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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...chromosome integrity, piRNA clusters encoding host defenses against selfish elements, and virtually the entire Y Chromosome. These regions, formed by highly similar tandem arrays, pose significant challenges for experimental and computational studies, impeding sequence-level descriptions essential...
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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
....The Cys2-His2 zinc finger (ZNF) is a short nucleic acid binding domain widespread in eukaryotes. ZNFs are often arranged in tandemly repeated arrays, resulting in proteins with versatile nucleic acid binding ability (Wolfe et al. 2000; Klug 2010; Najafabadi et al. 2017). In metazoans, tandem-repeat ZNF...
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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
...satellites can arise.Eukaryotic s are inundated with two types of repetitive sequences: transposable elements (TEs), which are dispersed by a variety of transposition mechanisms, and satellite sequences, which are tandemly repeated sequences that expand, contract, and are homogenized by recombination events...
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LETTER: Abundance, Distribution, and Transcriptional Activity of Repetitive Elements in the Maize Genome
- Blake C. Meyers,
- Scott V. Tingey,
- and Michele Morgante
Genome Res. October 1, 2001 11: 1660-1676; Published in Advance September 20, 2001, doi:10.1101/gr.188201
...: In this window In a new window Figure 2. Number of hybridizing repetitive elements versus BAC clone size and complexity. BACs (652) from a high-density array were scored for the presence or absence of seven common retroelements (Huck, Prem-2, Opie, Grande, Prem-1, Zeon-1, and ANLI). ( A ) Repetitive elements...
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Chicken Special/Letters: The repetitive landscape of the chicken genome
- Thomas Wicker,
- Jon S. Robertson,
- Stefan R. Schulze,
- F. Alex Feltus,
- Vincent Magrini,
- Jason A. Morrison,
- Elaine R. Mardis,
- Richard K. Wilson,
- Daniel G. Peterson,
- Andrew H. Paterson,
- and Robert Ivarie
Genome Res. January 2005 15: 126-136; Published in Advance July 15, 2004, doi:10.1101/gr.2438004
...by their abundance in the HR Cot sequences. The extremely repetitive nature of these tandem arrays causes a major problem for the final assembly, as demonstrated by the fact that almost all identified instances of CNM or PO41 are located on the virtual chromosome ChrUn and are immediately flanked by gaps...
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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
...dispersed throughout the The ribosomal-only contigs 19 to 29 (Fig. 2A) display a conserved structural pattern characterized by 45S rDNA genes (18S–5.8S–28S) flanked by a large array of tandemly repeated elements (Fig. 2B,C). We could identify other characteristic motifs: a 160 bp sequence at the 3′ end...
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LETTER: Uneven chromosome contraction and expansion in the maize genome
- Rémy Bruggmann,
- Arvind K. Bharti,
- Heidrun Gundlach,
- Jinsheng Lai,
- Sarah Young,
- Ana C. Pontaroli,
- Fusheng Wei,
- Georg Haberer,
- Galina Fuks,
- Chunguang Du,
- Christina Raymond,
- Matt C. Estep,
- Renyi Liu,
- Jeffrey L. Bennetzen,
- Agnes P. Chan,
- Pablo D. Rabinowicz,
- John Quackenbush,
- W. Brad Barbazuk,
- Rod A. Wing,
- Bruce Birren,
- Chad Nusbaum,
- Steve Rounsley,
- Klaus F.X. Mayer,
- and Joachim Messing
Genome Res. October 2006 16: 1241-1251; Published in Advance August 10, 2006, doi:10.1101/gr.5338906
...intergenic regions and the genes themselves relative to rice. Intergenic regions The intergenic regions in all three chromosomes are composed of a mixture of low-copy noncoding sequences, also referred to as nonassigned intergenic sequences, and repetitive DNA elements. To separate these two categories, we...
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ARTICLE: The Small Chromosomes of Trypanosoma brucei Involved in Antigenic Variation Are Constructed Around Repetitive Palindromes
- Bill Wickstead,
- Klaus Ersfeld,
- and Keith Gull
Genome Res. June 2004 14: 1014-1024; doi:10.1101/gr.2227704
...and subtelomeric repeats, and other repetitive elements such as the 70-bp repeat. Of these classes, the most common seems to be telomeric repeats, which appear to start close to the end of nonrepetitive regions (confirmed by the limited sequence data available for these regions) and show considerable heterogeneity...
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LETTER: Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium
- Jennifer S. Hawkins,
- HyeRan Kim,
- John D. Nason,
- Rod A. Wing,
- and Jonathan F. Wendel
Genome Res. October 2006 16: 1252-1261; Published in Advance September 5, 2006, doi:10.1101/gr.5282906
...representing different Gossypium s and one phylogenetic outgroup View this table: In this window In a new window Table 2. Repetitive element copy number and density estimates Several conserved coding domains for diverse repetitive sequences were recovered from the WGS libraries when queried against Arabidopsis...
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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
....Satellite DNAs (satDNAs) are the most abundant and rapidly evolving noncoding DNA of all eukaryotic s. In contrast to other groups of repetitive elements such as interspersed transposable elements (TEs), which are scattered throughout the , satDNAs are characterized by monomer sequences tandemly arranged...
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