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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
...Stenocereus gummosus, and D. m. sonorensis is also a columnar cacti dweller, using Stenocereus thurberi (Newby and Etges 1998). Therefore, this set of species from the buzzatii and mojavensis clusters provides an excellent model to investigate the molecular mechanisms underlying host shift evolution...
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Research: Transposable element insertions in fission yeast drive adaptation to environmental stress
- Caroline Esnault,
- Michael Lee,
- Chloe Ham,
- and Henry L. Levin
Genome Res. January 2019 29: 85-95; Published in Advance December 12, 2018, doi:10.1101/gr.239699.118
....gene.2012.07.042 ↵Chuong EB, Elde NC, Feschotte C. 2016. Regulatory evolution of innate immunity through co-option of endogenous retroviruses. Science 351: 1083–1087. doi:10.1126/science.aad5497 ↵Curcio MJ, Lutz S, Lesage P. 2015. The Ty1 LTR-retrotransposon of budding yeast, Saccharomyces cerevisiae...
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LETTER: Drosophila Euchromatic LTR Retrotransposons are Much Younger Than the Host Species in Which They Reside
- Nathan J. Bowen and
- John F. McDonald
Genome Res. September 1, 2001 11: 1527-1540; Published in Advance August 16, 2001, doi:10.1101/gr.164201
...). The main distinguishing characteristic is that some LTR retrotransposons, such as Ty1 in yeast, do not contain an envelope gene, which renders retroviruses infectious. Many LTR retrotransposons, such as gypsy from D. melanogaster , however, do encode Envelope proteins and are infectious ( Song et al. 1994...
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LETTER: Genomic Evolution of the Long Terminal Repeat Retrotransposons in Hemiascomycetous Yeasts
- Cécile Neuvéglise,
- Horst Feldmann,
- Elisabeth Bon,
- Claude Gaillardin,
- and and Serge Casaregola
Genome Res. June 1, 2002 12: 930-943; doi:10.1101/gr.219202
...retrotransposons exist in a wide range of eukaryotes including insects, plants, fungi, yeasts, and fishes. Recently, fossils of LTR retrotransposons were identified in mammals at a very low copy number ( Volff et al. 2001 ). The structure of LTR retrotransposons is comparable to that of the retroviruses...
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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
...into the of the host. LTR retrotransposons are also genetically similar to endogenous retroviruses in that they are integrated in the germline of their host. Therefore, LTR retrotransposons serve as excellent model systems for understanding the evolutionary impact that they and endogenous retroviruses have on the host...
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Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
....In plant s, the predominant association between transposons and centromeres involves retrotransposons. However, in fungi and animals, a notable connection exists between Pogo DNA elements and the centromeres. The mammalian CENP-B protein and the fission yeast Abp1, Cbh1, and Cbh2 proteins are centromere...
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Research: Accumulation and ineffective silencing of transposable elements on an avian W Chromosome
- Vera M. Warmuth,
- Matthias H. Weissensteiner,
- and Jochen B.W. Wolf
Genome Res. April 2022 32: 671-681; Published in Advance February 11, 2022, doi:10.1101/gr.275465.121
...-strand transcript, including the proteins encoded by the gag and pol genes. Over time, mutations in the host will lead to a deterioration of TE sequence and a corresponding decrease in activity. Transcribed LTR retrotransposons in our system fall predominantly into young age bins (<8% divergence from the consensus...
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Research: Retrotransposon profiling of RNA polymerase III initiation sites
- Xiaojie Qi,
- Kenneth Daily,
- Kim Nguyen,
- Haoyi Wang,
- David Mayhew,
- Paul Rigor,
- Sholeh Forouzan,
- Mark Johnston,
- Robi David Mitra,
- Pierre Baldi,
- and Suzanne Sandmeyer
Genome Res. April 2012 22: 681-692; Published in Advance January 27, 2012, doi:10.1101/gr.131219.111
...of Medicine, Washington University, St. Louis, Missouri 63108, USA Although retroviruses are relatively promiscuous in choice of integration sites, retrotransposons can display marked integration specificity. In yeast and slime mold, some retrotransposons are associated with tRNA genes (t...
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Research: Local features determine Ty3 targeting frequency at RNA polymerase III transcription start sites
- Kurt Patterson,
- Farbod Shavarebi,
- Christophe Magnan,
- Ivan Chang,
- Xiaojie Qi,
- Pierre Baldi,
- Virginia Bilanchone,
- and Suzanne B. Sandmeyer
Genome Res. August 2019 29: 1298-1309; Published in Advance June 27, 2019, doi:10.1101/gr.240861.118
...(Sultana et al. 2017; Gilbert and Feschotte 2018; Klein and O'Neill 2018). The genomic distribution of retrotransposons and retroviruses is not random (Kvaratskhelia et al. 2014; Sandmeyer et al. 2015; Lesbats et al. 2016; Sultana et al. 2017). Because sites of integration can be key determinants...
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LETTER: Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica
- Andrew J. Gentles,
- Matthew J. Wakefield,
- Oleksiy Kohany,
- Wanjun Gu,
- Mark A. Batzer,
- David D. Pollock,
- and Jerzy Jurka
Genome Res. July 2007 17: 992-1004; Published in Advance May 10, 2007, doi:10.1101/gr.6070707
...in Monodelphis than in human or mouse. In particular, 2.1% of the opossum is identified as copies of L3 elements, which is seven times higher than the 0.3% found in human. Endogenous retroviruses We identified at least 45 families of endogenous retroviruses (ERV; LTR retrotransposons) that have recognizable...

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