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Research: Haplotype-resolved telomere-to-telomere genome of Aphelenchus avenae implicates P5CS in nematode desiccation stress response
- Yali Zhang,
- Yayi Zhou,
- Yangyang Chen,
- Xueyu Wang,
- Boyan Hu,
- Shahid Siddique,
- Romnick A. Latina,
- Veronica I. Casey,
- Dexin Bo,
- Yucheng Liao,
- Min Zhang,
- Ming Sun,
- Fengjuan Zhang,
- and Dadong Dai
Genome Res. April 2026 36: 726-739; Published in Advance March 23, 2026, doi:10.1101/gr.281016.125
...identify the stress response gene P5CS in A. avenae nematodes. Aap5cs RNAi experiments demonstrate that knockdown of Aap5cs results in increased accumulation of reactive oxygen species under desiccation stress and reduced desiccation survival time, suggesting that Aap5cs plays a role in the stress response...
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Resource: Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival
- Marina Athanasouli,
- Tobias Loschko,
- and Christian Rödelsperger
Genome Res. October 2025 35: 2363-2374; Published in Advance August 5, 2025, doi:10.1101/gr.280848.125
...genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus. BMC Genomics 21: 708. doi:10.1186/s12864-020-07100-0 ↵Athanasouli M, Akduman N, Röseler W, Theam P, Rödelsperger C. 2023. Thousands of Pristionchus pacificus orphan genes were integrated...
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Method: Highly efficient and scarless genome editing via essential gene-coupled homology-directed repair
- Joo Hye Yeo,
- Hyongbum Henry Kim,
- Sang Ho Oh,
- and Jinu Lee
Genome Res. April 15, 2026 gr.281194.125; Published in Advance April 15, 2026, doi:10.1101/gr.281194.125
...strategies, including small-molecule treatments and marker-based 32 selection, are constrained by cytotoxicity, genomic scarring, and inconsistent 33 performance. Here, we present ESS-HDR (essential gene–supported scarless HDR), a 34 robust, drug- and marker-free platform that selectively enriches HDR...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...al. 2024). However, whether genomic mechanisms govern these slow rates of molecular evolution, and whether they are restricted to a subset of the , such as protein-coding genes (Takezaki 2018; Brownstein et al. 2024) and fourfold degenerate sites (Venkatesh et al. 2014; Gemmell et al. 2020), remain...
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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
...studies have sought to catalog driver events occurring in hundreds of cancer genes across different tumor types (Martincorena and Campbell 2015; Chung et al. 2016; Tokheim and Karchin 2019; Dietlein et al. 2020; Kumar et al. 2020; The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium 2020...
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Research: A genome-wide survey reveals a diverse array of enhancers coordinates the Drosophila innate immune response
- Lianne B Cohen,
- Tamara Hadzic,
- Caitlin Sauer,
- Julia R Gibbs,
- and Zeba Wunderlich
Genome Res. April 15, 2026 gr.281432.125; Published in Advance April 15, 2026, doi:10.1101/gr.281432.125
...Methods 547 Genome-wide reporter library construction 548 To generate a -wide reporter library, genomic DNA was isolated from both male and 549 female iso-1 flies, fragmented via sonication, and size selected (500-750 bps). To prepare and 550 clone these fragments into the the pSTARR-seq fly plasmid (AddGene...
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Research: Fusion, fission, and scrambling of the bilaterian genome in Bryozoa
- Thomas D. Lewin,
- Isabel Jiah-Yih Liao,
- Mu-En Chen,
- John D.D. Bishop,
- Peter W.H. Holland,
- and Yi-Jyun Luo
Genome Res. January 2025 35: 78-92; Published in Advance January 6, 2025, doi:10.1101/gr.279636.124
...Figure 5. Shared derived chromosome features between bryozoans and brachiopods support the Lophophorata hypothesis. (A) Chromosome-scale gene linkage between the bryozoan M. membranacea and the brachiopod L. anatina. Horizontal bars represent chromosomes. Vertical lines connect the genomic position...
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Research: Genetic exchange with an outcrossing sister species causes severe genome-wide dysregulation in a selfing Caenorhabditis nematode
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- Yongbin Li,
- Xiao Liu,
- Peter Sarkies,
- and Zhongying Zhao
Genome Res. November/December 2022 32: 2015-2027; Published in Advance November 9, 2022, doi:10.1101/gr.277205.122
...investigate this issue by using the nematode Caenorhabditis briggsae, which reproduces as a hermaphrodite, and its outcrossing sister species Caenorhabditis nigoni. We hypothesize that selfing species might develop some barriers to prevent gene intrusions through gene regulation. We therefore examined gene...
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Method: Pangenome-based genome inference using integer programming
- Ghanshyam Chandra,
- Md Helal Hossen,
- Stephan Scholz,
- Alexander T. Dilthey,
- Daniel Gibney,
- and Chirag Jain
Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
...: chirag@iisc.ac.inAbstractAffordable genotyping methods are essential in genomics. Commonly used genotyping methods primarily support single-nucleotide variants and short indels but neglect structural variants. Additionally, accuracy of read alignments to a reference is unreliable in highly polymorphic...
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Method: Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis
- Alejandro Ceron-Noriega,
- Miguel V. Almeida,
- Michal Levin,
- and Falk Butter
Genome Res. January 2023 33: 112-128; Published in Advance January 18, 2023, doi:10.1101/gr.277070.122
...of nematodes is believed to date back to ∼650–750 million years, generating a large and phylogenetically diverse group to be explored. However, for most species high-quality gene annotations are incomprehensive or missing. Combining short-read RNA sequencing with mass spectrometry–based proteomics and machine...

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