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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
.... (E) Mapping quality (MAPQ) distributions of Hi-C reads whose paired mates contained rDNA subtype-specific or non-subtype-specific 31-mers, categorized by the nuclear haplotype they mapped against.Detailed analyses of sequencing reads revealed two major rDNA subtypes (1 and 2) supported by substantial...
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Research: Continuous infiltration and evolutionary trajectory of nuclear organelle DNA in Oryza
- Chenbo Gong,
- Yicheng Huang,
- Mengmeng Liu,
- Yong Zhou,
- Yinwei Xu,
- Nahed Mohammed,
- Xintong Qiao,
- Andrea Zuccolo,
- Weibo Xie,
- Rod A. Wing,
- Jianwei Zhang,
- Fei Zhou,
- and Yongjun Lin
Genome Res. June 2025 35: 1349-1363; Published in Advance April 25, 2025, doi:10.1101/gr.279609.124
...rearranged DNA originating from both mtDNA and ptDNA (Noutsos et al. 2005; Portugez et al. 2018). Triticeae species tend to have more nuclear organellar genes than other Poaceae species (Chen et al. 2023). In Asian cultivated rice, several NUPT and NUMT events occur specifically in one subspecies (Huang et...
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Research: Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries
- Shaoqiang Hu,
- Xiangguo Zeng,
- Yuguo Liu,
- Yongping Li,
- Minghao Qu,
- Wen-Biao Jiao,
- Yongchao Han,
- and Chunying Kang
Genome Res. October 2024 34: 1582-1594; Published in Advance October 15, 2024, doi:10.1101/gr.279378.124
...in Arabidopsis (Jiang et al. 2011). Somaclonal variation occurs at multiple levels, including cytological abnormalities, DNA sequence changes, and epigenetic alterations (Abu-Qaoud and Sami 2010). In cotton, the -wide analysis revealed thousands of single nucleotide variants (SNVs) and hundreds of insertions...
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Research: Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensation
- David C.H. Metzger,
- Imogen Porter,
- Brendan Mobley,
- Benjamin A. Sandkam,
- Lydia J.M. Fong,
- Andrew P. Anderson,
- and Judith E. Mank
Genome Res. November 2023 33: 1917-1931; Published in Advance November 21, 2023, doi:10.1101/gr.278127.123
...-level assembly of P. picta with whole- bisulfite sequencing and RNA-seq data, we determine that the YY1 transcription factor (YY1) DNA binding motif is associated with male-specific hypomethylated regions on the X, but not the autosomes. These YY1 motifs are the result of a recent and rapid repetitive element...
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LETTER: Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome
- Regina S. Baucom,
- James C. Estill,
- Jim Leebens-Mack,
- and Jeffrey L. Bennetzen
Genome Res. February 2009 19: 243-254; Published in Advance November 24, 2008, doi:10.1101/gr.083360.108
....L. ( 2004 ) Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice . Genome Res. 14 : 860 – 869 . ↵ Mackay, T.F.C. , Lyman, R.F. , Jackson, M.S. ( 1992 ) Effects of P-element insertions on quantitative traits in Drosophila melanogaster . Genetics 130 : 315 – 332...
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Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
- Aleix Palahí i Torres,
- Lars Höök,
- Karin Näsvall,
- Daria Shipilina,
- Christer Wiklund,
- Roger Vila,
- Peter Pruisscher,
- and Niclas Backström
Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
...explanatory variables (GC content, gene density, DNA transposon, SINE, LINE, and LTR retrotransposon densities) on the recombination rate. This model revealed an overall significant association between the recombination rate and the explanatory variables (F(6) = 10.77, df = 603, P = 2.13 × 10...
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Resource: Integrated annotations and analyses of small RNA–producing loci from 47 diverse plants
- Alice Lunardon,
- Nathan R. Johnson,
- Emily Hagerott,
- Tamia Phifer,
- Seth Polydore,
- Ceyda Coruh,
- and Michael J. Axtell
Genome Res. March 2020 30: 497-513; Published in Advance March 16, 2020, doi:10.1101/gr.256750.119
...-directed DNA methylation (RdDM) pathway, involving 24 or 21–22 nt siRNAs. Twenty-four-nucleotide siRNAs are derived from Polymerase IV (Pol IV) transcripts that are converted to dsRNAs by RNA-dependent RNA polymerase 2 (RDR2), which are then processed by DCL3. They act in canonical RdDM, primarily targeting...
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Research: Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals
- Ulrike Böhme,
- Thomas D. Otto,
- James A. Cotton,
- Sascha Steinbiss,
- Mandy Sanders,
- Samuel O. Oyola,
- Antoine Nicot,
- Sylvain Gandon,
- Kailash P. Patra,
- Colin Herd,
- Ellen Bushell,
- Katarzyna K. Modrzynska,
- Oliver Billker,
- Joseph M. Vinetz,
- Ana Rivero,
- Chris I. Newbold,
- and Matthew Berriman
Genome Res. April 2018 28: 547-560; Published in Advance March 2, 2018, doi:10.1101/gr.218123.116
...and Plasmodium gallinaceum 8A. Our analyses provide insights into the evolution of unique features of mammalian-infective species and allow an exploration on how far the apparently shared features extend across the entire Plasmodium genus. We reveal surprising features involving gene content, gene family...
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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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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
...relies on the identification of LTR-RTs that are recent insertions and thus have at least some intact family members, tends to accentuate the early loss of events and under-represent the later loss events. Initial frequencies of DNA loss by UR and IR A previous study revealed rapid elimination of LTR...

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