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Research: Large tandem duplications affect gene expression, 3D organization, and plant–pathogen response
- Ariadna Picart-Picolo,
- Stefan Grob,
- Nathalie Picault,
- Michal Franek,
- Christel Llauro,
- Thierry Halter,
- Tom R. Maier,
- Edouard Jobet,
- Julie Descombin,
- Panpan Zhang,
- Vijayapalani Paramasivan,
- Thomas J. Baum,
- Lionel Navarro,
- Martina Dvořáčková,
- Marie Mirouze,
- and Frédéric Pontvianne
Genome Res. November 2020 30: 1583-1592; Published in Advance October 8, 2020, doi:10.1101/gr.261586.120
...on the short arm of Chromosome 4 (hk4s), a large heterochromatic region outside the pericentromeres, and a euchromatic region distal to the knob. Other TDDOs range in size from 60 to 370 kb long and are present on Chromosomes 1, 2, 4, and 5 (Fig. 1B). The absence/presence of TDDO4, the largest duplication...
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Method: HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
- Sergey Nurk,
- Brian P. Walenz,
- Arang Rhie,
- Mitchell R. Vollger,
- Glennis A. Logsdon,
- Robert Grothe,
- Karen H. Miga,
- Evan E. Eichler,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. September 2020 30: 1291-1305; Published in Advance August 14, 2020, doi:10.1101/gr.263566.120
...correction, and aggressive false overlap filtering. We benchmark HiCanu with a focus on the recovery of haplotype diversity, major histocompatibility complex (MHC) variants, satellite DNAs, and segmental duplications. For diploid human s sequenced to 30× HiFi coverage, HiCanu achieved superior accuracy...
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Research: Evidence for the fixation of gene duplications by positive selection in Drosophila
- Margarida Cardoso-Moreira,
- J. Roman Arguello,
- Srikanth Gottipati,
- L.G. Harshman,
- Jennifer K. Grenier,
- and Andrew G. Clark
Genome Res. June 2016 26: 787-798; Published in Advance April 12, 2016, doi:10.1101/gr.199323.115
...described, LD varies between populations, between the X and the autosomes, and between pericentromeric and normally recombining regions of chromosomes (Grenier et al. 2015). Therefore, we investigated the distribution of population-specific LD among SNPs located 5′ and 3′ for all duplications in our data...
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Research: Adaptation of centromeres to breakage through local genomic and epigenomic remodeling in wheat
- Jingwei Zhou,
- Yuhong Huang,
- Huan Ma,
- Yiqian Chen,
- Chuanye Chen,
- Fangpu Han,
- and Handong Su
Genome Res. November 2025 35: 2461-2471; Published in Advance September 30, 2025, doi:10.1101/gr.280913.125
...and duplications near centromere breakpoints. We reveal that the damaged centromeres possess a remarkable capacity for self-regulation, through employing structural modifications such as expansion, contraction, and neocentromere formation to maintain their functional integrity. Centromere breakage triggers...
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Research: Hominoid fission of chromosome 14/15 and the role of segmental duplications
- Giuliana Giannuzzi,
- Michele Pazienza,
- John Huddleston,
- Francesca Antonacci,
- Maika Malig,
- Laura Vives,
- Evan E. Eichler,
- and Mario Ventura
Genome Res. November 2013 23: 1763-1773; Published in Advance September 27, 2013, doi:10.1101/gr.156240.113
...–heterochromatin transition region (~20 Mb) acquired during the neocentromere establishment on chromosome 14, and find it was mainly derived through pericentromeric duplications from ancestral hominoid chromosomes homologous to human 2q14–qter and 10. Further, we show a relationship between evolutionary hotspots and low...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...chromatin modification. (B) The log2FE of H3K4me3, H3K27me3, and H3K9me3 along the euchromatic arms and pericentromeric region of Chromosome 2. Enrichment tracks from GSC-like cells are in green, whereas the tracks associated with CySC-like cells are in magenta. The distance between each mark along the x...
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ARTICLE: Interchromosomal segmental duplications of the pericentromeric region on the human Y chromosome
- Stefan Kirsch,
- Birgit Weiß,
- Tracie L. Miner,
- Robert H. Waterston,
- Royden A. Clark,
- Evan E. Eichler,
- Claudia Münch,
- Werner Schempp,
- and Gudrun Rappold
Genome Res. February 2005 15: 195-204; Published in Advance January 14, 2005, doi:10.1101/gr.3302705
...Interchromosomal segmental duplications of the pericentromeric region on the human Y chromosome Stefan Kirsch 1 , Birgit Weiß 1 , Tracie L. Miner 2 , Robert H. Waterston 2 , 5 , Royden A. Clark 3 , Evan E. Eichler 3 , Claudia...
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LETTER: A preliminary comparative analysis of primate segmental duplications shows elevated substitution rates and a great-ape expansion of intrachromosomal duplications
- Xinwei She,
- Ge Liu,
- Mario Ventura,
- Shaying Zhao,
- Doriana Misceo,
- Roberta Roberto,
- Maria Francesca Cardone,
- Mariano Rocchi,
- NISC Comparative Sequencing Program,
- Eric D. Green,
- Nicoletta Archidiacano,
- and Evan E. Eichler
Genome Res. May 2006 16: 576-583; Published in Advance April 10, 2006, doi:10.1101/gr.4949406
...support a model wherein interchromosomal duplication activity reached its peak during or after the separation of Old World monkeys and hominoid lineage (∼25 million years [Myr]). During this time, many of the duplicative transpositions of euchromatic DNA to pericentromeric and subtelomeric regions...
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Research: Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres
- Ursula Oggenfuss,
- Robert T. Todd,
- Natthapon Soisangwan,
- Bailey Kemp,
- Alison Guyer,
- Annette Beach,
- and Anna Selmecki
Genome Res. April 2025 35: 824-838; Published in Advance October 22, 2024, doi:10.1101/gr.279301.124
...with higher amounts of standing genetic variation, including single-nucleotide polymorphisms and structural variants (SVs), adapt more quickly than those with lower standing genetic variation (Feurtey et al. 2023). SVs consist of deletions, insertions, translocations, duplications, inversions, and complex...
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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
...into long arrays. Previous studies on many animal and plant species indicate preferential localization of satDNAs in the (peri)centromeric heterochromatin (Plohl et al. 2014). Heterochromatin represents a highly compact gene-poor specialized chromatin structure that is distinct from the gene...
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