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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 after centromere damage. Expanded centromeric domains remodeled to adopt a more open configuration, whereas contracted domains become more compact in CSDt lines (Fig. 5D). These findings indicated that centromeric chromatin is remodeled to maintain functionality following structural change. Similarly...
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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
...interspecies crossing, showed that regions of CENH3 ChIP-seq enrichment expanded from ∼1.8 Mb to ∼3.6 Mb, once in an oat nucleus (Jin et al. 2004; Wang et al. 2014). This indicates that the nuclear context, and likely trans-acting factors, can influence CENH3 occupancy on centromeric DNA sequences...
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Method: Fast sequence alignment for centromeres with RaMA
- Pinglu Zhang,
- Yanming Wei,
- Qinzhong Tian,
- Quan Zou,
- and Yansu Wang
Genome Res. May 2025 35: 1209-1218; Published in Advance February 12, 2025, doi:10.1101/gr.279763.124
...to complex regions like centromeres, composed of extra-long tandem repeats (ETRs). However, a significant gap remains as current methodologies are inadequate for producing sequence alignments that effectively capture genetic events within ETRs, highlighting a pressing need for improved alignment tools...
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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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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
...of highly uniform dimers flanked by more divergent dimers. An elevated mutational divergence was found between centromeres, two- to fourfold higher than at random loci, consistent with an error-prone repair process such as BIR. The investigators proposed a model in which highly identical repeats expand...
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Research: Differences in activity and stability drive transposable element variation in tropical and temperate maize
- Shujun Ou,
- Armin Scheben,
- Tyler Collins,
- Yinjie Qiu,
- Arun S. Seetharam,
- Claire C. Menard,
- Nancy Manchanda,
- Jonathan I. Gent,
- Michael C. Schatz,
- Sarah N. Anderson,
- Matthew B. Hufford,
- and Candice N. Hirsch
Genome Res. August 2024 34: 1140-1153; Published in Advance September 9, 2024, doi:10.1101/gr.278131.123
...content across 26 maize s, we developed panEDTA (Supplemental Code), which produces uniform TE annotations in a pan context (Fig. 1A). panEDTA is freely available at GitHub (https://github.com/oushujun/EDTA) and has been implemented in the browser-accessible, cloud-based platform Galaxy (The Galaxy...
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Resource: Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize
- Laura E. Tibbs-Cortes,
- Tingting Guo,
- Carson M. Andorf,
- Xianran Li,
- and Jianming Yu
Genome Res. August 2024 34: 1253-1263; Published in Advance September 13, 2024, doi:10.1101/gr.279027.124
...identification (Li et al. 2018b). This method has been applied in a sorghum biparental population (Li et al. 2018b; Mu et al. 2022), a rice backcross population (Guo et al. 2020), elite lines in wheat (Li et al. 2022), and diversity panels in maize, wheat, and oat (Li et al. 2021).We examined phenotypic...
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Research: miRNA-like secondary structures in maize (Zea mays) genes and transposable elements correlate with small RNAs, methylation, and expression
- Galen T. Martin,
- Edwin Solares,
- Jeanelle Guadardo-Mendez,
- Aline Muyle,
- Alexandros Bousios,
- and Brandon S. Gaut
Genome Res. November 2023 33: 1932-1946; Published in Advance November 2, 2023, doi:10.1101/gr.277459.122
...this method to the same set of 373,485 features as RNAfold but also to a larger, updated version of maize TE annotations (Stitzer et al. 2021), resulting in an expanded data set of 467,255 features (Table 2).For each sequence, LinearPartition calculated the partition function, summarized by the parameter Q...
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Research: Large haplotypes highlight a complex age structure within the maize pan-genome
- Jianing Liu and
- R. Kelly Dawe
Genome Res. March 2023 33: 359-370; Published in Advance February 28, 2023, doi:10.1101/gr.276705.122
...@uga.eduAbstractThe s of maize and other eukaryotes contain stable haplotypes in regions of low recombination. These regions, including centromeres, long heterochromatic blocks, and rDNA arrays, have been difficult to analyze with respect to their diversity and origin. Greatly improved assemblies are now available...
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Method: Predicted protein 3D structures provide essential insights into the genetic architecture underlying phenotypic diversity in maize
- Shuai Wang,
- Merritt Khaipho-Burch,
- Lynn C. Johnson,
- Zachary R. Miller,
- Peter J. Bradbury,
- Doug Speed,
- William J. Allen,
- M. Cinta Romay,
- Jiquan Xue,
- Edward S. Buckler,
- Guillaume P. Ramstein,
- and Baoxing Song
Genome Res. January 2026 36: 214-225; Published in Advance October 31, 2025, doi:10.1101/gr.280514.125
...Shuai Wang1,2, Merritt Khaipho-Burch3, Lynn C. Johnson4, Zachary R. Miller4, Peter J. Bradbury5, Doug Speed6, William J. Allen7, M. Cinta Romay4, Jiquan Xue1, Edward S. Buckler3,4,5, Guillaume P. Ramstein6 and Baoxing Song1,2 1Key Laboratory of Maize Biology and Genetic Breeding in Arid Areas...

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