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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
...Dynamic evolution of satellite DNAs drastically differentiates the s of Tribolium sibling species Damira Veseljak, Evelin Despot-Slade, Marin Volarić, Lucija Horvat, Tanja Vojvoda Zeljko, Nevenka Meštrović and Brankica Mravinac Ruđer Bošković Institute, Division of Molecular Biology, HR-10000...
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Research: Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events
- Marin Volarić,
- Evelin Despot-Slade,
- Damira Veseljak,
- Brankica Mravinac,
- and Nevenka Meštrović
Genome Res. November 2024 34: 1878-1894; Published in Advance October 22, 2024, doi:10.1101/gr.279225.124
...Long-read assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events Marin Volarić1,2, Evelin Despot-Slade1,2, Damira Veseljak1, Brankica Mravinac1 and Nevenka Meštrović1 1Ruđer Bošković Institute, 10000 Zagreb, Croatia...
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Perspective: The genetics and epigenetics of satellite centromeres
- Paul B. Talbert and
- Steven Henikoff
Genome Res. April 2022 32: 608-615; Published in Advance March 31, 2022, doi:10.1101/gr.275351.121
...of primate s: satellite DNA repeats and their evolutionary dynamics. Cells 9: 2714. doi:10.3390/cells9122714 ↵Alexandrov I, Kazakov A, Tumeneva I, Shepelev V, Yurov Y. 2001. α-Satellite DNA of primates: old and new families. Chromosoma 110: 253–266. doi:10.1007/s004120100146 ↵Aravind L, Iyer LM, Wu C. 2007...
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Research: Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development
- Song Zhang,
- Chao Wang,
- Shenghua Qin,
- Choulin Chen,
- Yongzhou Bao,
- Yuanyuan Zhang,
- Lingna Xu,
- Qingyou Liu,
- Yunxiang Zhao,
- Kui Li,
- Zhonglin Tang,
- and Yuwen Liu
Genome Res. December 2024 34: 2190-2202; Published in Advance October 21, 2024, doi:10.1101/gr.278344.123
...@caas.cn, liuyuwen@caas.cnAbstractSuper-enhancers (SEs) govern the expression of genes defining cell identity. However, the dynamic landscape of SEs and their critical constituent enhancers involved in skeletal muscle development remains unclear. In this study, using pig as a model, we employed cleavage under...
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Research: Birth, evolution, and transmission of satellite-free mammalian centromeric domains
- Solomon G. Nergadze,
- Francesca M. Piras,
- Riccardo Gamba,
- Marco Corbo,
- Federico Cerutti,
- Joseph G.W. McCarter,
- Eleonora Cappelletti,
- Francesco Gozzo,
- Rebecca M. Harman,
- Douglas F. Antczak,
- Donald Miller,
- Maren Scharfe,
- Giulio Pavesi,
- Elena Raimondi,
- Kevin F. Sullivan,
- and Elena Giulotto
Genome Res. June 2018 28: 789-799; Published in Advance April 30, 2018, doi:10.1101/gr.231159.117
...authors: elena.giulotto@unipv.it, kevin.sullivan@nuigalway.ie, elena.raimondi@unipv.itAbstractMammalian centromeres are associated with highly repetitive DNA (satellite DNA), which has so far hindered molecular analysis of this chromatin domain. Centromeres are epigenetically specified, and binding...
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Research: Analyses of 600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges
- John S. Sproul,
- Scott Hotaling,
- Jacqueline Heckenhauer,
- Ashlyn Powell,
- Dez Marshall,
- Amanda M. Larracuente,
- Joanna L. Kelley,
- Steffen U. Pauls,
- and Paul B. Frandsen
Genome Res. October 2023 33: 1708-1717; Published in Advance September 22, 2023, doi:10.1101/gr.277387.122
...Analyses of 600+ insect s reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges John S. Sproul1,2,3,12, Scott Hotaling4,5,12, Jacqueline Heckenhauer6,7,12, Ashlyn Powell8, Dez Marshall2, Amanda M. Larracuente3, Joanna L. Kelley4,9, Steffen U. Pauls6...
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Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
- A. Bernardo Carvalho,
- Bernard Y. Kim,
- and Fabiana Uno
Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
...reads produced by deep sequencing with state-of-the-art Nanopore (10.4 flow cells, 200× coverage) and PacBio (HiFi 50×). The same exons are accurately assembled using Illumina 67× coverage. We find that these missing exons are consistently located near simple satellite sequences, in which sequencing...
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Method: Double insertion of transposable elements provides a substrate for the evolution of satellite DNA
- Michael P. McGurk and
- Daniel A. Barbash
Genome Res. May 2018 28: 714-725; Published in Advance March 27, 2018, doi:10.1101/gr.231472.117
...—to investigating the evolutionary dynamics of repetitive DNA. But the existence of TE-derived satellites provides a potential opportunity: Rather than searching for the emergence of satellites from all possible single-copy sequences, tandems arising from repeats that are normally dispersed rather than tandemly...
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Research: Epigenetic and evolutionary features of ape subterminal heterochromatin
- DongAhn Yoo,
- Katherine M. Munson,
- and Evan E. Eichler
Genome Res. January 2026 36: 38-49; Published in Advance October 22, 2025, doi:10.1101/gr.280987.125
...of these regions in chimpanzees and gorillas. Detailed analyses of the composition of the associated terminal 32 bp satellite array from chimpanzee (termed pCht) and intervening segmental duplication (SD) spacers confirm two independent origins in the Pan and gorilla lineages. In chimpanzee and bonobo, we estimate...
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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
...(Fig. 6). TEs were detected in each of the seven assemblies, with proportions ranging from 15.6% to 19.3% of a ’s content (Supplemental Figs. S12–S18). The seven s contained LINEs, low complexity families, LTR elements, satellites and simple repeats, SINEs. The TE distribution was highly biased along...

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