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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
...showing the presence (red) or deletion (green) of specific terminal chromosomal fragments in various ditelosomic lines. PCR amplifications were conducted using primers targeting regions flanking the breakpoints in Chromosome 1, 6, and 7. (E) Copy number variations (CNVs) in genomic regions adjacent...
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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
...maintain a high level of genetic variation in the absence of meiosis. Notably, C. albicans copy number breakpoints colocalize with SVs and repetitive regions, further suggesting that the presence of heterozygous SVs could lead to chromosomal rearrangements (Todd et al. 2019). SVs and TEs in particular...
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Research: Genetic and phenotypic intra-species variation in Candida albicans
- Matthew P. Hirakawa,
- Diego A. Martinez,
- Sharadha Sakthikumar,
- Matthew Z. Anderson,
- Aaron Berlin,
- Sharvari Gujja,
- Qiandong Zeng,
- Ethan Zisson,
- Joshua M. Wang,
- Joshua M. Greenberg,
- Judith Berman,
- Richard J. Bennett,
- and Christina A. Cuomo
Genome Res. March 2015 25: 413-425; Published in Advance December 11, 2014, doi:10.1101/gr.174623.114
...is a commensal fungus of the human gastrointestinal tract and a prevalent opportunistic pathogen. To examine diversity within this species, extensive genomic and phenotypic analyses were performed on 21 clinical C. albicans isolates. Genomic variation was evident in the form of polymorphisms, copy number...
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Perspective: Short arms of human acrocentric chromosomes and the completion of the human genome sequence
- Stylianos E. Antonarakis
Genome Res. April 2022 32: 599-607; Published in Advance March 31, 2022, doi:10.1101/gr.275350.121
...these short arms of Chromosomes 13, 14, 15, 21, and 22 contain the ribosomal DNA (rDNA) genes, which are of paramount importance for human biology. The sequences of SAACs show an extensive variation in the copy number of the various repetitive elements, the full extent of which is currently unknown...
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Research: Organelle DNA rearrangement mapping reveals U-turn-like inversions as a major source of genomic instability in Arabidopsis and humans
- Éric Zampini,
- Étienne Lepage,
- Samuel Tremblay-Belzile,
- Sébastien Truche,
- and Normand Brisson
Genome Res. May 2015 25: 645-654; Published in Advance March 23, 2015, doi:10.1101/gr.188573.114
..., and the small-single copy region (SSC) are depicted as a long gray bar, a red bar, and a short gray bar, respectively. (B) Rearrangement breakpoint positions of wild-type Arabidopsis thaliana (Col-0) mitochondria. Each tile represents a region spanning 10 kb along each axis. Tile intensity represents the number...
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Resource: Single haplotype assembly of the human genome from a hydatidiform mole
- Karyn Meltz Steinberg,
- Valerie A. Schneider,
- Tina A. Graves-Lindsay,
- Robert S. Fulton,
- Richa Agarwala,
- John Huddleston,
- Sergey A. Shiryev,
- Aleksandr Morgulis,
- Urvashi Surti,
- Wesley C. Warren,
- Deanna M. Church,
- Evan E. Eichler,
- and Richard K. Wilson
Genome Res. December 2014 24: 2066-2076; Published in Advance November 4, 2014, doi:10.1101/gr.180893.114
.... 2068 Genome Research www..org (Hewitt et al. 1994). Repeat copy-number variation is associated with facioscapulohumeral muscular dystrophy (MIM 158900) (Bosnakovski et al. 2008). Both of these genes are now annotated in GRCh38 with information from the CHM1 data. Clinical allele analysis Using data...
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ARTICLE: Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution
- Stephen Richards,
- Yue Liu,
- Brian R. Bettencourt,
- Pavel Hradecky,
- Stan Letovsky,
- Rasmus Nielsen,
- Kevin Thornton,
- Melissa J. Hubisz,
- Rui Chen,
- Richard P. Meisel,
- Olivier Couronne,
- Sujun Hua,
- Mark A. Smith,
- Peili Zhang,
- Jing Liu,
- Harmen J. Bussemaker,
- Marinus F. van Batenburg,
- Sally L. Howells,
- Steven E. Scherer,
- Erica Sodergren,
- Beverly B. Matthews,
- Madeline A. Crosby,
- Andrew J. Schroeder,
- Daniel Ortiz-Barrientos,
- Catharine M. Rives,
- Michael L. Metzker,
- Donna M. Muzny,
- Graham Scott,
- David Steffen,
- David A. Wheeler,
- Kim C. Worley,
- Paul Havlak,
- K. James Durbin,
- Amy Egan,
- Rachel Gill,
- Jennifer Hume,
- Margaret B. Morgan,
- George Miner,
- Cerissa Hamilton,
- Yanmei Huang,
- Lenée Waldron,
- Daniel Verduzco,
- Kerstin P. Clerc-Blankenburg,
- Inna Dubchak,
- Mohamed A.F. Noor,
- Wyatt Anderson,
- Kevin P. White,
- Andrew G. Clark,
- Stephen W. Schaeffer,
- William Gelbart,
- George M. Weinstock,
- and Richard A. Gibbs
Genome Res. January 2005 15: 1-18; doi:10.1101/gr.3059305
...constitutes a single repetitive element family that has numerous degenerate copies in the D. pseudoobscura . The higher frequency of the breakpoint motif within the junction sequences on Muller elements C and E led to higher breakpoint similarity than Muller elements A, B, and D when a nonparametric Kruskal...
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Research: Gene amplification as double minutes or homogeneously staining regions in solid tumors: Origin and structure
- Clelia Tiziana Storlazzi,
- Angelo Lonoce,
- Maria C. Guastadisegni,
- Domenico Trombetta,
- Pietro D'Addabbo,
- Giulia Daniele,
- Alberto L'Abbate,
- Gemma Macchia,
- Cecilia Surace,
- Klaas Kok,
- Reinhard Ullmann,
- Stefania Purgato,
- Orazio Palumbo,
- Massimo Carella,
- Peter F. Ambros,
- and Mariano Rocchi
Genome Res. September 2010 20: 1198-1206; Published in Advance July 14, 2010, doi:10.1101/gr.106252.110
...,000 probes for the detection of copy number variation. Sample preparation, hybridization, and scanning were performed using GeneChip Instrument System hardware according to the manufacturer’s specifications (Affymetrix). Quality controls and LOH analysis have been performed using Affymetrix Genotyping...
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LETTER: Segmental duplications and evolutionary plasticity at tumor chromosome break-prone regions
- Eva Darai-Ramqvist,
- Agneta Sandlund,
- Stefan Müller,
- George Klein,
- Stefan Imreh,
- and Maria Kost-Alimova
Genome Res. March 2008 18: 370-379; Published in Advance January 29, 2008, doi:10.1101/gr.7010208
...found that the borders of evolutionarily conserved chromosomal regions often coincide with tumor-associated deletion breakpoints within human 3p12-p22. Moreover, a detailed analysis of a frequently deleted region at 3p21.3 (CER1) showed associations between tumor breaks and gene duplications. We now...
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ARTICLE: Structure and Evolution of the Smith-Magenis Syndrome Repeat Gene Clusters, SMS-REPs
- Sung-Sup Park,
- Paweł Stankiewicz,
- Weimin Bi,
- Christine Shaw,
- Jessica Lehoczky,
- Ken Dewar,
- Bruce Birren,
- and James R. Lupski
Genome Res. May 1, 2002 12: 729-738; doi:10.1101/gr.82802
.... A third copy, the middle SMS-REP, has been mapped in 17p11.2 between the proximal and distal SMS-REPs ( Chen et al. 1997 ). The chromosome 17p11.2 genomic region is involved in several other rearrangements. Isodicentric chromosomes idic(17)(p11), with breakpoints mapping within or just adjacent to the SMS...

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