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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
...different preferences. Transposable elements are a source of genetic novelty between populations and species, driving rapid adaptive evolution. However, the extent of TEs’ contribution to host shift remains unexplored. Here, we perform genomic and transcriptomic analyses in six s of cactophilic species...
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Research: Unexpectedly low recombination rates and presence of hotspots in termite genomes
- Turid Everitt,
- Tilman Rönneburg,
- Daniel Elsner,
- Anna Olsson,
- Yuanzhen Liu,
- Tuuli Larva,
- Judith Korb,
- and Matthew T. Webster
Genome Res. May 2025 35: 1124-1137; Published in Advance March 20, 2025, doi:10.1101/gr.279180.124
...and recombination in both s (Spearman's ρ = 0.051, P < 2.22 × 10−16 for M. bellicosus; Spearman's ρ = 0.055, P < 2.22 × 10−16 for C. secundus). SINE and LINE elements are also only weakly associated with recombination rate in both s (SINEs: Spearman's ρ = −0.012, not significant for M. bellicosus, and Spearman's ρ...
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Research: KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution
- Kai Otsuka,
- Akihiko Sakashita,
- So Maezawa,
- Richard M. Schultz,
- and Satoshi H. Namekawa
Genome Res. March 2025 35: 417-431; Published in Advance March 12, 2025, doi:10.1101/gr.279924.124
...of peaks versus the theoretically expected numbers of peaks. Binomial test. (***) P < 0.001. (E–G) Violin plots showing the data distribution of normalized H3K9me3 signals at each KZFP-bound LINEs (E), LTRs (F), and SINEs (G) compared with enrichment at all interspersed copies in KIT+ spermatogonia...
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Resource: Inversion variants in human and primate genomes
- Claudia Rita Catacchio,
- Flavia Angela Maria Maggiolini,
- Pietro D'Addabbo,
- Miriana Bitonto,
- Oronzo Capozzi,
- Martina Lepore Signorile,
- Mattia Miroballo,
- Nicoletta Archidiacono,
- Evan E. Eichler,
- Mario Ventura,
- and Francesca Antonacci
Genome Res. May 18, 2018 ; Published in Advance May 18, 2018, doi:10.1101/gr.234831.118
...that overlap with segmental duplications at their breakpoints in only 41% of the cases (seven out of 17) (Supplemental Table S3). Sequence analyses of the remaining macaque inversions show that 47% (eight out of 17) contain SINEs or LINEs at their breakpoints (Supplemental Table S8). We annotated...
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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...of fragments acting as enhancers, whereas another SINE superfamily (RST) was significantly enriched but with a much lower effect size estimate (Fig. 6D). The transcriptionally inducing fragments from these three superfamilies were enriched for a total of 38 unique TF binding motifs (RLC = 12, RST = 8, and RLX...
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Method: Identification of bona fide B2 SINE retrotransposon transcription through single-nucleus RNA-seq of the mouse hippocampus
- Sara B. Linker,
- Lynne Randolph-Moore,
- Kalyani Kottilil,
- Fan Qiu,
- Baptiste N. Jaeger,
- Jerika Barron,
- and Fred H. Gage
Genome Res. November 2020 30: 1643-1654; Published in Advance October 29, 2020, doi:10.1101/gr.262196.120
...-of concept analysis by exploring SINE expression in response to behaviorally relevant neuronal activity.The SINE family of TEs, which includes Alu and SVA in primates and B1 and B2 in rodents, is involved in biological processes such as cellular stress in response to heat shock, viral infection, or DNA...
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Research: High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis
- Yuan Lu,
- Edward Rice,
- Kang Du,
- Susanne Kneitz,
- Magali Naville,
- Corentin Dechaud,
- Jean-Nicolas Volff,
- Mikki Boswell,
- William Boswell,
- LaDeana Hillier,
- Chad Tomlinson,
- Kremitzki Milin,
- Ronald B. Walter,
- Manfred Schartl,
- and Wesley C. Warren
Genome Res. April 2023 33: 557-571; Published in Advance May 5, 2023, doi:10.1101/gr.277434.122
...element; (RLC) Copia; (RLG) Gypsy; (RLX) LTR retrotransposon; (RPX) Penelope; (RYX) DIRS; (RXX) unclassified retrotransposon; (RIX) LINE; (RSX) SINE. (B) TE landscapes in Xiphophorus species and medaka species. TE insertions were compared between each other for each identified TE family; the distribution...
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Research: Large palindromes on the primate X Chromosome are preserved by natural selection
- Emily K. Jackson,
- Daniel W. Bellott,
- Ting-Jan Cho,
- Helen Skaletsky,
- Jennifer F. Hughes,
- Tatyana Pyntikova,
- and David C. Page
Genome Res. August 2021 31: 1337-1352; Published in Advance July 21, 2021, doi:10.1101/gr.275188.120
...To ensure consistency in palindrome annotation between species, we began by re-annotating human X palindromes. We identified palindromic amplicons by searching the reference sequence of the human X Chromosome for inverted repeats >8 kb in length (which excludes repetitive elements such as LINEs and SINEs...
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Research: Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
- David Thybert,
- Maša Roller,
- Fábio C.P. Navarro,
- Ian Fiddes,
- Ian Streeter,
- Christine Feig,
- David Martin-Galvez,
- Mikhail Kolmogorov,
- Václav Janoušek,
- Wasiu Akanni,
- Bronwen Aken,
- Sarah Aldridge,
- Varshith Chakrapani,
- William Chow,
- Laura Clarke,
- Carla Cummins,
- Anthony Doran,
- Matthew Dunn,
- Leo Goodstadt,
- Kerstin Howe,
- Matthew Howell,
- Ambre-Aurore Josselin,
- Robert C. Karn,
- Christina M. Laukaitis,
- Lilue Jingtao,
- Fergal Martin,
- Matthieu Muffato,
- Stefanie Nachtweide,
- Michael A. Quail,
- Cristina Sisu,
- Mario Stanke,
- Klara Stefflova,
- Cock Van Oosterhout,
- Frederic Veyrunes,
- Ben Ward,
- Fengtang Yang,
- Golbahar Yazdanifar,
- Amonida Zadissa,
- David J. Adams,
- Alvis Brazma,
- Mark Gerstein,
- Benedict Paten,
- Son Pham,
- Thomas M. Keane,
- Duncan T. Odom,
- and Paul Flicek
Genome Res. April 2018 28: 448-459; Published in Advance March 21, 2018, doi:10.1101/gr.234096.117
...LTR and SINE elements and appear to have greatly accelerated activity when compared to the rate found in primates (ANCOVA, P-value < 10−3) (Fig. 2B,C). This result is consistent with previous reports showing increased lineage-specific LINE activity in mouse as compared to human (Mouse Genome...
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Method: Epigenomic differences in the human and chimpanzee genomes are associated with structural variation
- Xiaoyu Zhuo,
- Alan Y. Du,
- Erica C. Pehrsson,
- Daofeng Li,
- and Ting Wang
Genome Res. February 2021 31: 279-290; Published in Advance December 10, 2020, doi:10.1101/gr.263491.120
..., duplications, inversions, insertions, and translocations, are responsible for the majority of genetic differences within populations and between species. The 1000 Genomes Project estimated that an individual carries a median of 8.9 Mb of SVs versus 3.6 Mb of single-nucleotide variants (SNVs) (Sudmant et al...

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