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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
.... For detailed sample identification, mycorrhizal synthesis preparation, and library construction, see the Supplemental Methods.Genome survey and assemblyIllumina reads were quality checked with FastQC v0.11.7 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and trimmed with Trimmomatic v0.39 (-phred33...
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Resource: The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
- Hsin-Yen Larry Wu,
- Isaiah D. Kaufman,
- and Polly Yingshan Hsu
Genome Res. September 2025 35: 2130-2142; Published in Advance July 22, 2025, doi:10.1101/gr.280480.125
...available TI-seq data (Willems et al. 2017), a technique similar to Ribo-seq but enriching for initiating ribosomes, which assists in the identification of translation initiation sites (Ingolia et al. 2011; Lee et al. 2012; Willems et al. 2017; Li and Liu 2020). The TI-seq data show two major peaks...
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Research: Xist upstream deletion leads to dysregulation of Xist and autosomal gene expression
- Sudeshna Majumdar,
- Lakshmi Sowjanya Bammidi,
- Hemant C. Naik,
- Avinchal Manhas,
- Runumi Baro,
- Akash Kalita,
- Amlan Jyoti Naskar,
- Sundarraj Nidharshan,
- Girija S. Bariha,
- Dimple Notani,
- and Srimonta Gayen
Genome Res. September 2025 35: 1992-2010; Published in Advance August 6, 2025, doi:10.1101/gr.279822.124
..., this region has been referred to as being conducive to retrotransposition and harbors two ribosomal protein pseudogenes (pS19X and pS12X) (Fig. 2A; Rougeulle and Avner 1996; Romer and Ashworth 2000). Notably, this region is enriched with long interspersed elements (LINEs) and short interspersed elements...
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Review: De novo gene birth and the conundrum of ORFan genes in bacteria
- Md. Hassan uz-Zaman and
- Howard Ochman
Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124
..., Ishihama Y, Mori H. 2016. Comprehensive identification of translation start sites by tetracycline-inhibited ribosome profiling. DNA Res 23: 193–201. doi:10.1093/dnares/dsw008 ↵Nayfach S, Shi ZJ, Seshadri R, Pollard KS, Kyrpides NC. 2019. New insights from uncultivated s of the global human gut microbiome...
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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
...in CGC1-specific gDNA, we also predicted genes and transcripts in CGC1 sequences shared with N2. WormBase curators have spent decades evaluating gene predictions in N2 and found many to be repetitive elements or pseudogenes. Thus, we treated these new predictions in N2-shared genomic sequence...
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Research: Variation in the fitness impact of translationally optimal codons among animals
- Florian Bénitière,
- Tristan Lefébure,
- and Laurent Duret
Genome Res. March 2025 35: 446-458; Published in Advance February 10, 2025, doi:10.1101/gr.279837.124
...that favors the transmission of G:C alleles over A:T alleles (Duret and Galtier 2009). NSPs affect all genomic compartments (coding or noncoding) and, notably, have a strong impact on SCU (e.g., Pouyet et al. 2017; Long et al. 2018). Besides NSPs, SCU can also be affected by selection. Indeed, it has been...
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Research: Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging
- Amy R. Vandiver,
- Allen Herbst,
- Paul Stothard,
- and Jonathan Wanagat
Genome Res. January 2025 35: 55-65; Published in Advance November 27, 2024, doi:10.1101/gr.279072.124
...potential differences in the distribution of mtDNA deletions between tissues. The identification of this unstudied class of mitochondrial transcripts will facilitate further studies to clarify these differences and gain insight into tissue specificity of mitochondrial genomic variation.Limitations of our...
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Resource: Generation and analysis of a mouse multitissue genome annotation atlas
- Matthew Adams and
- Christopher Vollmers
Genome Res. November 2024 34: 2108-2117; Published in Advance October 23, 2024, doi:10.1101/gr.279217.124
...DNA consensus reads—averaging 5.4 million reads per tissue for a dozen tissues. Using the Mandalorion tool, we processed these reads to generate the Tissue-level Atlas of Mouse Isoforms which is available as a trackhub for the UCSC Genome Browser and contains at least one full-length isoform for the vast...
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Resource: Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding
- Kai Li,
- Melissa L. Smith,
- J. Chris Blazier,
- Kelli J. Kochan,
- Jonathan M.D. Wood,
- Kerstin Howe,
- Anne E. Kwitek,
- Melinda R. Dwinell,
- Hao Chen,
- Julia L. Ciosek,
- Patrick Masterson,
- Terence D. Murphy,
- Theodore S. Kalbfleisch,
- and Peter A. Doris
Genome Res. November 2024 34: 2081-2093; Published in Advance November 8, 2024, doi:10.1101/gr.279292.124
..., Terence D. Murphy7, Theodore S. Kalbfleisch1 and Peter A. Doris8 1Gluck Equine Genomics Center, University of Kentucky, Lexington, Kentucky 40503, USA; 2Department of Biochemistry and Molecular Biology, University of Louisville School of Medicine, Louisville, Kentucky 40202, USA; 3Texas A&M Institute...
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Perspective: Ribosome decision graphs for the representation of eukaryotic RNA translation complexity
- Jack A.S. Tierney,
- Michał Świrski,
- Håkon Tjeldnes,
- Jonathan M. Mudge,
- Joanna Kufel,
- Nicola Whiffin,
- Eivind Valen,
- and Pavel V. Baranov
Genome Res. April 2024 34: 530-538; Published in Advance May 7, 2024, doi:10.1101/gr.278810.123
...′-untranslated regions of eukaryotic mRNAs. Science 352: 1413–1416. doi:10.1126/science.aad9868 ↵Ingolia NT, Ghaemmaghami S, Newman JRS, Weissman JS. 2009. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324: 218–223. doi:10.1126/science.1168978 ↵Ingolia...
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