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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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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
...this resource alongside other Pezizomycetes s, we (1) reconstructed a robust timeline for Tuberaceae emergence and diversification, (2) deciphered the evolutionary dynamics of TEs across the clade, and (3) assessed the impact of massive TE bursts on architecture and gene-family evolution.ResultsA high...
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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
...period following doubling.The two most influential mutational mechanisms that have shaped eukaryotic evolution are whole- duplications (WGDs) and transposable element (TE) activity. Both WGDs and TEs drive size evolution. However, as mobile genetic elements with capacity to replicate (Feschotte...
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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
...the expression (RNA-seq data) of all ERV types in mouse spermatogenesis.Because rapid gene evolution is a hallmark of germline genes expressed in testis (Soumillon et al. 2013), we suspected that rapidly evolving KZFP genes are expressed during spermatogenesis. Furthermore, our recent study demonstrated dynamic...
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Research: Physiological intron retaining transcripts in the cytoplasm abound during human motor neurogenesis
- Marija Petrić Howe,
- Hamish Crerar,
- Jacob Neeves,
- Jasmine Harley,
- Giulia E. Tyzack,
- Pierre Klein,
- Andres Ramos,
- Rickie Patani,
- and Raphaëlle Luisier
Genome Res. October 2022 32: 1808-1825; Published in Advance September 30, 2022, doi:10.1101/gr.276898.122
...identifies a previously unrecognized class of cytoplasmic intronic sequences with potential regulatory function beyond gene expression.Intron retention (IR), a mode of alternative splicing (AS) whereby one or more introns are retained within mature polyadenylated mRNAs, has been greatly understudied...
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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
...contributed equally to this work. Corresponding authors: jnw72@cornell.edu, cf458@cornell.eduAbstractCys2-His2 zinc finger genes (ZNFs) form the largest family of transcription factors in metazoans. ZNF evolution is highly dynamic and characterized by the rapid expansion and contraction of numerous...
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Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
- Xinghua Li,
- Judith E. Mank,
- and Liping Ban
Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
...of the X Chromosome to test for temporal dynamics to Fast-X evolution, and find evidence of a recent burst evolution for new X-linked genes in contrast to slow evolution of X-conserved genes.Grasshoppers (order Orthoptera, suborder Caelifera) represent an important phylogenetic and developmental comparison...
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Research: GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes
- Anguo Liu,
- Nini Wang,
- Guoxiang Xie,
- Yang Li,
- Xixi Yan,
- Xinmei Li,
- Zhenliang Zhu,
- Zhuohui Li,
- Jing Yang,
- Fanxin Meng,
- Mingle Dou,
- Weihuang Chen,
- Nange Ma,
- Yu Jiang,
- Yuanpeng Gao,
- and Yu Wang
Genome Res. October 2023 33: 1673-1689; Published in Advance October 26, 2023, doi:10.1101/gr.277784.123
...GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian s Anguo Liu1,2,7, Nini Wang1,3,7, Guoxiang Xie1,2,7, Yang Li1,2, Xixi Yan1,2, Xinmei Li1,2, Zhenliang Zhu2,4,5, Zhuohui Li1,2, Jing Yang2,4,5, Fanxin Meng1, Mingle Dou1,2, Weihuang Chen1, Nange...
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Method: Genome-reconstruction for eukaryotes from complex natural microbial communities
- Patrick T. West,
- Alexander J. Probst,
- Igor V. Grigoriev,
- Brian C. Thomas,
- and Jillian F. Banfield
Genome Res. April 2018 28: 569-580; Published in Advance March 1, 2018, doi:10.1101/gr.228429.117
...complex promoter regions, regulatory signals, and genes spliced into introns and exons, variable between species. For this reason, it is not surprising that we found that prokaryotic gene predictors underperform when used on eukaryotic sequences. This can impact binning by affecting taxonomic profiling...
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Research: Intron evolution in Neurospora: the role of mutational bias and selection
- Yu Sun,
- Carrie A. Whittle,
- Pádraic Corcoran,
- and Hanna Johannesson
Genome Res. January 2015 25: 100-110; Published in Advance October 23, 2014, doi:10.1101/gr.175653.114
...investigation. Population-level analyses are keys to fully understanding intron evolution, since intra-species dynamics ultimately determine whether introns become fixed or lost in the . Until now, however, few studies have used a population genetic approach to study intron evolution. Population data from...

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