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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
...of Sciences, Beijing 100101, China; 4University of the Chinese Academy of Sciences, Beijing 100049, China ↵5 These authors contributed equally to this work. Corresponding author: shandong@mail.hzau.edu.cnAbstractCentromeres, characterized by their unique chromatin attributes, are indispensable...
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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
...clinical isolate, indicating that SVs represent a significant source of intraspecies genetic variation. We identify multiple, distinct SVs at the centromeres of Chromosome 4 and Chromosome 5, including inversions and transposon polymorphisms. These two chromosomes are often aneuploid in drug...
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Method: scSHEFT enables multiomics label transfer from scRNA-seq to scATAC-seq through dual alignment
- Zhitao Huang,
- Ruiqing Zheng,
- Pengzhen Jia,
- Xuhua Yan,
- Jinmiao Chen,
- and Min Li
Genome Res. February 2026 36: 387-396; Published in Advance January 20, 2026, doi:10.1101/gr.280410.125
...information. To achieve a balance between interomics alignment and intraomics heterogeneity, we propose a dual alignment strategy. Specifically, scSHEFT employs an anchor-based approach to align interomics anchor pairs and a contrastive-based strategy to preserve cellular heterogeneity within each omics layer...
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Method: Accurate short-read alignment through r-index-based pangenome indexing
- Rahul Varki,
- Massimiliano Rossi,
- Eddie Ferro,
- Marco Oliva,
- Erik Garrison,
- Ben Langmead,
- and Christina Boucher
Genome Res. July 2025 35: 1609-1620; Published in Advance June 12, 2025, doi:10.1101/gr.279858.124
...Accurate short-read alignment through r-index-based pan indexing Rahul Varki1,4, Massimiliano Rossi1,4, Eddie Ferro1, Marco Oliva1, Erik Garrison2, Ben Langmead3 and Christina Boucher1 1Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida 32611...
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Method: Efficient integration of spatial omics data for joint domain detection, matching, and alignment with stMSA
- Han Shu,
- Jing Chen,
- Chang Xu,
- Jialu Hu,
- Yongtian Wang,
- Jiajie Peng,
- Qinghua Jiang,
- Xuequn Shang,
- and Tao Wang
Genome Res. October 2025 35: 2285-2299; Published in Advance August 14, 2025, doi:10.1101/gr.280584.125
...technologies. Furthermore, stMSA effectively deciphers complex developmental trajectories by integrating spatial proteomics and transcriptomics data and excels in cross-slice matching and alignment for 3D tissue reconstruction.Spatial omics (SO) technologies have greatly enhanced our understanding of molecular...
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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
...Matthew Naish and Ian R. Henderson Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom Corresponding author: irh25@cam.ac.ukAbstractCentromeres are essential regions of eukaryotic chromosomes responsible for the formation of kinetochore complexes, which connect...
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Method: Haplotype-aware sequence alignment to pangenome graphs
- Ghanshyam Chandra,
- Daniel Gibney,
- and Chirag Jain
Genome Res. September 2024 34: 1265-1275; Published in Advance July 16, 2024, doi:10.1101/gr.279143.124
...Haplotype-aware sequence alignment to pan graphs Ghanshyam Chandra1, Daniel Gibney2 and Chirag Jain1 1Department of Computational and Data Sciences, Indian Institute of Science, Bangalore Karnataka 560012, India; 2Department of Computer Science, The University of Texas at Dallas, Richardson, Texas...
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Method: Automated annotation of human centromeres with HORmon
- Olga Kunyavskaya,
- Tatiana Dvorkina,
- Andrey V. Bzikadze,
- Ivan A. Alexandrov,
- and Pavel A. Pevzner
Genome Res. June 2022 32: 1137-1151; Published in Advance May 11, 2022, doi:10.1101/gr.276362.121
...-standing questions about the architecture and evolution of human centromeres. They also emphasized the need for centromere annotation (partitioning human centromeres into monomers and higher-order repeats [HORs]). Although there was a half-century-long series of semi-manual studies of centromere architecture...
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Perspective: The genetics and epigenetics of satellite centromeres
- Paul B. Talbert and
- Steven Henikoff
Genome Res. April 2022 32: 608-615; Published in Advance March 31, 2022, doi:10.1101/gr.275351.121
...Paul B. Talbert and Steven Henikoff Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA Corresponding authors: ptalbert@fredhutch.org, steveh@fhcrc.orgAbstractCentromeres, the chromosomal loci where spindle fibers attach during cell division...
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Research: Convergent recombination cessation between mating-type genes and centromeres in selfing anther-smut fungi
- Fantin Carpentier,
- Ricardo C. Rodríguez de la Vega,
- Sara Branco,
- Alodie Snirc,
- Marco A. Coelho,
- Michael E. Hood,
- and Tatiana Giraud
Genome Res. June 2019 29: 944-953; Published in Advance May 1, 2019, doi:10.1101/gr.242578.118
...the concatenated alignments of the nine and 10 genes with both alleles available in all s and located between the HD-proximal region and the centromere, or the PR-proximal region and the centromere, respectively. We calibrated the tree nodes using the speciation date between Microbotryum lychnidis...

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