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Research: Centromere location in Arabidopsis is unaltered by extreme divergence in CENH3 protein sequence
- Shamoni Maheshwari,
- Takayoshi Ishii,
- C. Titus Brown,
- Andreas Houben,
- and Luca Comai
Genome Res. March 2017 27: 471-478; Published in Advance February 21, 2017, doi:10.1101/gr.214619.116
...shown that centromeres built on L. oleraceum CENH3 are deficient in comparison to wild type, because when outcrossed, they missegregate dramatically. We also tested A. thaliana centromeres assembled with Z. mays CENH3 in crosses to wild type and observed extensive missegregation leading to seed death...
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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
...DNA-rich s of two closely related Tribolium insects that produce sterile hybrids. In Tribolium freemani, we identify 135 satDNAs, accounting for 38.7% of the . Comparative analysis with the Tribolium castaneum satellitome reveals that the drastic difference occurs in their centromeric regions, which share...
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Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
.... The embryo sac contains the egg cell, which is fertilized by pollen to produce progeny seed. The green arrows indicate the theoretical path a selfish centromere could follow to overtransmit itself in a non-Mendelian manner, causing meiotic drive. (B) StainedGlass sequence identity heat maps comparing CEN1...
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Research: Efficient neocentromere formation is suppressed by gene conversion to maintain centromere function at native physical chromosomal loci in Candida albicans
- Jitendra Thakur and
- Kaustuv Sanyal
Genome Res. April 2013 23: 638-652; Published in Advance February 25, 2013, doi:10.1101/gr.141614.112
...(3–5 kb) in Chr5 and Chr1 deletion experiments ranging from 6 to 12 kb (see the coordinates given above). These results, taken together, strongly suggest that CEN-proximal sites are the most preferred sites for centromere seeding in C. albicans. Real-time qPCR analysis revealed significant reduction...
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Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
- Yao Wang,
- Dong Yu,
- Yue Mei,
- ZhiDa Fu,
- Jian Lin,
- Di Wu,
- Yuan Yang,
- and Hongli Yan
Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
...observed in only two paired nontumor samples (Fig. 5A–I; Supplemental Table S2). Ideograms of major HBV-mediated interchromosomal translocations (supported by three or more chimeric reads) revealed that these events frequently resulted in telomere or centromere deletion and occasionally led to dual...
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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
...definition of satellite DNA refers to clusters of tandem repetitions extending for several megabases, the tandem repeat expansions that we observed at these five centromeres may well be considered as an early seed of chromosome-specific centromeric satellites. In this view, these five neocentromeres cannot...
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Method: Genetic complexity of killer-cell immunoglobulin-like receptor genes in human pangenome assemblies
- Tsung-Kai Hung,
- Wan-Chi Liu,
- Sheng-Kai Lai,
- Hui-Wen Chuang,
- Yi-Che Lee,
- Hong-Ye Lin,
- Chia-Lang Hsu,
- Chien-Yu Chen,
- Ya-Chien Yang,
- Jacob Shujui Hsu,
- and Pei-Lung Chen
Genome Res. August 2024 34: 1211-1223; Published in Advance September 9, 2024, doi:10.1101/gr.278358.123
...-quality assemblies from the Human Pan Reference Consortium (HPRC), we present a novel bioinformatic tool, the structural KIR annoTator (SKIRT), to investigate gene diversity and facilitate precise KIR allele analysis. In 47 HPRC-phased assemblies, SKIRT identifies a recurrent novel KIR2DS4/3DL1 fusion gene...
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Research: Small polymorphisms are a source of ancestral bias in structural variant breakpoint placement
- Peter A. Audano and
- Christine R. Beck
Genome Res. January 2024 34: 7-19; Published in Advance January 4, 2024, doi:10.1101/gr.278203.123
...by chance near SV breakpoints after the SV occurred. An additional 11 (15%) segregated with the rightmost breakpoint but were also identified in non-SV alleles, indicating either the SV or the SNV might be recurrent, and of these, two (18%) reached significance (P < 0.01, FET).A model for breakpoint bias...
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Research: Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary
- Satyam P. Srivastav,
- Cédric Feschotte,
- and Andrew G. Clark
Genome Res. May 2024 34: 711-724; Published in Advance May 15, 2024, doi:10.1101/gr.278062.123
...to the origin of piCs. We propose that piC evolution begins with the emergence of piRNAs from individual insertions of a few select TE families prone to seed new piCs that subsequently expand by accretion of insertions from most other TE families during evolution to form larger “trap” clusters. Our study shows...
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Method: Phased nanopore assembly with Shasta and modular graph phasing with GFAse
- Ryan Lorig-Roach,
- Melissa Meredith,
- Jean Monlong,
- Miten Jain,
- Hugh E. Olsen,
- Brandy McNulty,
- David Porubsky,
- Tessa G. Montague,
- Julian K. Lucas,
- Chris Condon,
- Jordan M. Eizenga,
- Sissel Juul,
- Sean K. McKenzie,
- Sara E. Simmonds,
- Jimin Park,
- Mobin Asri,
- Sergey Koren,
- Evan E. Eichler,
- Richard Axel,
- Bruce Martin,
- Paolo Carnevali,
- Karen H. Miga,
- and Benedict Paten
Genome Res. March 2024 34: 454-468; Published in Advance April 16, 2024, doi:10.1101/gr.278268.123
...in comparison to phasing time, as homology detection primarily relies on locality-sensitive hashing (see Methods) to find candidate matches between nodes. Both of these steps are multithreaded, but the phasing step does not benefit from running with more threads than there are independent samples (random seeds...

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