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Research: Natural diversity of telomere length distributions across 100 Saccharomyces cerevisiae strains
- Clotilde Garrido,
- Cintia Gómez-Muñoz,
- Etienne Kornobis,
- Nicolas Agier,
- Oana Ilioaia,
- Gilles Fischer,
- and Zhou Xu
Genome Res. March 2026 36: 522-533; Published in Advance January 16, 2026, doi:10.1101/gr.281132.125
..., relatively little is known about TL regulation and distribution in natural yeast strains. Recent large-scale population genomics studies revealed great genetic diversity encompassing, beyond single-nucleotide polymorphisms, structural variations, aneuploidies, and polyploidies (Peter et al. 2018; O...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...of meiotic crossing over, the variation patterns suggest mechanisms such as unequal sister chromatid exchange. We also examine the prevalence and scale of concerted evolution in the histone and Stellate clusters and discuss the mechanisms underlying these observed patterns.Tandem repetitive sequences...
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Method: High-resolution genotype-free mapping of genetic variation with CRI-SPA-Map
- Sheila Lutz,
- Megan Lawler,
- Samuel Amidon,
- and Frank W Albert
Genome Res. March 23, 2026 gr.281514.125; Published in Advance March 23, 2026, doi:10.1101/gr.281514.125
...the identification of 58 individual genes and variants whose variation shapes complex phenotypes challenging. 59 The yeast Saccharomyces cerevisiae is a key model for the dissection of genetically complex 60 traits (Liti and Louis 2012). The uniformly high meiotic recombination rate along the 61 coupled...
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Resource: Chromosome-level subgenome-aware de novo assembly provides insight into Saccharomyces bayanus genome divergence after hybridization
- Cory Gardner,
- Junhao Chen,
- Christina Hadfield,
- Zhaolian Lu,
- David Debruin,
- Yu Zhan,
- Maureen J. Donlin,
- Tae-Hyuk Ahn,
- and Zhenguo Lin
Genome Res. November 2024 34: 2133-2146; Published in Advance September 17, 2024, doi:10.1101/gr.279364.124
...diversification, adaptation, and speciation. To better understand the changes that occurred in the different subs of a hybrid species and how they facilitate adaptation, we have completed chromosome-level de novo assemblies of all chromosomes for a recently formed hybrid yeast, Saccharomyces bayanus strain CBS380...
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Research: Highly complete long-read genomes reveal pangenomic variation underlying yeast phenotypic diversity
- Cory A. Weller,
- Ilya Andreev,
- Michael J. Chambers,
- Morgan Park,
- NISC Comparative Sequencing Program,
- Joshua S. Bloom,
- and Meru J. Sadhu
Genome Res. May 2023 33: 729-740; Published in Advance May 1, 2023, doi:10.1101/gr.277515.122
...Highly complete long-read s reveal pangenomic variation underlying yeast phenotypic diversity Cory A. Weller1,8,10, Ilya Andreev1,8,11, Michael J. Chambers1,8, Morgan Park2, NISC Comparative Sequencing Program2,9, Joshua S. Bloom3,4,5,6,7 and Meru J. Sadhu1 1Computational and Statistical Genomics...
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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
...of ribosomal RNA genes are observed in other species such as budding yeast and humans (Hori et al. 2023), we investigated how the 45S rDNA array of CGC1 differs from arrays in other C. elegans strains. For this, we analyzed publicly available PacBio HiFi read data sets from two strains “DLW N2 Bristol...
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Method: Delineating yeast cleavage and polyadenylation signals using deep learning
- Emily Kunce Stroup and
- Zhe Ji
Genome Res. July 2024 34: 1066-1080; Published in Advance June 24, 2024, doi:10.1101/gr.278606.123
...on multiple alignments (Siepel et al. 2005; Rhind et al. 2011). We examined the conservation of S. pombe poly(A) sequences using the alignments across four Schizosaccharomyces yeasts, the conservation of S. cerevisiae sites across seven Saccharomyces yeasts, and the human site conservation across 100...
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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
...between tRNA abundance and their respective gene copy number, with an adjusted R2 > 0.91 for yeasts (Saccharomyces cerevisiae and Schizosaccharomyces pombe), 0.79 for D. melanogaster, and 0.62 for H. sapiens (Behrens et al. 2021). These results suggest that tRNA gene copy number is a good predictor of t...
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Research: Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages
- Tracy Jiaye Lee,
- Yu-Ching Liu,
- Wei-An Liu,
- Yu-Fei Lin,
- Hsin-Han Lee,
- Huei-Mien Ke,
- Jen-Pan Huang,
- Mei-Yeh Jade Lu,
- Chia-Lun Hsieh,
- Kuo-Fang Chung,
- Gianni Liti,
- and Isheng Jason Tsai
Genome Res. May 2022 32: 864-877; Published in Advance March 31, 2022, doi:10.1101/gr.276286.121
...diversity sheltered from human influences, making it a powerful model system in microbial ecology.The yeast genus Saccharomyces, which includes S. cerevisiae, is a powerful model system for revealing patterns of genomic variation underlying reproductive isolation and adaptation in eukaryotic microorganisms...
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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
...to high homogenization within a single cluster (Ganley and Kobayashi 2011; Hori et al. 2021; Garcia et al. 2024). The complex IGS region, similarly to what is observed in humans and budding yeast (Ganley and Kobayashi 2011; Hori et al. 2021), is composed of tandemly arranged repeats and can undergo...

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