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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
...provides novel insights into the genomic regulatory landscape underlying antiviral 33 immunity in a farmed fish with a complex . 34 Introduction 35 The innate immune response to viral infection, which is mainly based on the type I interferon 36 (type I IFN) pathway is crucial to both disease progression...
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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
.... briggsae strains and nine C. nigoni strains, including both reference strains. Through comparative pan-genomic analyses of both nematode species, we aim to identify the critical structural and genetic variations that drive intra- and interspecific evolution, ultimately leading to speciation...
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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
...identify sequence variations relative to a reference . These genomic variations encompass a spectrum of sizes, from single-nucleotide variants (SNVs) and short insertions or deletions (indels, <50 bp) to SVs (≥50 bp). Thus, identifying the proper reference for long-read alignment is critical as it might...
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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
...–driven evolution for more than a century. Despite strong efforts, knowledge on genomic organization and molecular differentiation of the sex chromosome pair remains unsatisfactory and partly contradictory with respect to regions of reduced recombination. Especially the border between pseudoautosomal and male...
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Research: Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription
- Christine R. Keenan,
- Hannah D. Coughlan,
- Nadia Iannarella,
- Andres Tapia del Fierro,
- Andrew Keniry,
- Timothy M. Johanson,
- Wing Fuk Chan,
- Alexandra L. Garnham,
- Lachlan W. Whitehead,
- Marnie E. Blewitt,
- Gordon K. Smyth,
- and Rhys S. Allan
Genome Res. April 2024 34: 556-571; Published in Advance May 6, 2024, doi:10.1101/gr.279119.124
....79 and bin size 6 kbp; KO: gap penalty 9.1 and bin size 8 kbp). LADs called on the Y and scaffold chromosomes were excluded from subsequent analyses. LADs were also defined with methods based on circular binary segmentation (CBS) and LADetector (Harr et al. 2015; Luperchio et al. 2017). With the down...
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Research: Genomic architecture constrained placental mammal X Chromosome evolution
- Wesley A. Brashear,
- Kevin R. Bredemeyer,
- and William J. Murphy
Genome Res. August 2021 31: 1353-1365; Published in Advance July 22, 2021, doi:10.1101/gr.275274.121
...constraints on the three-dimensional genomic architecture necessary for X-Chromosome inactivation. Species with rearranged X Chromosomes have retained the ancestral order and relative spacing of loci critical for superloop formation during X-Chromosome inactivation, suggesting that selection for compensatory...
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Research: Genomic insights into metabolic flux in hummingbirds
- Ariel Gershman,
- Quinn Hauck,
- Morag Dick,
- Jerrica M. Jamison,
- Michael Tassia,
- Xabier Agirrezabala,
- Saad Muhammad,
- Raafay Ali,
- Rachael E. Workman,
- Mikel Valle,
- G. William Wong,
- Kenneth C. Welch, Jr.,
- and Winston Timp
Genome Res. May 2023 33: 703-714; Published in Advance May 8, 2023, doi:10.1101/gr.276779.122
...and annotation. Our genomic and transcriptomic data found positive selection of key metabolic genes in nectivorous avian species and deletion of critical genes (SLC2A4, GCK) involved in glucostasis in other vertebrates. We found expression of a fructose-specific version of SLC2A5 putatively in place of insulin...
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Research: Targeted and complete genomic sequencing of the major histocompatibility complex in haplotypic form of individual heterozygous samples
- Taishan Hu,
- Timothy L. Mosbruger,
- Nikolaos G. Tairis,
- Amalia Dinou,
- Pushkala Jayaraman,
- Mahdi Sarmady,
- Kingham Brewster,
- Yang Li,
- Tristan J. Hayeck,
- Jamie L. Duke,
- and Dimitri S. Monos
Genome Res. October 2024 34: 1500-1513; Published in Advance September 26, 2024, doi:10.1101/gr.278588.123
..., NY 10029, USA; 9Department of Genomic and Data Sciences, Spark Therapeutics, Philadelphia, PA 19104, USA Corresponding author: monosd@chop.eduAbstractThe human major histocompatibility complex (MHC) is a ∼4 Mb genomic segment on Chromosome 6 that plays a pivotal role in the immune response. Despite...
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Research: Multi-omics analyses demonstrate a critical role for EHMT1 methyltransferase in transcriptional repression during oogenesis
- Hannah Demond,
- Courtney W. Hanna,
- Juan Castillo-Fernandez,
- Fátima Santos,
- Evangelia K. Papachristou,
- Anne Segonds-Pichon,
- Kamal Kishore,
- Simon Andrews,
- Clive S. D'Santos,
- and Gavin Kelsey
Genome Res. January 2023 33: 18-31; Published in Advance January 23, 2023, doi:10.1101/gr.277046.122
...transcriptional repression in the oocyte, partially independent of EHMT2, and is critical for oogenesis and oocyte developmental competence.The mammalian germline is the context for widespread epigenetic changes, in which the somatic epigenetic signature is erased and replaced by a germline signature...
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Research: Chromosome-specific telomere lengths and the minimal functional telomere revealed by nanopore sequencing
- Samantha L. Sholes,
- Kayarash Karimian,
- Ariel Gershman,
- Thomas J. Kelly,
- Winston Timp,
- and Carol W. Greider
Genome Res. April 2022 32: 616-628; Published in Advance October 26, 2021, doi:10.1101/gr.275868.121
...restriction sites on different chromosomes are at different locations, the absolute size of each smear differs. Frequently, the restriction enzyme XhoI is used to cut genomic DNA because many telomeres have a conserved XhoI restriction site in the Y′ subtelomere element. Multiple telomeres are then visualized...

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