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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
...are emerging as a model system to understand the molecular evolution of living fossil lineages (Braasch et al. 2016; Thompson et al. 2021; Brownstein et al. 2022a, 2024; Simakov et al. 2022). To better understand rates of genomic evolution in gars, we estimated nucleotide substitution and structural change...
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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
...haplotypes rev2. https://zenodo.org/records/13889312 ↵Sibbesen JA, Maretty L, Danish Pan-Genome Consortium, Krogh A. 2018. Accurate genotyping across variant classes and lengths using variant graphs. Nat Genet 50: 1054–1059. doi:10.1038/s41588-018-0145-5 ↵Sirén J, Monlong J, Chang X, Novak AM, Eizenga JM...
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Method: ERC2.0 evolutionary rate covariation update improves inference of functional interactions across large phylogenies
- Jordan H. Little,
- Guillermo Hoffmann Meyer,
- Aakash Grover,
- Alex Michael Francette,
- Raghavendran Partha,
- Karen M. Arndt,
- Martin Smith,
- Nathan Clark,
- and Maria Chikina
Genome Res. September 2025 35: 2041-2051; Published in Advance August 7, 2025, doi:10.1101/gr.280586.125
...functional predictions of ERC have been empirically validated, its predictive power has hitherto been limited by its inability to tackle the large numbers of species in contemporary comparative genomics data sets. This study introduces ERC2.0, an enhanced methodology for studying ERC across phylogenies...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
..., Section 3.Comparative genomics of the histone clusterFigure 3A shows a schematic view of the histone locus across four different assemblies: iso-1 (FlyBase), iso-1 (HiFi), A4, and A3. The iso-1 FlyBase assembly contains a gap represented by empty space and is scaled to match our assembly's 113 copies...
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Research: Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes
- Diana Lobo,
- Hernán E. Morales,
- Cock Van Oosterhout,
- José Vicente López-Bao,
- Pedro Silva,
- Luis Llaneza,
- Carolina Pacheco,
- Diana Castro,
- Germán Hernández-Alonso,
- George Pacheco,
- John Archer,
- M. Thomas P. Gilbert,
- Nuno Ferrand,
- and Raquel Godinho
Genome Res. March 2025 35: 432-445; Published in Advance February 14, 2025, doi:10.1101/gr.279093.124
...introgressed genomic regions, mostly stochastically distributed across individuals (Supplemental Figs. S2, S3).Unlike neutral ancient introgression, if introgression conveys a selective advantage, population genetic theory predicts that introgressed genomic regions should be present at high frequency within...
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Method: Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT and otter
- Niccoló Tesi,
- Alex Salazar,
- Yaran Zhang,
- Sven van der Lee,
- Marc Hulsman,
- Lydian Knoop,
- Sanduni Wijesekera,
- Jana Krizova,
- Anne-Fleur Schneider,
- Maartje Pennings,
- Kristel Sleegers,
- Erik-Jan Kamsteeg,
- Marcel Reinders,
- and Henne Holstege
Genome Res. November 2024 34: 1942-1953; Published in Advance October 15, 2024, doi:10.1101/gr.279351.124
...to incorrect assessments of allele-sequences, including disease-associated TRs in patients.Here, we present TREAT (Tandem REpeat Annotation Toolkit), a unified workflow for characterizing TRs across multiple s, cross-compatible with diverse long-read technologies and data-types (e.g., read-alignments and de...
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Method: Combining DNA and protein alignments to improve genome annotation with LiftOn
- Kuan-Hao Chao,
- Jakob M. Heinz,
- Celine Hoh,
- Alan Mao,
- Alaina Shumate,
- Mihaela Pertea,
- and Steven L. Salzberg
Genome Res. February 2025 35: 311-325; Published in Advance December 27, 2024, doi:10.1101/gr.279620.124
..., and Arabidopsis thaliana. It can further map annotation effectively across species pairs as far apart as mouse and rat or Drosophila melanogaster and Drosophila erecta.Recent advancements in sequencing technologies have resulted in an exponential increase in available assemblies. Long-read sequencing technology...
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Research: Proteome-wide structural analysis quantifies structural conservation across distant species
- Shijie Zhang,
- Teng Zhang,
- and Yuan Fu
Genome Res. November 2023 33: 1975-1993; Published in Advance November 22, 2023, doi:10.1101/gr.277771.123
...structurally conserved protein list of the twilight zone when comparing H. sapiens to E. coli (Table 2; Supplemental Table S2). Incidentally, it is known that membrane proteins are less conserved than water-soluble proteins across the tree of life in terms of sequence, presumably due to a stronger adaptive...
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Resource: Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding
- Kai Li,
- Melissa L. Smith,
- J. Chris Blazier,
- Kelli J. Kochan,
- Jonathan M.D. Wood,
- Kerstin Howe,
- Anne E. Kwitek,
- Melinda R. Dwinell,
- Hao Chen,
- Julia L. Ciosek,
- Patrick Masterson,
- Terence D. Murphy,
- Theodore S. Kalbfleisch,
- and Peter A. Doris
Genome Res. November 2024 34: 2081-2093; Published in Advance November 8, 2024, doi:10.1101/gr.279292.124
...for Genome Sciences and Society, Texas A&M University, College Station, Texas 77843, USA; 4Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, United Kingdom; 5Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA; 6Department of Pharmacology...
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Method: Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe
- Arnaud Belcour,
- Jeanne Got,
- Méziane Aite,
- Ludovic Delage,
- Jonas Collén,
- Clémence Frioux,
- Catherine Leblanc,
- Simon M. Dittami,
- Samuel Blanquart,
- Gabriel V. Markov,
- and Anne Siegel
Genome Res. June 2023 33: 972-987; Published in Advance July 19, 2023, doi:10.1101/gr.277056.122
...distant algae, underlining the potential of AuCoMe to accelerate the broad exploration of metabolic evolution across the tree of life.The comparison of genomic data gave rise to today's view of the three domains of life: bacteria, archaea, and eukaryotes, which are divided into several supergroups (Burki...

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