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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
...the consequences of centromere breakage on wheat genomic architecture, we analyzed the CS ditelosomic (CSDt) lines from homoeologous groups 1, 6, and 7 chromosomes. Cytogenetic analysis confirmed the presence of telosomic chromosomes carrying either the short or long arm (Supplemental Fig. S1). Telomeric signals...
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Research: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
- Rita Tam,
- Mareike Möller,
- Runpeng Luo,
- Zhenyan Luo,
- Ashley Jones,
- Sambasivam Periyannan,
- John P. Rathjen,
- and Benjamin Schwessinger
Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
...expression analysis with our ONT cDNA data sets to identify candidate Avr effector genes. We searched for secretome genes that are upregulated early in wheat infection (4, 6, and 8 dpi) relative to UG, as their functions likely correlate with pathogenesis. A total of 1318 secretome genes were found...
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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...distributed along the . However, because some TE families tend to have certain preferences to where they are inserted in the (Chuong et al. 2017), we take into account the genomic context when calculating the expected counts following the methodology described by Bogdan et al. (2020). Specifically...
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Research: Crossover-active regions of the wheat genome are distinguished by DMC1, the chromosome axis, H3K27me3, and signatures of adaptation
- Andrew J. Tock,
- Daniel M. Holland,
- Wei Jiang,
- Kim Osman,
- Eugenio Sanchez-Moran,
- James D. Higgins,
- Keith J. Edwards,
- Cristobal Uauy,
- F. Chris H. Franklin,
- and Ian R. Henderson
Genome Res. September 2021 31: 1614-1628; Published in Advance August 23, 2021, doi:10.1101/gr.273672.120
...) (Marcussen et al. 2014). Wheat chromosomes are large (473–830 Mb), with high transposable element (TE) content, and comprise one of the most complex assembled s (IWGSC 2018).Pronounced compartmentalization of features occurs along the wheat chromosomes. For example, crossover rate, gene density...
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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
...of kinetochore attachment sites along chromosomes. We discuss how variation in CENH3 loading can drive elimination during early cell divisions of plant embryogenesis. We review how epigenetic state may influence centromere identity and discuss evolutionary models that seek to explain the paradoxically rapid...
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LETTER: Comparative DNA Sequence Analysis of Wheat and Rice Genomes
- Mark E. Sorrells,
- Mauricio La Rota,
- Catherine E. Bermudez-Kandianis,
- Robert A. Greene,
- Ramesh Kantety,
- Jesse D. Munkvold,
- Miftahudin,
- Ahmed Mahmoud,
- Xuefeng Ma,
- Perry J. Gustafson,
- Lili L. Qi,
- Benjamin Echalier,
- Bikram S. Gill,
- David E. Matthews,
- Gerard R. Lazo,
- Shiaoman Chao,
- Olin D. Anderson,
- Hugh Edwards,
- Anna M. Linkiewicz,
- Jorge Dubcovsky,
- Eduard D. Akhunov,
- Jan Dvorak,
- Deshui Zhang,
- Henry T. Nguyen,
- Junhua Peng,
- Nora L.V. Lapitan,
- Jose L. Gonzalez-Hernandez,
- James A. Anderson,
- Khwaja Hossain,
- Venu Kalavacharla,
- Shahryar F. Kianian,
- Dong-Woog Choi,
- Timothy J. Close,
- Muharrem Dilbirligi,
- Kulvinder S. Gill,
- Camille Steber,
- Mary K. Walker-Simmons,
- Patrick E. McGuire,
- and Calvin O. Qualset
Genome Res. August 2003 13: 1818-1827; doi:10.1101/gr.1113003
...rates along chromosome arms that were suggested to promote more rapid rates of transcriptome evolution in distal, high-recombination regions than in proximal, low-recombination regions ( Akhunov et al. 2003 ). The physical location of these nonconserved, multicopy regions in wheat were not consistent...
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LETTER: Variation in crossing-over rates across chromosome 4 of Arabidopsis thaliana reveals the presence of meiotic recombination “hot spots”
- Jan Drouaud,
- Christine Camilleri,
- Pierre-Yves Bourguignon,
- Aurélie Canaguier,
- Aurélie Bérard,
- Daniel Vezon,
- Sandra Giancola,
- Dominique Brunel,
- Vincent Colot,
- Bernard Prum,
- Hadi Quesneville,
- and Christine Mézard
Genome Res. January 2006 16: 106-114; Published in Advance December 12, 2005, doi:10.1101/gr.4319006
...in a multiple regression analysis, correlation with the G+C content becomes negative ( Kong et al. 2002 ; Jensen-Seaman et al. 2004 ). In wheat, barley, and maize, gene-rich regions are more recombinationally active than gene-poor regions (for review, see Schnable et al. 1998 ). In humans, female CO rates...
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Research: Patching gaps in plant genomes results in gene movement and erosion of colinearity
- Thomas Wicker,
- Jan P. Buchmann,
- and Beat Keller
Genome Res. September 2010 20: 1229-1237; Published in Advance June 7, 2010, doi:10.1101/gr.107284.110
...plant s during evolution. [Supplemental material is available online at http://www..org.] The genes of closely related species are usually found in similar order along chromosomes. This ‘‘colinearity’’ reflects descent froma commonancestor.While gene order in animal s is well-conserved over hundreds...
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LETTER: Uneven chromosome contraction and expansion in the maize genome
- Rémy Bruggmann,
- Arvind K. Bharti,
- Heidrun Gundlach,
- Jinsheng Lai,
- Sarah Young,
- Ana C. Pontaroli,
- Fusheng Wei,
- Georg Haberer,
- Galina Fuks,
- Chunguang Du,
- Christina Raymond,
- Matt C. Estep,
- Renyi Liu,
- Jeffrey L. Bennetzen,
- Agnes P. Chan,
- Pablo D. Rabinowicz,
- John Quackenbush,
- W. Brad Barbazuk,
- Rod A. Wing,
- Bruce Birren,
- Chad Nusbaum,
- Steve Rounsley,
- Klaus F.X. Mayer,
- and Joachim Messing
Genome Res. October 2006 16: 1241-1251; Published in Advance August 10, 2006, doi:10.1101/gr.5338906
...2006 ). Within the cereals, conserved genetic markers can readily be found, and are largely collinear ( Gale and Devos 1998 ). However, sizes vary greatly, as illustrated by the difference between the 389-Mb rice ( International Rice Genome Sequencing Project 2005 ) and the 16,000-Mb hexaploid wheat...
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Letter: Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?
- Zhixi Tian,
- Carene Rizzon,
- Jianchang Du,
- Liucun Zhu,
- Jeffrey L. Bennetzen,
- Scott A. Jackson,
- Brandon S. Gaut,
- and Jianxin Ma
Genome Res. December 2009 19: 2221-2230; Published in Advance September 29, 2009, doi:10.1101/gr.083899.108
...resamplings. dCorrelation based on the proportion of LTR-RTs (DNA %) and proportion of genes (DNA %). Tian et al. 2226 Genome Research www..org Discussion The rice is organized along recombinational gradients The accrual and elimination of LTR-RT DNA have been well documented in Arabidopsis, rice, and several...

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