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Research: GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes
- Anguo Liu,
- Nini Wang,
- Guoxiang Xie,
- Yang Li,
- Xixi Yan,
- Xinmei Li,
- Zhenliang Zhu,
- Zhuohui Li,
- Jing Yang,
- Fanxin Meng,
- Mingle Dou,
- Weihuang Chen,
- Nange Ma,
- Yu Jiang,
- Yuanpeng Gao,
- and Yu Wang
Genome Res. October 2023 33: 1673-1689; Published in Advance October 26, 2023, doi:10.1101/gr.277784.123
...of the substitution counts in uc.359 in Cervidae with those expected under neutral evolution indicated that uc.359 is still subject to strong purifying selection (Supplemental Fig. S16). Therefore, we speculated that a recombination event occurred in the cervid ancestor that shaped this cervid-specific GC-biased...
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Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
- Aleix Palahí i Torres,
- Lars Höök,
- Karin Näsvall,
- Daria Shipilina,
- Christer Wiklund,
- Roger Vila,
- Peter Pruisscher,
- and Niclas Backström
Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
...elements (TEs), which tend to accumulate in regions of low recombination rate (Bartolomé et al. 2002; Xu and Du 2014). The frequency of recombination events can also directly affect nucleotide composition through GC-biased gene conversion (gBGC), a process that facilitates the fixation of strong (G and C...
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Method: Quantification of GC-biased gene conversion in the human genome
- Sylvain Glémin,
- Peter F. Arndt,
- Philipp W. Messer,
- Dmitri Petrov,
- Nicolas Galtier,
- and Laurent Duret
Genome Res. August 2015 25: 1215-1228; Published in Advance May 20, 2015, doi:10.1101/gr.185488.114
..., a large fraction of the is affected by short episodes of strong gBGC.The process of GC-biased gene conversion (gBGC) has a major impact on the evolution of mammalian s (Duret and Galtier 2009; Romiguier et al. 2010; Katzman et al. 2011) and is known or suspected to a play a role in many other groups...
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Review: Recent advances in methods to characterize archaic introgression in modern humans
- David Peede,
- Mayra M. Bañuelos,
- Jazeps Medina Tretmanis,
- Miriam Miyagi,
- and Emilia Huerta-Sánchez
Genome Res. February 2026 36: 239-256; Published in Advance January 16, 2026, doi:10.1101/gr.278993.124
..., such as Neanderthals and Denisovans, into the s of modern humans due to historical gene flow events is known as archaic introgression. As new methods and data sets uncover a more complex intermingling between our ancestors and archaic humans than previously thought, the relevance of archaic introgression has only...
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Research: Lambdoid phages with abundant Chi recombination hotspots reflect diverse viral strategies for recombination-dependent growth
- Clarence Zheng,
- Sherwood R. Casjens,
- Alan R. Davidson,
- Susan K. Amundsen,
- and Gerald R. Smith
Genome Res. August 2025 35: 1767-1780; Published in Advance July 10, 2025, doi:10.1101/gr.280248.124
..., but characterization of their roles in phage lifecycles is limited, and their impact on phage replication is controversial. To address these issues, we have searched for phages whose growth is impacted by the major recombination-promoting helicase-nuclease of Escherichia coli, the RecBCD enzyme. Although no phages...
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Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
- Yao Wang,
- Dong Yu,
- Yue Mei,
- ZhiDa Fu,
- Jian Lin,
- Di Wu,
- Yuan Yang,
- and Hongli Yan
Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
...recombination in the human . Notably, integrated HBV enhancer I (HBV-Enh I) is detected in six of seven tumor tissues and is associated with aberrant gene expression. HBV integration induces oncogenic SVs, such as focal MYC amplification and NAV2 deletion, and directly modulates gene expression. Additionally...
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Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
- Sophia N. Lee,
- Erin C. Banda,
- Lu Qiao,
- Sarah L. Thompson,
- Karan Singh,
- Ryan A. Hagenson,
- Teresa Davoli,
- Stefan F. Pinter,
- and Jason M. Sheltzer
Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125
...of Chromosome 8 and restore euploidy in cells derived from an individual with a complex rearrangement of Chromosome 8p. Transcriptomic analysis revealed 361 differentially expressed genes between the proband and the euploid revertant, highlighting genes both within and outside the 8p region that may contribute...
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Resource: Exploration of fine-scale recombination rate variation in the domestic horse
- Samantha K. Beeson,
- James R. Mickelson,
- and Molly E. McCue
Genome Res. October 2019 29: 1744-1752; Published in Advance August 21, 2019, doi:10.1101/gr.243311.118
...stability in the Icelandic horse breed. Anim Genet 43: 447–449. doi:10.1111/j.1365-2052.2011.02266.x ↵Coop G, Wen X, Ober C, Pritchard JK, Przeworski M. 2008. High-resolution mapping of crossovers reveals extensive variation in fine-scale recombination patterns among humans. Science 319: 1395–1398. doi:10...
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Research: Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans
- Xavi Guitart,
- David Porubsky,
- DongAhn Yoo,
- Max L. Dougherty,
- Philip C. Dishuck,
- Katherine M. Munson,
- Alexandra P. Lewis,
- Kendra Hoekzema,
- Jordan Knuth,
- Stephen Chang,
- Tomi Pastinen,
- and Evan E. Eichler
Genome Res. November 2024 34: 1798-1810; Published in Advance August 6, 2024, doi:10.1101/gr.279299.124
...conversion of all gene family copies in each lineage. In contrast, the gelada and rhesus macaque show both shared and lineage-specific groups, suggesting TBC1D3 expanded before and after speciation. Using 25 and 6.5 million years ago (mya) as times of human–macaque and human–chimpanzee divergence, we...
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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
...features, revealing 212 strong consistency with RNA-based cell annotations (Supplemental Fig. S8A). We validated 213 chromatin accessibility at marker genes for cell subclasses (Fig. 3A). Next, we performed peak 214 calling on each subclass to identify reproducible peaks following a previous established...
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