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Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
- Aleix Palahí i Torres,
- Lars Höök,
- Karin Näsvall,
- Daria Shipilina,
- Christer Wiklund,
- Roger Vila,
- Peter Pruisscher,
- and Niclas Backström
Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
...explanatory variables (GC content, gene density, DNA transposon, SINE, LINE, and LTR retrotransposon densities) on the recombination rate. This model revealed an overall significant association between the recombination rate and the explanatory variables (F(6) = 10.77, df = 603, P = 2.13 × 10...
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Research: Epigenetic activation of meiotic recombination near Arabidopsis thaliana centromeres via loss of H3K9me2 and non-CG DNA methylation
- Charles J. Underwood,
- Kyuha Choi,
- Christophe Lambing,
- Xiaohui Zhao,
- Heïdi Serra,
- Filipe Borges,
- Joe Simorowski,
- Evan Ernst,
- Yannick Jacob,
- Ian R. Henderson,
- and Robert A. Martienssen
Genome Res. April 2018 28: 519-531; Published in Advance March 12, 2018, doi:10.1101/gr.227116.117
...al. 2015). At the fine-scale, plant crossover hotspots occur at gene promoters and terminators, and recombination is promoted by euchromatic modifications, including histone variant H2A.Z (Choi et al. 2013; Hellsten et al. 2013; Wijnker et al. 2013; Shilo et al. 2015). Acquisition of DNA methylation...
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Letter: Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization
- Xiyin Wang,
- Haibao Tang,
- John E. Bowers,
- and Andrew H. Paterson
Genome Res. June 2009 19: 1026-1032; Published in Advance April 16, 2009, doi:10.1101/gr.087288.108
...). Second, repetitive elements are often enriched in pericentromeric regions, which reduce large-scale sequence similarity between homoeologous segments by inducing DNA rearrangements and mutations. In both rice and sorghum, long-terminal repeat (LTR) elements are substantially enriched...
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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
...; Naish et al. 2021). High-copy tandem repeats are traditionally termed satellites, as following density gradient centrifugation, the repeats form satellite bands owing to different buoyant density compared with the bulk genomic DNA (Kit 1961; Thakur et al. 2021; Altemose 2022). Typically, individual...
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REVIEW: Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health
- Victoria P. Belancio,
- Dale J. Hedges,
- and Prescott Deininger
Genome Res. March 2008 18: 343-358; Published in Advance February 6, 2008, doi:10.1101/gr.5558208
...exceptions, the majority of this repetitive DNA consists of class I retrotransposon elements, which copy themselves in the via an RNA-based intermediate. Within the human , the non-long-terminal-repeat (non-LTR) retrotransposon, L1, is the dominant family of elements driving amplification ( Fig. 1...
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Research: Differences in activity and stability drive transposable element variation in tropical and temperate maize
- Shujun Ou,
- Armin Scheben,
- Tyler Collins,
- Yinjie Qiu,
- Arun S. Seetharam,
- Claire C. Menard,
- Nancy Manchanda,
- Jonathan I. Gent,
- Michael C. Schatz,
- Sarah N. Anderson,
- Matthew B. Hufford,
- and Candice N. Hirsch
Genome Res. August 2024 34: 1140-1153; Published in Advance September 9, 2024, doi:10.1101/gr.278131.123
...regions that coincide with late DNA replication during the S phase, whereas the ji family is found in early replication regions that are usually enriched with genes (Wear et al. 2017). Together, Young tropical amplifying Ty3 and Young temperate removing Ty1 LTR families contributed nearly half (42...
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LETTER: Doubling genome size without polyploidization: Dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice
- Benoit Piegu,
- Romain Guyot,
- Nathalie Picault,
- Anne Roulin,
- Abhijit Saniyal,
- Hyeran Kim,
- Kristi Collura,
- Darshan S. Brar,
- Scott Jackson,
- Rod A. Wing,
- and Olivier Panaud
Genome Res. October 2006 16: 1262-1269; Published in Advance September 8, 2006, doi:10.1101/gr.5290206
...of DNA and contributing to size reduction in Arabidopsis and rice ( Petrov 2002 ; Ma et al. 2004 ). Analysis by sequence alignment of Wallabi , Kangourou , and RIRE1 LTR-retrotransposon families from the three fully sequenced BAC clones ( Fig. 3 ) revealed the presence of limited small deletions...
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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
...are not detectable in the current version. C. albicans TE families include DNA transposons and retrotransposons with LINE and LTR-retrotransposons (Wicker et al. 2007). LTR-retrotransposons contain LTR on each side of the element, which can undergo ectopic recombination, removing the majority of the retrotransposon...
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Letter: Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression
- Jesse D. Hollister and
- Brandon S. Gaut
Genome Res. August 2009 19: 1419-1428; Published in Advance May 28, 2009, doi:10.1101/gr.091678.109
...against TEs near genes has not been elucidated fully for any organism and particularly for these species in which ectopic recombination may be infrequent. Epigenetic pathways also shape the proliferation and accumulation of TE sequences. In many eukaryotic lineages, TEs are targeted for DNA methylation...
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Research: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster
- Anna Grandchamp,
- Lucas Kühl,
- Marie Lebherz,
- Kathrin Brüggemann,
- John Parsch,
- and Erich Bornberg-Bauer
Genome Res. June 2023 33: 872-890; Published in Advance July 13, 2023, doi:10.1101/gr.277482.122
..., multiple studies across many taxa showed that some novel genes arise de novo, that is, from previously noncoding DNA. To characterize the underlying mutations that allowed de novo gene emergence and their order of occurrence, homologous regions must be detected within noncoding sequences in closely related...

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