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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...complete and gap-free (Hillier et al. 2005). It was thus surprising when, 14 years later, our attempt to reproduce a perfect isogenic copy of the reference C. elegans instead showed that it was neither complete nor gap-free (Yoshimura et al. 2019), as discrepancies observed by others were by then also...
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Method: Minimizing reference bias with an imputed personalized reference
- Kavya Vaddadi,
- Mao-Jan Lin,
- Sina Majidian,
- Taher Mun,
- and Ben Langmead
Genome Res. March 5, 2026 gr.280989.125; Published in Advance March 5, 2026, doi:10.1101/gr.280989.125
...Giraffe with linear and pan references, and personalizedpan approaches (Supplemental Table S10). Within the GRCh38 Complex Medically Relevant Gene (CMRG) regions tailored for HG002 (Wagner et al. 2022), the impute-first workflows had slightly lower F1 score (0.9445– 0.9524) compared to the Giraffe pan (0...
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Research: Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
- Bertille Montibus,
- James A. Cain,
- Rocio T. Martinez-Nunez,
- and Rebecca J. Oakey
Genome Res. December 2024 34: 2163-2175; Published in Advance November 22, 2024, doi:10.1101/gr.279430.124
...the requirement of rapid evolution, and yet, still contain genomic overlaps (Veeramachaneni et al. 2004). In eukaryotes, the first of these was identified in 1986 in Drosophila and mouse (Henikoff et al. 1986; Spencer et al. 1986; Williams and Fried 1986).In 2019, a study in humans estimated that ∼26...
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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
...with particular reference to the “innovation–amplification–divergence” model of neofunctionalization (Näsvall et al. 2012), in which a pre-existing, weak, secondary gene function (“innovation”) confers advantage owing to changes in the environment, leading to selection for increased gene copy (“amplification...
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Method: Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS
- Qunlun Shen,
- Shuqin Zhang,
- and Shihua Zhang
Genome Res. November 2025 35: 2527-2538; Published in Advance October 1, 2025, doi:10.1101/gr.280821.125
...: zhangs@fudan.edu.cn, zsh@amss.ac.cnAbstractCell type annotation is a critical and essential task in single-cell data analysis. Various reference-based methods have provided rapid annotation for diverse single-cell data. However, selection of the optimal references and methods is often overlooked...
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Method: Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration
- Zepu Miao and
- Jia-Xing Yue
Genome Res. February 2025 35: 296-310; Published in Advance January 13, 2025, doi:10.1101/gr.279461.124
...data set, users can interactively visualize, navigate, and query the pan graph via a primary linear reference–based coordinate system. An example of the human APOE gene region (Chr 19: 44,905,000–44,910,000, GRCh38 coordinates) of the HRPC Minigraph-Cactus pan graph is shown here. The APOE gene bears...
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Research: Third-generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants
- Jing Xia,
- Aarthi Venkat,
- Rachel E. Bainbridge,
- Michael L. Reese,
- Karine G. Le Roch,
- Ferhat Ay,
- and Jon P. Boyle
Genome Res. May 2021 31: 834-851; Published in Advance April 27, 2021, doi:10.1101/gr.262816.120
...26 show that copy number can change during sexual recombination because the copy number in these F1 progeny clones does not match copy number in either parent. (D–F) Whole-chromosome alignments between ME49ToxoDB-48 and our Nanopore assemblies at loci harboring tandem gene arrays. Gray boxes with red...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...hypersensitivity), high nucleosomal turnover (e.g., high levels of rapid-turnover histones H2A.Z and H3.3), specific epigenetic markers (e.g., high ratio of H3K4me1 and H3K4me2 to H3K4me3, high ratio of 5hmC to 5mC, enrichment of H3K27ac), chromatin loops in direct contact with the core promoter (enrichment...
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Research: Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly
- Kang Du,
- Oliver Deusch,
- Ilja Bezrukov,
- Christa Lanz,
- Yann Guiguen,
- Margarete Hoffmann,
- Anette Habring,
- Detlef Weigel,
- Manfred Schartl,
- and Christine Dreyer
Genome Res. March 2025 35: 489-498; Published in Advance March 5, 2025, doi:10.1101/gr.279582.124
.... Evol Appl 13: 2791–2806. doi:10.1111/eva.13084 ↵Metzger DCH, Sandkam BA, Darolti I, Mank JE. 2021. Rapid evolution of complete dosage compensation in Poecilia. Genome Biol Evol 13: evab155. doi:10.1093/gbe/evab155 ↵Morris J, Darolti I, Bloch NI, Wright AE, Mank JE. 2018. Shared and species...
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Research: Copy number variation alters local and global mutational tolerance
- Grace Avecilla,
- Pieter Spealman,
- Julia Matthews,
- Elodie Caudal,
- Joseph Schacherer,
- and David Gresham
Genome Res. August 2023 33: 1340-1353; Published in Advance August 31, 2023, doi:10.1101/gr.277625.122
...or duplication of segments of DNA. Amplification of segments of DNA sequence, a type of copy number variation (CNV), is an important source of rapid adaptive evolution. In the short term, gene amplification can result in increased gene expression, which provides a selective advantage facilitating adaptation...
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