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Method: Robust 16S rRNA classification based on a compressed LCA index
- Omar Ahmed,
- Christina Boucher,
- and Ben Langmead
Genome Res. December 2025 35: 2650-2660; Published in Advance August 25, 2025, doi:10.1101/gr.279846.124
...in CliffyCliffy can perform both read-level classification and abundance profiling. Given a sequencing read, Cliffy begins at the end of the read and performs maximal left-extension using a backward search on the tree-ordered text of the taxonomy. Once the backward search range is empty, Cliffy resets...
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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
...the new s, we show that gars have the slowest rates of genomic structural and sequence evolution of all vertebrates. In species of the two living gar genera Atractosteus and Lepisosteus, 83.35% of the s remain identical even though they diverged over 100 million years ago. Genome size variation among gars...
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Resource: Whole-genome sequencing of diverse 351 cultured prokaryotes including as-yet-unsequenced type strains
- Shingo Kato,
- Sachiko Masuda,
- Arisa Shibata,
- Takashi Itoh,
- Mitsuo Sakamoto,
- Ken Shirasu,
- and Moriya Ohkuma
Genome Res. April 2026 36: 875-884; Published in Advance April 7, 2026, doi:10.1101/gr.281026.125
...305-0074, Japan; 2Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan Corresponding authors: skato@riken.jp, mohkuma@riken.jpAbstractGenome sequences provide fundamental information for both basic and applied life sciences. Whole...
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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
...enhancers from the S2* cells have an overlap of at least 100 bp with 123 STARR-seq enhancers found in S2 cells (Arnold et al. 2013). Overall, the consensus enhancers 124 resemble previously identified Drosophila enhancers, in both sequence and genomic regions. 125 126 To determine if we identified enhancers...
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Research: Age-dependent mutational loads in human tRNA genes are tumor-specific and result in chimeric tRNA sequences that could disrupt the genetic code
- Marina Murillo,
- Marina Salvadores,
- Aina Vaquer Picó,
- Lina Tsapanou,
- Adrian Gabriel Torres,
- Fran Supek,
- and Lluis Ribas de Pouplana
Genome Res. April 15, 2026 gr.281022.125; Published in Advance April 15, 2026, doi:10.1101/gr.281022.125
...the genomic coordinates of tDNAs we used the 375 RIdeogram v0.2.2 package from R. Genomic distances between consecutive tDNAs were computed 376 18 and used to plot their cumulative distribution using ecdf (empirical cumulative distribution function) 377 (Supplemental Fig. S1A). Taking into account the profile...
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Research: Phylogenetic relatedness rather than aquatic habitat fosters horizontal transfer of transposable elements in animals
- Héloïse Muller,
- Rosina Savisaar,
- Jean Peccoud,
- Sylvain Charlat,
- and Clément Gilbert
Genome Res. September 2025 35: 2011-2022; Published in Advance August 8, 2025, doi:10.1101/gr.280432.125
..., to evaluate the suspected positive effects of aquatic habitat and of phylogenetic relatedness on HTT. Among the 6043 independent HTT events recovered, the vast majority (>85%) involve DNA transposons, of which Mariner-like and hAT-like elements have the highest rates of horizontal transfer and of intragenomic...
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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
...biology approach, we compile the first cross-species interactome of P. pacificus by statistically linking bacterial genomic and nematode transcriptomic data.ResultsSequencing of 84 bacteria establishes the genomic basis to study host–microbe interactionsIn order to establish a phylogenomic framework...
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Method: Polyomino reconstructs spatial transcriptomic profiles with single-cell resolution via a region-allocation method
- Quanyou Cai,
- Lihui Lin,
- Xin Liu,
- and Jiekai Chen
Genome Res. November 2025 35: 2513-2526; Published in Advance October 22, 2025, doi:10.1101/gr.280532.125
...Visium spots by leveraging structural priors and expression profiles, without requiring parametric assumptions.View larger version: In this window In a new window Figure 5. Analysis in colorectal cancer liver metastasis data. (A) Spatial transcriptomics sequencing data (Visium) of colorectal cancer liver...
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Method: Identification of the shortest species-specific oligonucleotide sequences
- Ioannis Mouratidis,
- Maxwell A. Konnaris,
- Nikol Chantzi,
- Candace S.Y. Chan,
- Michail Patsakis,
- Kimonas Provatas,
- Austin Montgomery,
- Fotis A. Baltoumas,
- Congzhou M. Sha,
- Manvita Mareboina,
- Georgios A. Pavlopoulos,
- Dionysios V. Chartoumpekis,
- and Ilias Georgakopoulos-Soares
Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
...-mer profiles (Bize et al. 2021). Previous efforts have identified sequences that are clustered in specific taxonomies or are conserved; examples include OrthoVenn3, which identifies orthologous clusters and detects conserved and variable genomic structures (Sun et al. 2023) and Telobase, which provides...
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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
...derivative of the N2 strain. We use improved long-read sequencing and manual assembly of 43 recalcitrant genomic regions to overcome deficiencies of prior N2 and VC2010 assemblies and to assemble tandem repeat loci, including a 772 kb sequence for the 45S rRNA genes. Although many differences from earlier...
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