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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
...and manual methods to build a curated TE library for each species based on the classification of TEs (Wicker et al. 2007). The method was designed to perform polishing steps in both TE consensus and copies to remove artifacts (see Methods). The total number of TE consensuses (LTRs separated from internal...
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Research: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
- Rita Tam,
- Mareike Möller,
- Runpeng Luo,
- Zhenyan Luo,
- Ashley Jones,
- Sambasivam Periyannan,
- John P. Rathjen,
- and Benjamin Schwessinger
Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
...diverse and enriched with LTR retrotransposonsWe set out to identify Pst104E's centromeric regions and analyzed their sequence composition. Basidiomycete centromeres are often characterized by hypermethylated TE-rich and gene-poor regions (Guin et al. 2020). We estimated their positions from the Hi...
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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
...,B), with one characterized by the insertion of a nonrepetitive genomic region of 480 bp of unknown origin, followed by a solo-LTR (Supplemental Fig. S12C,D). On the other hand, 5S rDNA genes present lower sequence similarity levels that can drop down to 80.8% of identity between 5S_14 and 5S_22 paralogs...
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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
...; Wlodzimierz et al. 2023b), whereas in other s, retrotransposons correspond to the CENH3-occupied sequences themselves (Fig. 1E; Table 1). For example, monocot centromeres frequently contain a high frequency of Gypsy-LTR chromovirus retrotransposons, including CRM in maize, CRR in rice, and Cereba and Quinta...
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Research: Evolution of genome structure in the Drosophila simulans species complex
- Mahul Chakraborty,
- Ching-Ho Chang,
- Danielle E. Khost,
- Jeffrey Vedanayagam,
- Jeffrey R. Adrion,
- Yi Liao,
- Kristi L. Montooth,
- Colin D. Meiklejohn,
- Amanda M. Larracuente,
- and J.J. Emerson
Genome Res. March 2021 31: 380-396; Published in Advance February 9, 2021, doi:10.1101/gr.263442.120
...(Drosophila 12 Genomes Consortium 2007; Lerat et al. 2011; Kofler et al. 2015; Bargues and Lerat 2017). Non-LTR retrotransposons comprise the majority (52%) of the old TEs found in all four mel-complex species, whereas DNA transposons comprise most (71%) of the younger fixed TE sequences found only in the sim...
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Research: Transposable elements drive the evolution of metazoan zinc finger genes
- Jonathan N. Wells,
- Ni-Chen Chang,
- John McCormick,
- Caitlyn Coleman,
- Nathalie Ramos,
- Bozhou Jin,
- and Cédric Feschotte
Genome Res. August 2023 33: 1325-1339; Published in Advance September 15, 2023, doi:10.1101/gr.277966.123
...by LTR elements (odds ratio = 6.56, P-value = 1.2 × 10−8, Fisher's exact test) (Supplemental Fig. 10A). Because LTRs include many of the youngest TE families in the zebrafish (Chang et al. 2022), we reasoned that their enrichment among up-regulated genes and TE families may reflect a tendency for young...
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Resource: A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes
- Jing Liu,
- Zongji Wang,
- Jing Li,
- Luohao Xu,
- Jiaqi Liu,
- Shaohong Feng,
- Chunxue Guo,
- Shengchan Chen,
- Zhanjun Ren,
- Jinpeng Rao,
- Kai Wei,
- Yuezhou Chen,
- Erich D. Jarvis,
- Guojie Zhang,
- and Qi Zhou
Genome Res. March 2021 31: 497-511; Published in Advance January 6, 2021, doi:10.1101/gr.271569.120
...-range linkage information (Fig. 1C). This was reflected by the increased annotated repeat content (9.9% vs. 7.2%) of droZJU1.0 versus droNov1 s, which is mainly concentrated at several long terminal repeat (LTR) retrotransposon families (Supplemental Fig. S2). We annotated a total of 20,823 consensus gene...
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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
...as is standard for RNA-seq analysis of genes. After normalization based on total counts, we determined the expression of all TE elements within hippocampal nuclei (Fig. 1C). Although passenger transcripts detected expression of long-terminal repeat containing elements (LTR), LINEs, satellite RNA, and SINEs, bona...
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Research: Transposon accumulation at xenobiotic gene family loci in aphids
- Tobias Baril,
- Adam Pym,
- Chris Bass,
- and Alex Hayward
Genome Res. October 2023 33: 1718-1733; Published in Advance October 18, 2023, doi:10.1101/gr.277820.123
..., such as LTR retrotransposons, in altering host gene expression (Chung et al. 2007). This may suggest that other processes beyond TE-mediated increases in expression are involved in the patterns of enrichment we uncover, although it is entirely possible that the DNA TEs involved also contain sequences relevant...
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Resource: Structural variants in 3000 rice genomes
- Roven Rommel Fuentes,
- Dmytro Chebotarov,
- Jorge Duitama,
- Sean Smith,
- Juan Fernando De la Hoz,
- Marghoob Mohiyuddin,
- Rod A. Wing,
- Kenneth L. McNally,
- Tatiana Tatarinova,
- Andrey Grigoriev,
- Ramil Mauleon,
- and Nickolai Alexandrov
Genome Res. May 2019 29: 870-880; Published in Advance April 16, 2019, doi:10.1101/gr.241240.118
...) families of transposable elements (Fig. 1C). Peaks at 237, 433, and 466 bp consisted of the OsT38 family of Tc1-mariner (Lu et al. 2012) elements, mPing elements (Jiang et al. 2003; Naito et al. 2014), and the long terminal repeat (LTR) of the gypsy-type retrotransposon RIRE2 (Ohtsubo et al. 1999...
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