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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
....DiscussionInsect host shift and its role in speciation have been the subject of research to understand the evolution of reproductive isolating barriers and adaptation to local environments. Indeed, many insects have finely tuned adaptations to locate, feed, reproduce, and develop on the host tissue. Adaptations to new...
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Research: Degrees of convergent evolution in rodent adaptations to arid environments
- Domitille Chalopin,
- Carine Rey,
- Jeremy Ganofsky,
- Juliana Blin,
- Pascale Chevret,
- Marion Mouginot,
- Laurent Guéguen,
- Bastien Boussau,
- Sophie Pantalacci,
- and Marie Sémon
Genome Res. March 2026 36: 472-486; Published in Advance January 21, 2026, doi:10.1101/gr.280089.124
..., Université de Lyon, Lyon 69007, France; 4Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR 5558, Université Claude Bernard Lyon 1, Villeurbanne 69622, France ↵5 These authors contributed equally to this work. Corresponding authors: domitille.chalopin-fillot@u-bordeaux.fr, sophie...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...Evolution of -wide methylation profiling technologies Carolina Montano1,2 and Winston Timp1 1Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA; 2Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia...
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Research: Birth of protein-coding exons by ancient domestication of LINE-1 retrotransposon
- Koichi Kitao,
- Kenji Ichiyanagi,
- and So Nakagawa
Genome Res. June 2025 35: 1287-1300; Published in Advance May 8, 2025, doi:10.1101/gr.280007.124
...domestication has occurred multiple times in vertebrate evolution.DiscussionLINEs are some of the most active transposons in vertebrates. Among them, L1 is the only LINE that remains active in the human (Hoyt et al. 2022). L1 ORF1p is an RNA-binding protein that assembles to package L1 RNA (Hohjoh and Singer...
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Resource: Streamlined spatial and environmental expression signatures characterize the minimalist duckweed Wolffia australiana
- Tom Denyer,
- Pin-Jou Wu,
- Kelly Colt,
- Bradley W. Abramson,
- Zhili Pang,
- Pavel Solansky,
- Allen Mamerto,
- Tatsuya Nobori,
- Joseph R. Ecker,
- Eric Lam,
- Todd P. Michael,
- and Marja C.P. Timmermans
Genome Res. July 2024 34: 1106-1120; Published in Advance July 1, 2024, doi:10.1101/gr.279091.124
...developmental and environmental expression signatures observed thus far, gene expression associated with photosynthesis in guard cells may override that of their epidermal origin.The Wolffia atlas captures developmental time between mother and daughter frondsWolffia reproduces through budding, and in some...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...6BT, United Kingdom; 2Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom; 3Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, United Kingdom; 4University College London Cancer...
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Research: Plant genome evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence
- Scott Ferguson,
- Ashley Jones,
- Kevin Murray,
- Rose Andrew,
- Benjamin Schwessinger,
- and Justin Borevitz
Genome Res. April 2024 34: 606-619; Published in Advance April 8, 2024, doi:10.1101/gr.277999.123
...Plant evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence Scott Ferguson1,4, Ashley Jones1,4, Kevin Murray1,2, Rose Andrew3, Benjamin Schwessinger1 and Justin Borevitz1 1Research School of Biology, Australian National University, Canberra...
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Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
...the same centromere is widespread (Dover 1982; Rudd et al. 2006; Wlodzimierz et al. 2023b). Analysis of variants within the Arabidopsis satellites showed signatures of sequence homogenization, reminiscent of concerted evolution in other tandem repeat arrays (Coen et al. 1982; Durfy and Willard 1990; Liao...
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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
.... 2020; Langmüller et al. 2023). These selection signatures on TE insertions in noncoding regions indicate selective forces on TE-CRE evolution, which is also evident from several analyses in our study.We find clear underrepresentation of TE sequences in accessible chromatin (Fig. 2A), and in particular...
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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
...the evolution of species-specific gene regulatory networks. Although likely true, this feature cannot be the initial driver of their rapid evolution, because TE domestication is a process that takes place over many generations, whereas selection primarily acts on currently extant individuals (Sniegowski...
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