianwei Zhang,
- Fei Zhou,
- and Yongjun Lin
Genome Res. June 2025 35: 1349-1363; Published in Advance April 25, 2025, doi:10.1101/gr.279609.124
...) and the plastid acetyl-CoA carboxylase subunit D (accD) gene (Harris et al. 2013; Rousseau-Gueutin et al. 2013), have been lost and transferred to the nucleus multiple times during angiosperm evolution. There are abundant copies of organellar genes in the nuclear of each accession (Supplemental Tables S6, S7...

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