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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
...Caenorhabditis briggsae and its sister species Caenorhabditis nigoni provide an ideal model system to address this question, as they exhibit extensive genomic divergence with limited gene flow from C. briggsae to C. nigoni. Despite previous comparative genomic studies, a comprehensive analysis of both...
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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
...) regulatory divergence between paralogous 96 genes contributes to their differential expression during the antiviral response; and (iii) 97 expanded or salmonid-specific gene families exhibit distinct regulatory signatures that reflect 98 their functional roles in immunity. 99 To test these hypotheses, we...
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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
...not be expected in relation to Eurasian wolves, thus suggesting postdivergence gene flow between Iberian wolves and dogs.To further dissect the evolutionary history of this genomic region, we compared the population phylogenetic trees for the entire Chromosome 2 and for the 500 kb region using TreeMix (Pickrell...
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Method: Autoencoders for genomic variation analysis
- Margarita Geleta,
- Daniel Mas Montserrat,
- Xavier Giro-i-Nieto,
- and Alexander G. Ioannidis
Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
...et al. 2020) and SALAI-Net (Sabat Oriol et al. 2022).Genomic sequence simulationAlthough the number of sequenced s has grown substantially over the years, there is a clear disparity among the ancestries represented. The proportion of participants of non-European descent has remained constant (Wojcik...
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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
...under the “innovation–amplification–divergence” model of neofunctionalization (Näsvall et al. 2012). In essence, a tumor may increase its adaptability to a dynamic landscape of selection pressures by exploiting an expanded repertoire of potential functional modifications. Gene duplication, allowing...
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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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Method: Automated interpretable artificial intelligence genomic prediction with AIGP
- Lei Wei,
- Ziqin Jiang,
- Baoliang Fan,
- Yidan Yan,
- Zhenqiang Xu,
- Xiaoxiang Hu,
- and Yuzhe Wang
Genome Res. March 5, 2026 gr.281006.125; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
...and enable independent feature importance 331 assessment(Wang et al. 2020; Zhu et al. 2025a), and 3) incorporation of in silico mutational 332 landscapes (Chen et al. 2022) and gene-editing datasets. Multimodal integration will advance 333 phenotype prediction from single-source models to large...
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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
...(TEs) and other repetitive sequences are known to be one of the major causes of structural variations within individuals and species, promoting expansion, gene duplication, gene loss, genomic rearrangements, and reshaping of the overall genomic regulatory network (Bourque et al. 2018). Among fungi...
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Research: Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma
- Meilong Shi,
- Chuanqi Teng,
- Shan Zhang,
- Xiaobo He,
- Lingyun Xu,
- Fengxian Han,
- Rongqi Wen,
- Ganjun Yu,
- Jingwen Liu,
- Yang Feng,
- Yanfeng Wu,
- Yan Ren,
- Gang Jin,
- and Jing Li
Genome Res. February 2026 36: 275-290; Published in Advance January 8, 2026, doi:10.1101/gr.280528.125
...). In the 7413 upregulated DETEs, 36.4% were classified as LINE elements, and 35.8% belonged to SINE, and 0.18% of the 770,551 LTR genomic copies were upregulated. Unlike previous reports linking TE expression to instability, we found no association with gene mutations or tumor markers (Fig. 1C; Supplemental Fig...
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Research: Different trajectories of polyploidization shape the genomic landscape of the Brettanomyces bruxellensis yeast species
- Chris Eberlein,
- Omar Abou Saada,
- Anne Friedrich,
- Warren Albertin,
- and Joseph Schacherer
Genome Res. December 2021 31: 2316-2326; Published in Advance November 23, 2021, doi:10.1101/gr.275380.121
...divergence and speciation (Leitch and Leitch 2008; Soltis et al. 2015). Polyploidy can be beneficial under certain environmental circumstances and increases the potential for adaptability, taking advantage of evolutionary innovations from neo- and subfunctionalization of duplicated genes (Sanchez-Perez et al...
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