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Research: A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility
- Angelo A. Ruggieri,
- Luca Livraghi,
- James J. Lewis,
- Elizabeth Evans,
- Francesco Cicconardi,
- Laura Hebberecht,
- Yadira Ortiz-Ruiz,
- Stephen H. Montgomery,
- Alfredo Ghezzi,
- José Arcadio Rodriguez-Martinez,
- Chris D. Jiggins,
- W. Owen McMillan,
- Brian A. Counterman,
- Riccardo Papa,
- and Steven M. Van Belleghem
Genome Res. October 2022 32: 1862-1875; Published in Advance September 15, 2022, doi:10.1101/gr.276839.122
...A butterfly pan- reveals that a large amount of structural variation underlies the evolution of chromatin accessibility Angelo A. Ruggieri1, Luca Livraghi2,3, James J. Lewis4, Elizabeth Evans1, Francesco Cicconardi5, Laura Hebberecht5, Yadira Ortiz-Ruiz1,6, Stephen H. Montgomery5, Alfredo Ghezzi1...
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Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
- Aayush Grover,
- Till Muser,
- Liine Kasak,
- Lin Zhang,
- Ekaterina Krymova,
- and Valentina Boeva
Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
...–specific regulatory features that underlie chromatin accessibility.View larger version: In this window In a new window Figure 4. Interpreting sequence features underlying model predictions. (A–D) Proportion of identified transcription factor motifs in different cell lines: (A) GM12878, (B) K562, (C) IMR-90, and (D...
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Research: Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements
- Fu Xiang Quah,
- Miguel Vasconcelos Almeida,
- Moritz Blumer,
- Chengwei Ulrika Yuan,
- Bettina Fischer,
- Kirsten See,
- Ben Jackson,
- Richard Zatha,
- Bosco Rusuwa,
- George F. Turner,
- M. Emília Santos,
- Hannes Svardal,
- Martin Hemberg,
- Richard Durbin,
- and Eric Miska
Genome Res. May 2025 35: 1094-1107; Published in Advance April 10, 2025, doi:10.1101/gr.279674.124
...Lake Malawi cichlid pan graph reveals extensive structural variation driven by transposable elements Fu Xiang Quah1,2, Miguel Vasconcelos Almeida1, Moritz Blumer2, Chengwei Ulrika Yuan1,2, Bettina Fischer2, Kirsten See1, Ben Jackson2, Richard Zatha3, Bosco Rusuwa3, George F. Turner4, M. Emília...
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Research: Large haplotypes highlight a complex age structure within the maize pan-genome
- Jianing Liu and
- R. Kelly Dawe
Genome Res. March 2023 33: 359-370; Published in Advance February 28, 2023, doi:10.1101/gr.276705.122
...method also revealed ∼19 million structural variations (Supplemental Figs. S4, S5; Supplemental Tables S1, S2); a greatly expanded list (relative to an earlier database of ∼0.79 million [Hufford et al. 2021]), which is available for use in mapping and association studies. By comparing s in an all...
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Research: Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
- Kevin W. Currin,
- Hannah J. Perrin,
- Gautam K. Pandey,
- Abdalla A. Alkhawaja,
- Swarooparani Vadlamudi,
- Annie E. Musser,
- Amy S. Etheridge,
- K. Alaine Broadaway,
- Jonathan D. Rosen,
- Arushi Varshney,
- Amarjit S. Chaudhry,
- Paul J. Gallins,
- Fred A. Wright,
- Yi-hui Zhou,
- Stephen C.J. Parker,
- Laura M. Raffield,
- Erin G. Schuetz,
- Federico Innocenti,
- and Karen L. Mohlke
Genome Res. July 2025 35: 1485-1502; Published in Advance May 20, 2025, doi:10.1101/gr.279741.124
...with this principle, genetic variants have been shown to explain a larger proportion of variation in chromatin accessibility than gene expression (Liang et al. 2021). Additional approaches, such as Hi-C (Jung et al. 2019) and chromatin coaccessibility (Thurman et al. 2012; Kumasaka et al. 2019; Currin et al. 2021...
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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
...The grasshopper reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution Xinghua Li1,2, Judith E. Mank3 and Liping Ban1 1Department of Grassland Resources and Ecology, College of Grassland Science and Technology, China Agricultural University...
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Method: Statistically rigorous and computationally efficient chromatin stripe detection with Quagga
- Fan Feng,
- Sean Moran,
- Anders S. Hansen,
- Xiaotian Zhang,
- and Jie Liu
Genome Res. January 2026 36: 159-168; Published in Advance November 12, 2025, doi:10.1101/gr.280132.124
...and convenient tool to help scientists explore the relationships between chromatin architectural stripes and important biological questions.Chromatin conformation capture (3C) techniques, especially proximity ligation–based methods, have revealed that the hierarchical structures of DNA break down into distinct...
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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
...a moderate signal for habitat-related convergent evolution of gene expression levels, whereas the Murinae_expr data set displays a stronger signal.Transcriptome convergence is associated with convergent shifts in kidney cell compositionTissue bulk RNA-seq data reflect variation in both expression per cell...
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Resource: The SynMall resource for characterizing the functional impact of synonymous variation
- Chen Ye,
- Xiaoyan Li,
- Na Cheng,
- Yansen Su,
- and Junfeng Xia
Genome Res. February 2026 36: 421-431; Published in Advance December 17, 2025, doi:10.1101/gr.281257.125
...-derived attributes, and residue-level protein characteristics such as intrinsic disorder, secondary structure, and solvent accessibility. Beyond these handcrafted features, SynMall also integrates 10 biological language models, considering their growing success in variant effect prediction tasks (Cheng et al. 2023...
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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
...Stenocereus gummosus, and D. m. sonorensis is also a columnar cacti dweller, using Stenocereus thurberi (Newby and Etges 1998). Therefore, this set of species from the buzzatii and mojavensis clusters provides an excellent model to investigate the molecular mechanisms underlying host shift evolution...

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