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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...). The existence of F1 and F2 A. spatula × Lepisosteus spp. crosses is surprising because these genera diverged from one another during the Cretaceous period, between 97 and 120 million years ago (Grande 2010; Brownstein et al. 2022a). The slow rate of genomic evolution in gars may enable gars to hybridize across...
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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...) and genomic size (∼0.6 Mbp) (Supplemental Fig. S3), TAD border insulation strength (R2 = 0.77–1.00) (Supplemental Fig. S4) and intra-TAD contact frequencies (R2 = 0.91–1.00) (Supplemental Fig. S5), and genomic positions of both TADs (Jaccard index [JI] = 0.76–0.80; called at 50 kb resolution), and sub...
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Research: H3K27 and H3K9 methylation mask potential CTCF binding sites to maintain 3D genome integrity
- Kei Fukuda,
- Chikako Shimura,
- and Yoichi Shinkai
Genome Res. October 2025 35: 2199-2210; Published in Advance August 5, 2025, doi:10.1101/gr.280732.125
..., Yamanashi 400-8510, Japan Corresponding authors: yshinkai@riken.jp, k.fukuda@yamanashi.ac.jpAbstractThe three-dimensional (3D) structure is essential for gene regulation and various genomic functions. CTCF plays a key role in organizing topologically associated domains (TADs) and promoter-enhancer loops...
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Resource: Building better genome annotations across the tree of life
- Adam H. Freedman and
- Timothy B. Sackton
Genome Res. May 2025 35: 1261-1276; Published in Advance April 15, 2025, doi:10.1101/gr.280377.124
...of bioinformatics tools and resources to interrogate s for evolutionary patterns and features of biomedical interest. But even as s became available for other model organisms such as mouse (Mus musculus) (Mouse Genome Sequencing Consortium et al. 2002) and rhesus macaque (Macaca mulatta) (Rhesus Macaque Genome...
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Resource: Chromosome-level subgenome-aware de novo assembly provides insight into Saccharomyces bayanus genome divergence after hybridization
- Cory Gardner,
- Junhao Chen,
- Christina Hadfield,
- Zhaolian Lu,
- David Debruin,
- Yu Zhan,
- Maureen J. Donlin,
- Tae-Hyuk Ahn,
- and Zhenguo Lin
Genome Res. November 2024 34: 2133-2146; Published in Advance September 17, 2024, doi:10.1101/gr.279364.124
.... This high score indicates a successful capture of the genomic features we aimed to assemble.We aimed to address the inherent complexity of the diploid of S. bayanus CBS380 by assembling the two subs separately. We used the MinION platform's long-read technology to generate the sequence and, of the different...
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Research: Fusion, fission, and scrambling of the bilaterian genome in Bryozoa
- Thomas D. Lewin,
- Isabel Jiah-Yih Liao,
- Mu-En Chen,
- John D.D. Bishop,
- Peter W.H. Holland,
- and Yi-Jyun Luo
Genome Res. January 2025 35: 78-92; Published in Advance January 6, 2025, doi:10.1101/gr.279636.124
...as macrosynteny, is seen between bilaterian phyla as divergent as Chordata, Echinodermata, Mollusca, and Nemertea. Here, we report a unique pattern of evolution in Bryozoa, an understudied phylum of colonial invertebrates. Using comparative genomics, we reconstruct the chromosomal evolutionary history of five...
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Method: Pangenome-based genome inference using integer programming
- Ghanshyam Chandra,
- Md Helal Hossen,
- Stephan Scholz,
- Alexander T. Dilthey,
- Daniel Gibney,
- and Chirag Jain
Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
...: chirag@iisc.ac.inAbstractAffordable genotyping methods are essential in genomics. Commonly used genotyping methods primarily support single-nucleotide variants and short indels but neglect structural variants. Additionally, accuracy of read alignments to a reference is unreliable in highly polymorphic...
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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
....zambonelli@unibo.itAbstractThe genus Tuber (family: Tuberaceae) includes the most economically valuable ectomycorrhizal (ECM), truffle-forming fungi. Previous genomic analyses revealed that massive transposable element (TE) proliferation represents a convergent genomic feature of ECM fungi, including Tuberaceae. Repetitive sequences...
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Research: Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma
- Mauro Castellarin,
- René L. Warren,
- J. Douglas Freeman,
- Lisa Dreolini,
- Martin Krzywinski,
- Jaclyn Strauss,
- Rebecca Barnes,
- Peter Watson,
- Emma Allen-Vercoe,
- Richard A. Moore,
- and Robert A. Holt
Genome Res. February 2012 22: 299-306; Published in Advance October 18, 2011, doi:10.1101/gr.126516.111
...disproportionate between tumor and control were to the of Fusobacterium nucleatum subsp. nucleatum (American Type Culture Collection [ATCC] 25586), a Gram-negative anaerobe. F. nucleatum was the organism with the highest number of hits overall (21% of all alignments), and nine of the 11 subjects showed at least...
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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
....Cytosine methylation plays a critical role in genomic imprinting, gene regulation, X-Chromosome inactivation (XCI), cellular differentiation, aging, and tumorigenesis. Cells have an extensive system of proteins that establish these methylation patterns through de novo methylation or demethylation, copy methylation...
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