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Research: Haplotype-resolved telomere-to-telomere genome of Aphelenchus avenae implicates P5CS in nematode desiccation stress response
- Yali Zhang,
- Yayi Zhou,
- Yangyang Chen,
- Xueyu Wang,
- Boyan Hu,
- Shahid Siddique,
- Romnick A. Latina,
- Veronica I. Casey,
- Dexin Bo,
- Yucheng Liao,
- Min Zhang,
- Ming Sun,
- Fengjuan Zhang,
- and Dadong Dai
Genome Res. April 2026 36: 726-739; Published in Advance March 23, 2026, doi:10.1101/gr.281016.125
...) and was subsequently confirmed to play a role in desiccation tolerance in animals such as nematodes (Browne et al. 2002). The LEA proteins eliminate the aggregation of water-soluble proteins in cells caused by desiccation which increases cytoplasmic viscosity. It also participates in repairing desiccation-induced DNA...
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Research: Epigenetic activation of meiotic recombination near Arabidopsis thaliana centromeres via loss of H3K9me2 and non-CG DNA methylation
- Charles J. Underwood,
- Kyuha Choi,
- Christophe Lambing,
- Xiaohui Zhao,
- Heïdi Serra,
- Filipe Borges,
- Joe Simorowski,
- Evan Ernst,
- Yannick Jacob,
- Ian R. Henderson,
- and Robert A. Martienssen
Genome Res. April 2018 28: 519-531; Published in Advance March 12, 2018, doi:10.1101/gr.227116.117
...at multiple scales (Supplemental Table S17). For example, Pearson's r values between replicate libraries at the 10-kb scale were between 0.91 and 0.99 (Supplemental Table S17). Further normalization was performed using a single-ended Col genomic DNA library with reads trimmed to 50 base pairs, which were...
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Chicken Special/Letters: The repetitive landscape of the chicken genome
- Thomas Wicker,
- Jon S. Robertson,
- Stefan R. Schulze,
- F. Alex Feltus,
- Vincent Magrini,
- Jason A. Morrison,
- Elaine R. Mardis,
- Richard K. Wilson,
- Daniel G. Peterson,
- Andrew H. Paterson,
- and Robert Ivarie
Genome Res. January 2005 15: 126-136; Published in Advance July 15, 2004, doi:10.1101/gr.2438004
...Abstract Cot-based cloning and sequencing (CBCS) is a powerful tool for isolating and characterizing the various repetitive components of any genome, combining the established principles of DNA reassociation kinetics with high-throughput sequencing. CBCS was used to generate sequence libraries...
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Research: Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution
- Florent Murat,
- Jian-Hong Xu,
- Eric Tannier,
- Michael Abrouk,
- Nicolas Guilhot,
- Caroline Pont,
- Joachim Messing,
- and Jérôme Salse
Genome Res. November 2010 20: 1545-1557; Published in Advance September 28, 2010, doi:10.1101/gr.109744.110
...). One of the grass subfamilies investigated here is the Pooideae, which includes important crops like wheat, barley, and oats. Because most of these s contain large amounts of repetitive DNA, Brachypodium, with a very small , has been sequenced as a representative of this subfamily. To reconstruct...
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LETTER: Genome Size Reduction through Illegitimate Recombination Counteracts Genome Expansion in Arabidopsis
- Katrien M. Devos,
- James K.M. Brown,
- and Jeffrey L. Bennetzen
Genome Res. July 1, 2002 12: 1075-1079; doi:10.1101/gr.132102
.... ↵ Shirasu K. , Schulman A.H. , Lahaye T. , Schulze-Lefert P. ( 2000 ) A contiguous 66-kb barley DNA sequence provides evidence for reversible expansion. Genome Res. 10 : 908 – 915 . ↵ Sugawara N. , Haber J.E. ( 1992 ) Characterization of double-strand break-induced recombination: Homology requirements...
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LETTER: Incongruent Patterns of Local and Global Genome Size Evolution in Cotton
- Corrinne E. Grover,
- HyeRan Kim,
- Rod A. Wing,
- Andrew H. Paterson,
- and Jonathan F. Wendel
Genome Res. August 2004 14: 1474-1482; Published in Advance July 15, 2004, doi:10.1101/gr.2673204
...in the same nucleus at the time of polyploid formation, ∼1–2 Mya. Gene content, order, and spacing are largely conserved between the two genomes, although a few transposable elements and a single cpDNA fragment distinguish the two homoeologs. Sequence conservation is high in both intergenic and genic regions...
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LETTER: Analyses of LTR-Retrotransposon Structures Reveal Recent and Rapid Genomic DNA Loss in Rice
- Jianxin Ma,
- Katrien M. Devos,
- and Jeffrey L. Bennetzen
Genome Res. May 2004 14: 860-869; Published in Advance April 12, 2004, doi:10.1101/gr.1466204
...: 312 -316. ↵ Shirasu, K., Schulman, A.H., Lahaye, T., and Schulze-Lefert, P. 2000 . A contiguous 66-kb barley DNA sequence provides evidence for reversible expansion. Genome Res. 10 : 908 -915. ↵ Song, R., Llaca, V., and Messing, J. 2002 . Mosaic organization of orthologous sequences in grass s. Genome...
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REPORT: Conservation of Microstructure between a Sequenced Region of the Genome of Rice and Multiple Segments of the Genome of Arabidopsis thaliana
- Klaus Mayer,
- George Murphy,
- Renato Tarchini,
- Rolf Wambutt,
- Guido Volckaert,
- Thomas Pohl,
- Andreas Düsterhöft,
- Willem Stiekema,
- Karl-Dieter Entian,
- Nancy Terryn,
- Kai Lemcke,
- Dirk Haase,
- Caroline R. Hall,
- Anne-Marie van Dodeweerd,
- Scott V. Tingey,
- Hans-Werner Mewes,
- Michael W. Bevan,
- and Ian Bancroft
Genome Res. July 1, 2001 11: 1167-1174; Published in Advance June 12, 2001, doi:10.1101/gr.161701
...(29%) have EST matches leads us to predict a total gene number for rice of ∼35,000. This would be consistent with a model in which the majority of the rice genes are contained in gene-rich regions comprising 50% of the genomic DNA of rice (220 Mb), with these gene-rich regions typically containing...
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LETTER: Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium
- Jennifer S. Hawkins,
- HyeRan Kim,
- John D. Nason,
- Rod A. Wing,
- and Jonathan F. Wendel
Genome Res. October 2006 16: 1252-1261; Published in Advance September 5, 2006, doi:10.1101/gr.5282906
...1 Iowa State University, Department of Ecology, Evolution and Organismal Biology, Ames, Iowa 50011, USA; 2 University of Arizona, Department of Plant Sciences, Arizona Genomics Institute, Tucson, Arizona 85721, USA Abstract The DNA content of eukaryotic nuclei (C...
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LETTER: Abundance, Distribution, and Transcriptional Activity of Repetitive Elements in the Maize Genome
- Blake C. Meyers,
- Scott V. Tingey,
- and Michele Morgante
Genome Res. October 1, 2001 11: 1660-1676; Published in Advance September 20, 2001, doi:10.1101/gr.188201
...A library (the cne1g library) of small-insert genomic DNA was prepared using nebulized maize total genomic DNA from the inbred line B73. After joining forward and reverse sequences from each clone, the total number of sequences was 2157, representing 1.41×106 bp (GenBank accession numbers BH126890 – BH...

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