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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
...et al. 2001; Casola et al. 2008).TE insertions in S. pombe have also been discussed in the context of adaptation to environmental disturbance, or stress response. TE expression has been shown to be induced under stress conditions (Chen et al. 2003; Sehgal et al. 2007), and an enhancer sequence...
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Research: Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres
- Ursula Oggenfuss,
- Robert T. Todd,
- Natthapon Soisangwan,
- Bailey Kemp,
- Alison Guyer,
- Annette Beach,
- and Anna Selmecki
Genome Res. April 2025 35: 824-838; Published in Advance October 22, 2024, doi:10.1101/gr.279301.124
...with higher amounts of standing genetic variation, including single-nucleotide polymorphisms and structural variants (SVs), adapt more quickly than those with lower standing genetic variation (Feurtey et al. 2023). SVs consist of deletions, insertions, translocations, duplications, inversions, and complex...
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Research: Continuous infiltration and evolutionary trajectory of nuclear organelle DNA in Oryza
- Chenbo Gong,
- Yicheng Huang,
- Mengmeng Liu,
- Yong Zhou,
- Yinwei Xu,
- Nahed Mohammed,
- Xintong Qiao,
- Andrea Zuccolo,
- Weibo Xie,
- Rod A. Wing,
- Jianwei Zhang,
- Fei Zhou,
- and Yongjun Lin
Genome Res. June 2025 35: 1349-1363; Published in Advance April 25, 2025, doi:10.1101/gr.279609.124
...also increase the complexity of NORGs.NORG fragmentation triggered by transposable elementsCollinearity analysis revealed sequence insertions in 71 ONGs in one or more accessions, which resulted in the splitting of single NORGs into multiple fragments with very large distances between each other...
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Research: Rates and spectra of de novo structural mutations in Chlamydomonas reinhardtii
- Eugenio López-Cortegano,
- Rory J. Craig,
- Jobran Chebib,
- Eniolaye J. Balogun,
- and Peter D. Keightley
Genome Res. January 2023 33: 45-60; Published in Advance December 12, 2022, doi:10.1101/gr.276957.122
....keightley@ed.ac.ukAbstractGenetic variation originates from several types of spontaneous mutation, including single-nucleotide substitutions, short insertions and deletions (indels), and larger structural changes. Structural mutations (SMs) drive evolution and are thought to play major roles in evolutionary adaptation, speciation...
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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
...assessments. Our study establishes a fundamental genomic resource for future research on truffle genomics and showcases a clear example of how establishment and self-perpetuating expansion of heterochromatin can drive massive size variation owing to activity of selfish genetic elements.Transposable elements...
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PERSPECTIVE: Fish genomics and biology
- Hugues Roest Crollius and
- Jean Weissenbach
Genome Res. December 2005 15: 1675-1682; doi:10.1101/gr.3735805
...evolution of one of the two copies, in agreement with the latter model and supporting the view that (and hence gene) duplication is a driving force behind the emergence of functional novelty. The ancestral teleost duplication provided its owner with a powerful toolkit to adapt and diversify: twice as many...
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Resource: Long-read sequencing reveals intra-species tolerance of substantial structural variations and new subtelomere formation in C. elegans
- Chuna Kim,
- Jun Kim,
- Sunghyun Kim,
- Daniel E. Cook,
- Kathryn S. Evans,
- Erik C. Andersen,
- and Junho Lee
Genome Res. June 2019 29: 1023-1035; Published in Advance May 23, 2019, doi:10.1101/gr.246082.118
...that harsh environmental stimuli or stresses, yet to be identified, may have induced Chr VR–specific DSBs in CB4856 ancestors and that these stimuli activated the intrinsic subtelomeric recombination mechanisms by which a new subtelomere was formed by ALT and BIR. We did not fail to notice that telomerase...
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Review: Origins, evolution, and phenotypic impact of new genes
- Henrik Kaessmann
Genome Res. October 2010 20: 1313-1326; Published in Advance July 22, 2010, doi:10.1101/gr.101386.109
...these copies after acquisition or evolution of promoters in their 59 flanking regions that may drive their transcription. (Pink rightangled arrow) TSS, (transparent pink box) additionally transcribed flanking sequence at the insertion site. 1314 Genome Research www..org Kaessmann Duplication of noncoding RNAs...
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PERSPECTIVE: The opossum genome: Insights and opportunities from an alternative mammal
- Paul B. Samollow
Genome Res. August 2008 18: 1199-1215; doi:10.1101/gr.065326.107
...and the functional attributes of their components. Comparative analyses using the opossum genome have already provided a wealth of new evidence regarding the importance of noncoding elements in the evolution of mammalian genomes, the role of transposable elements in driving genomic innovation, and the relationships...

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