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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
...Corresponding authors: mhufford@iastate.edu, cnhirsch@umn.eduAbstractMuch of the profound interspecific variation in content has been attributed to transposable elements (TEs). To explore the extent of TE variation within species, we developed an optimized open-source algorithm, panEDTA, to de novo annotate TEs...
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Research: Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis
- Alexandra Dallaire,
- Bethan F. Manley,
- Maya Wilkens,
- Iliana Bista,
- Clement Quan,
- Edouard Evangelisti,
- Charles R. Bradshaw,
- Navin B. Ramakrishna,
- Sebastian Schornack,
- Falk Butter,
- Uta Paszkowski,
- and Eric A. Miska
Genome Res. December 2021 31: 2290-2302; Published in Advance November 12, 2021, doi:10.1101/gr.275752.121
...adaptation. Here, we assessed the potential of transposable elements for generating such genomic diversity. The dynamic expression of TEs during Rhizophagus irregularis spore development suggests ongoing TE activity. We find Mutator-like elements located near genes belonging to highly expanded gene families...
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Research: Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements
- Yuyun Zhang,
- Zijuan Li,
- Yu'e Zhang,
- Kande Lin,
- Yuan Peng,
- Luhuan Ye,
- Yili Zhuang,
- Meiyue Wang,
- Yilin Xie,
- Jingyu Guo,
- Wan Teng,
- Yiping Tong,
- Wenli Zhang,
- Yongbiao Xue,
- Zhaobo Lang,
- and Yijing Zhang
Genome Res. December 2021 31: 2276-2289; Published in Advance September 9, 2021, doi:10.1101/gr.275658.121
.... 2017; Zhao et al. 2018). The read density distributions for TFBSs in TEs and non-TE regions were very similar (Fig. 4B). Transposable elements are generally repressed by DNA methylation, with low chromatin accessibility. In this study, we observed that 40,807 collapsed TFBSs (with overlapping TFBSs...
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Resource: Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish
- Hyung Joo Lee,
- Yiran Hou,
- Ju Heon Maeng,
- Nakul M. Shah,
- Yujie Chen,
- Heather A. Lawson,
- Hongbo Yang,
- Feng Yue,
- and Ting Wang
Genome Res. July 2022 32: 1424-1436; Published in Advance June 1, 2022, doi:10.1101/gr.276052.121
...probability greater than 0.95 were used as CTCF-bound sites. To confirm whether those sites were bound by CTCF, we used CTCF ChIP-seq data of zebrafish 24 h postfertilization (GEO; GSE133437) (Pérez-Rico et al. 2020). Heat maps of ATAC insert read counts and CTCF ChIP-seq signals over -wide CTCF motif sites...
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LETTER: Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: New functional implications for MITEs
- Hanhui Kuang,
- Chellappan Padmanabhan,
- Feng Li,
- Ayako Kamei,
- Pudota B. Bhaskar,
- Shu Ouyang,
- Jiming Jiang,
- C. Robin Buell,
- and Barbara Baker
Genome Res. January 2009 19: 42-56; Published in Advance November 26, 2008, doi:10.1101/gr.078196.108
...Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: New functional implications for MITEs Hanhui Kuang 1 , 2 , 6 , Chellappan Padmanabhan 1 , 2 , 6 , Feng Li 1 , 2 , 6...
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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
...of transposable elements (TEs), their association with specific sequences, their chromosomal distribution, and their evolution. Using homology-based sequence identification, we found that the sequenced strain of S. pombe contained only one family of full-length transposons. This family, Tf2, consisted of 13 full...
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Research: Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species
- Damira Veseljak,
- Evelin Despot-Slade,
- Marin Volarić,
- Lucija Horvat,
- Tanja Vojvoda Zeljko,
- Nevenka Meštrović,
- and Brankica Mravinac
Genome Res. November 2025 35: 2445-2460; Published in Advance September 16, 2025, doi:10.1101/gr.280516.125
...-independent identification of satDNAs, we resequenced its using Illumina sequencing. The Illumina reads were processed by the TAREAN pipeline, which predicted satDNA candidates from short reads via graph-based clustering (Supplemental Table S1). The TAREAN-predicted sequences were mapped to the T. freemani reference...
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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: Haplotype-resolved telomere-to-telomere genome of Aphelenchus avenae implicates P5CS in nematode desiccation stress response
- Yali Zhang,
- Yayi Zhou,
- Yangyang Chen,
- Xueyu Wang,
- Boyan Hu,
- Shahid Siddique,
- Romnick A. Latina,
- Veronica I. Casey,
- Dexin Bo,
- Yucheng Liao,
- Min Zhang,
- Ming Sun,
- Fengjuan Zhang,
- and Dadong Dai
Genome Res. April 2026 36: 726-739; Published in Advance March 23, 2026, doi:10.1101/gr.281016.125
...for their exceptional tolerance to dehydration, and multiple genes related to this trait have been identified. However, the absence of a chromosome-scale, high-contiguity for A. avenae has been a limitation in the -wide identification of gene families potentially involved in desiccation tolerance. In this study, we...
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RESEARCH: Transposable Elements and Genome Organization: A Comprehensive Survey of Retrotransposons Revealed by the Complete Saccharomyces cerevisiae Genome Sequence
- Jin M. Kim,
- Swathi Vanguri,
- Jef D. Boeke,
- Abram Gabriel,
- and Daniel F. Voytas
Genome Res. May 1, 1998 8: 464-478; doi:10.1101/gr.8.5.464
...repeats (LTRs) or LTR fragments. Overall, retrotransposon sequences constitute &gt;377 kb or 3.1% of the genome. Independent evolution of retrotransposon sequences was evidenced by the identification of a single-base pair insertion/deletion that distinguishes the highly similar Ty1 and Ty2 LTRs...

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