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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
...). For the X Chromosome (Muller element A), our assembly also introduced ∼3.9 Mb of new sequence, including ∼2.76 Mb of heterochromatin sequence adjacent to the rDNA array. For every major repeat category across all chromosomes except the dot, the HiFi assembly of iso-1 recovered more than previous assemblies...
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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
...Figure 5. Detection of extrachromosomal circular DNA (eccDNA) molecules containing Cast1, Cast2, Cast5, and Cast6 satDNA. Results of T. castaneum genomic DNA separation in 2D electrophoresis are shown on the left, and Southern blot hybridization with specific probes for each Cast element is shown...
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Research: Single-molecule sequencing resolves the detailed structure of complex satellite DNA loci in Drosophila melanogaster
- Daniel E. Khost,
- Danna G. Eickbush,
- and Amanda M. Larracuente
Genome Res. May 2017 27: 709-721; Published in Advance April 3, 2017, doi:10.1101/gr.213512.116
...the Doc5 elements, it does not appear that the movement of Rsp was mediated by TE activity. We speculate that intra-sister chromatid exchange events in the major Rsp locus—in this case, the most centromere-proximal repeats (Fig. 4A)—may have generated an extrachromosomal circular DNA, perhaps amplified...
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Research: The rate and spectrum of new mutations in mice inferred by long-read sequencing
- Eugenio López-Cortegano,
- Jobran Chebib,
- Anika Jonas,
- Anastasia Vock,
- Sven Künzel,
- Peter D. Keightley,
- and Diethard Tautz
Genome Res. January 2025 35: 43-54; Published in Advance December 2, 2024, doi:10.1101/gr.279982.124
.... 2021). However, SNORD clusters consist of tandem repeats that are substantially longer than the PacBio reads obtained here, and we were unable to detect evidence of copy-number variation in these loci. De novo extrachromosomal circular DNA (eccDNA) variants have previously been observed...
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Research: Telomerase-independent survival leads to a mosaic of complex subtelomere rearrangements in Chlamydomonas reinhardtii
- Frédéric Chaux,
- Nicolas Agier,
- Clotilde Garrido,
- Gilles Fischer,
- Stephan Eberhard,
- and Zhou Xu
Genome Res. September 2023 33: 1582-1598; Published in Advance August 14, 2023, doi:10.1101/gr.278043.123
...-1.Extrachromosomal telomeric DNA molecules, predominantly found as double-stranded or single-stranded circles, are detected in ALT tumors and proposed to be involved in telomere maintenance (Cesare and Reddel 2010). To detect potential circular DNA containing telomere sequences, we performed rolling circle...
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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
...of eccDNAs.View larger version: In this window In a new window Figure 7. Experimental evidence of TfSat01 and TfSat03 satDNA repeats in the extrachromosomal circular DNA (eccDNA) molecules and in prophase I associations of nonhomologous chromosomes. (A) 2D gel electrophoresis analysis of the eccDNAs in T...
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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
...the centromere of the Drosophila minichromosome Dp1187 . A combination of mapping and partial sequencing was used to infer a sequence assembly consisting of islands of complex DNA embedded in large regions of simple sequence repeat. Here, we have used gene targeting to introduce exogenous plasmids at various...

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