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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
...duplication events as a way of enhancing tumor adaptability. In addition, it is possible that some FIEs (including those in known cancer genes) result in neofunctional changes. Here, neofunctionalization refers to the emergence of a tumor-beneficial protein function that is distinct from the wild...
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Research: Adaptation of centromeres to breakage through local genomic and epigenomic remodeling in wheat
- Jingwei Zhou,
- Yuhong Huang,
- Huan Ma,
- Yiqian Chen,
- Chuanye Chen,
- Fangpu Han,
- and Handong Su
Genome Res. November 2025 35: 2461-2471; Published in Advance September 30, 2025, doi:10.1101/gr.280913.125
...for Chinese Spring wheat and both short-arm (S) and long-arm (L) telosomes of ditelosomic lines. The bottom track presents annotated gene distributions. Triangles in the CS tracks denote primer positions used for PCR validation of genomic regions near breakpoints. (D) Agarose gel electrophoresis results...
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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
..., presumably via accelerated recombination during fbxn gene duplication, thereby reinforcing genetic divergence among populations and between species.An unusually conserved genomic region is identified surrounding Cni-neib-1Given the highly dynamic nature of fbxn genes across C. nigoni populations...
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Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
- Shahmir Naseer,
- Thomas C Clark,
- Bertrand Collet,
- Pooran Dewari,
- Damir Baranasic,
- Daniel J Macqueen,
- Pierre Boudinot,
- and Samuel A.M. Martin
Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
...substantial. In this study, we examined the -wide regulatory basis for 16 antiviral gene expression responses in Atlantic salmon (Salmo salar), representing a teleost 17 family that underwent a whole duplication (WGD) event ~100 Mya. We stimulate 18 fish systemically with polyinosinic:polycytidylic acid (poly...
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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
...regulatory phenotypes have been partly linked to divergent TE insertions in promoters of gene duplicates (Gillard et al. 2021; Sahlström et al. 2023), but the link between WGD and TE-CRE evolution has remained elusive. One hypothesis is that WGDs induce a genomic shock that results in bursts of TE activity...
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Research: Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera
- Peter O. Mulhair,
- Liam Crowley,
- Douglas H. Boyes,
- Amber Harper,
- Owen T. Lewis,
- Darwin Tree of Life Consortium,
- and Peter W.H. Holland
Genome Res. January 2023 33: 32-44; Published in Advance December 8, 2022, doi:10.1101/gr.277118.122
...A in Z. pyrina) and others having multiple copies of several of the four Shx genes (Supplemental Fig. S5). It is currently unclear whether these large gene arrays are adaptive, having been driven by selection, or whether they are neutral and a consequence of a genomic region prone to duplication...
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Research: Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites
- João L. Reis-Cunha,
- Samuel A. Pimenta-Carvalho,
- Laila V. Almeida,
- Anderson Coqueiro-dos-Santos,
- Catarina A. Marques,
- Jennifer A. Black,
- Jeziel Damasceno,
- Richard McCulloch,
- Daniella C. Bartholomeu,
- and Daniel C. Jeffares
Genome Res. March 2024 34: 441-453; Published in Advance April 11, 2024, doi:10.1101/gr.278550.123
...Ancestral aneuploidy and stable chromosomal duplication resulting in differential structure and gene expression control in trypanosomatid parasites João L. Reis-Cunha1,5, Samuel A. Pimenta-Carvalho2,5, Laila V. Almeida2, Anderson Coqueiro-dos-Santos2, Catarina A. Marques3, Jennifer A. Black3...
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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. March 4, 2026 gr.281113.125; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...,000 nuclei were loaded onto a 10x Chromium Controller following the 430 Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide (CG000338, 431 10x Genomics). Libraries underwent shallow sequencing (~1-5 million reads per library) on a 432 NextSeq 500 (Illumina) for quality control, followed...
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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
..., expanding the applicability of long-read sequencing across diverse genomic studies (Wenger et al. 2019; Koren et al. 2024). Both platforms are capable of DNA and cDNA sequencing and detecting DNA methylation. At the same time, ONT offers additional functionalities such as adaptive sampling and direct RNA...
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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
...to human-dominated landscapes.To test the “introgression fueled adaptation” hypothesis, we conducted a comprehensive genomic analysis of 48 historical (1912–2005) and 97 contemporary samples of Iberian wolves, alongside 67 worldwide wolves and 131 dogs (Fig. 1A,B; Supplemental Table S1). We used these data...
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