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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
...for the kidney. We combined publicly available data (cDNA from published s and kidney RNA-seq data) with newly generated RNA-seq data to obtain coding sequence and expression data in a variety of rodents, ensuring a reasonable overlap between the two types of data (12 families, 48 species out of which 33 species...
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Research: Genome-wide patterns of selection–drift variation strongly associate with organismal traits across the green plant lineage
- Kavitha Uthanumallian,
- Andrea Del Cortona,
- Susana M. Coelho,
- Olivier De Clerck,
- Sebastian Duchene,
- and Heroen Verbruggen
Genome Res. August 2024 34: 1130-1139; Published in Advance August 29, 2024, doi:10.1101/gr.279002.124
.../mci002 ↵Kapraun DF. 2006. Nuclear DNA content estimates in green algal lineages: Chlorophyta and Streptophyta. Ann Bot 99: 677–701. doi:10.1093/aob/mcl294 ↵Krasovec M, Eyre-Walker A, Sanchez-Ferandin S, Piganeau G. 2017. Spontaneous mutation rate in the smallest photosynthetic eukaryotes. Mol Biol Evol...
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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
..., Pennsylvania 19104, USA Corresponding authors: montanoc@chop.edu, wtimp@jhu.eduAbstractIn this mini-review, we explore the advancements in -wide DNA methylation profiling, tracing the evolution from traditional methods such as methylation arrays and whole- bisulfite sequencing to the cutting-edge single...
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Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
- Marian F. Laughery,
- Bastian Stark,
- Benjamin Morledge-Hampton,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
.... Single-stranded DNA with a free 3′OH generated from the UDG and APE1 digestions was ligated to a biotinylated first adapter (Fig. 1D, green), and ligation products were sonicated and purified using streptavidin beads. The complementary strand was synthesized by polymerase extension using a primer...
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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
...editing efficiency, we amplified genomic DNA from puromycin-selected, doubly transfected C1 cells using primers targeting regions surrounding sites recognized by sgRNAs in RE1, -2, or -3 (Supplemental Fig. S49A). PCR products were analyzed by gel electrophoresis, purified, and sequenced (Supplemental Fig...
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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
...-resolved assemblies. This graph is modeled as a DAG, in which each node is labeled with a DNA sequence, and edges represent the adjacency of these sequences along known haplotypes. Any path through this graph can represent an existing haplotype or a recombinant mosaic of segments from multiple haplotypes.In the Li...
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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
...sites from paralogs (blue), and likely functional sites predicted owing to high conservation within the CATH functional families (green), are mapped in an identical manner. Significant mutation clusters near functional sites were termed “tunable sites,” highlighting commonalities between mutations from...
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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
...Biopython (Cock et al. 2009) and Pyfaidx (https://github.com/mdshw5/pyfaidx) to extract both DNA and protein transcript sequences from the reference . These extracted sequences, stored as intermediate FASTA files, serve as inputs for the embedded Liftoff code and miniprot module through a Python subprocess...
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Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J Smith,
- and Falk Butter
Genome Res. January 28, 2026 gr.281000.125; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
...excision 506 repair in yeast and mammals: Translational implications1. Cancer Res 63: 549–54. 507 Kovalchuk I. 2016. Chapter 38 - Conserved and Divergent Features of DNA Repair: 508 Future Perspectives in Genome Instability Research. In Genome Stability (eds. I. 509 Kovalchuk and O. Kovalchuk), pp. 651...
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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
...in shaping evolution of retroelement-associated TE-CRE landscapes in Atlantic salmon.Although retroelements dominate the salmon TE-CRE landscape, the role of DNA transposons such as DTA and DTT elements in TE-CRE evolution cannot be neglected owing to their high genomic copy numbers (Figs. 1, 3A). Indeed...

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