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Research: Reactivation of transposable elements following hybridization in fission yeast
- Sergio Tusso,
- Fang Suo,
- Yue Liang,
- Li-Lin Du,
- and Jochen B.W. Wolf
Genome Res. February 2022 32: 324-336; Published in Advance December 14, 2021, doi:10.1101/gr.276056.121
...spanning a wide range of ancestral admixture proportions. A comprehensive TE inventory revealed exclusive presence of long terminal repeat (LTR) retrotransposons. Sequence analysis of active full-length elements, as well as solo LTRs, revealed a complex history of homologous recombination. Population...
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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
....zambonelli@unibo.itAbstractThe genus Tuber (family: Tuberaceae) includes the most economically valuable ectomycorrhizal (ECM), truffle-forming fungi. Previous genomic analyses revealed that massive transposable element (TE) proliferation represents a convergent genomic feature of ECM fungi, including Tuberaceae. Repetitive sequences...
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Method: Double insertion of transposable elements provides a substrate for the evolution of satellite DNA
- Michael P. McGurk and
- Daniel A. Barbash
Genome Res. May 2018 28: 714-725; Published in Advance March 27, 2018, doi:10.1101/gr.231472.117
...Michael P. McGurk and Daniel A. Barbash Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA Corresponding author: dab87@cornell.eduAbstractEukaryotic s are replete with repeated sequences in the form of transposable elements (TEs) dispersed across...
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ARTICLE: Retrotransposons and Their Recognition of pol II Promoters: A Comprehensive Survey of the Transposable Elements From the Complete Genome Sequence of Schizosaccharomyces pombe
- Nathan J. Bowen,
- I. King Jordan,
- Jonathan A. Epstein,
- Valerie Wood,
- and Henry L. Levin
Genome Res. September 2003 13: 1984-1997; doi:10.1101/gr.1191603
...Retrotransposons and Their Recognition of pol II Promoters: A Comprehensive Survey of the Transposable Elements From the Complete Genome Sequence of Schizosaccharomyces pombe Nathan J. Bowen 1 , 5 , I. King Jordan 2 , Jonathan A. Epstein 3 , Valerie...
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Research: Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments
- Barbara Dunn,
- Chandra Richter,
- Daniel J. Kvitek,
- Tom Pugh,
- and Gavin Sherlock
Genome Res. May 2012 22: 908-924; Published in Advance February 27, 2012, doi:10.1101/gr.130310.111
...substantial copy number variation among S. cerevisiae strains for subtelomeric regions, transposable elements, mitochondrial and episomal s, and in genomic regions not present in the reference S288c strain. Little is known about the latter regions, making this the first characterization of these regions...
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LETTER: Chromodomains direct integration of retrotransposons to heterochromatin
- Xiang Gao,
- Yi Hou,
- Hirotaka Ebina,
- Henry L. Levin,
- and Daniel F. Voytas
Genome Res. March 2008 18: 359-369; Published in Advance February 6, 2008, doi:10.1101/gr.7146408
...-poor, transposon-rich regions of their host s. ( A ) The genomic distribution of M. grisea MAGGY (group I) insertions. For each of the 75 MAGGY insertions in the completed sequence ( Dean et al. 2005 ), 20-kb windows at the site of insertion (10 kb upstream and downstream) were surveyed for genes and transposable...
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LETTER: Recombination Rate and the Distribution of Transposable Elements in the Drosophila melanogaster Genome
- Carène Rizzon,
- Gabriel Marais,
- Manolo Gouy,
- and Christian Biémont
Genome Res. March 1, 2002 12: 400-407; Published in Advance February 15, 2002, doi:10.1101/gr.210802
...: 7704 – 7711 . ↵ Kidwell M.G. , Evgen'ev M.B. ( 1999 ) How valuable are model organisms for transposable element studies? Genetica 107 : 103 – 111 . ↵ Kim J.M. , Vanguri S. , Boeke J.D. , Gabriel A. , Voytas D.F. ( 1998 ) Transposable elements and organization: A comprehensive survey of retrotransposons...
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Research: A genome-wide transcriptome and translatome analysis of Arabidopsis transposons identifies a unique and conserved genome expression strategy for Ty1/Copia retroelements
- Stefan Oberlin,
- Alexis Sarazin,
- Clément Chevalier,
- Olivier Voinnet,
- and Arturo Marí-Ordóñez
Genome Res. September 2017 27: 1549-1562; Published in Advance August 7, 2017, doi:10.1101/gr.220723.117
...and transcriptionally active transposons in A. thaliana is illustrated by our comprehensive analysis of the cotranscriptional and translational features of Ty1/Copia elements, a family of young and active retroelements in plant s, and how such features impact their biology. Genome-wide transcript profiling revealed...
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LETTER: Reconstruction of the genome origins and evolution of the hybrid lager yeast Saccharomyces pastorianus
- Barbara Dunn and
- Gavin Sherlock
Genome Res. October 2008 18: 1610-1623; Published in Advance September 11, 2008, doi:10.1101/gr.076075.108
...important lager beer yeast Saccharomyces pastorianus is such a hybrid, formed by the union of Saccharomyces cerevisiae and Saccharomyces bayanus -related yeasts; efforts to understand its complex genome, searching for both biological and brewing-related insights, have been underway since its hybrid...
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Research: Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus
- Nikolaos Vakirlis,
- Véronique Sarilar,
- Guénola Drillon,
- Aubin Fleiss,
- Nicolas Agier,
- Jean-Philippe Meyniel,
- Lou Blanpain,
- Alessandra Carbone,
- Hugo Devillers,
- Kenny Dubois,
- Alexandre Gillet-Markowska,
- Stéphane Graziani,
- Nguyen Huu-Vang,
- Marion Poirel,
- Cyrielle Reisser,
- Jonathan Schott,
- Joseph Schacherer,
- Ingrid Lafontaine,
- Bertrand Llorente,
- Cécile Neuvéglise,
- and Gilles Fischer
Genome Res. July 2016 26: 918-932; Published in Advance May 31, 2016, doi:10.1101/gr.204420.116
..., or the transposable element content. However, we found a clear positive correlation between sizes and the cumulative sizes of Reconstruction of history in Lachancea Genome Research 919 www..org intergenic regions and introns (Fig. 1B; Supplemental Fig. S3). The largest size variation in intergenic regions equals...

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