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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...method. (Right) Comparative genomic features between interspecific and intraspecific strains, including sizes (A), gene numbers (B), repeat content as a percentage of the (C), proportions of repeat types among total repeats (D), gene length distributions (E), and coding DNA sequence (CDS) length...
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Research: Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen
- Xingmin Han,
- Chenghui Xu,
- Yiyi Ren,
- Meiling Guo,
- Jiayue Yan,
- Xuan Wang,
- Chao Liu,
- Qin Gu,
- Xing-Xing Shen,
- Zhonghua Ma,
- and Yun Chen
Genome Res. November 2025 35: 2472-2487; Published in Advance October 14, 2025, doi:10.1101/gr.280560.125
...Xingmin Han1, Chenghui Xu1, Yiyi Ren1, Meiling Guo1, Jiayue Yan1, Xuan Wang1, Chao Liu1, Qin Gu2, Xing-Xing Shen1, Zhonghua Ma1 and Yun Chen1 1State Key Laboratory of Rice Biology and Breeding, Zhejiang Key Laboratory of Biology and Ecological Regulation of Crop Pathogens and Insects, Department...
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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: 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
...mechanisms, including TE mobilization or homologous repair following DNA-double-stranded breaks (Todd et al. 2019, Berdan et al. 2021).The human fungal pathogen Candida albicans is an asexual diploid organism that displays significant genomic plasticity (Vande Zande et al. 2023). SVs are important drivers...
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Research: Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza
- Rodolphe Dombey,
- Daniel Buendía-Ávila,
- Verónica Barragán-Borrero,
- Laura Diezma-Navas,
- Arturo Ponce-Mañe,
- José Mario Vargas-Guerrero,
- Rana Elias,
- and Arturo Marí-Ordóñez
Genome Res. March 2025 35: 522-544; Published in Advance March 4, 2025, doi:10.1101/gr.279532.124
...content of the Spirodela is similar to that of Arabidopsis (∼20%) (Wang et al. 2014). Therefore, reduced genomic TE load is unlikely to be the cause behind the low levels of DNA methylation and sRNAs in Spirodela. Furthermore, in Spirodela, several sRNA silencing components including some involved in Rd...
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Research: Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly
- Kang Du,
- Oliver Deusch,
- Ilja Bezrukov,
- Christa Lanz,
- Yann Guiguen,
- Margarete Hoffmann,
- Anette Habring,
- Detlef Weigel,
- Manfred Schartl,
- and Christine Dreyer
Genome Res. March 2025 35: 489-498; Published in Advance March 5, 2025, doi:10.1101/gr.279582.124
...Guanapo population. High-molecular-weight genomic DNA from the YY male was sequenced on the Pacific Biosciences platform, and both Y haplotypes were reconstructed by Trio binning. By mapping of male specific SNPs and RADseq sequences, we identify a single male specific-region of ∼5 Mb length at the distal...
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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
...; Naish et al. 2021). High-copy tandem repeats are traditionally termed satellites, as following density gradient centrifugation, the repeats form satellite bands owing to different buoyant density compared with the bulk genomic DNA (Kit 1961; Thakur et al. 2021; Altemose 2022). Typically, individual...
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Research: Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes
- Ting-Ying Wu,
- Ya-Ru Li,
- Kai-Jyun Chang,
- Jhen-Cheng Fang,
- Daisuke Urano,
- and Ming-Jung Liu
Genome Res. February 2024 34: 272-285; Published in Advance March 13, 2024, doi:10.1101/gr.278100.123
...), a highly conserved region across rice (Oryza sativa), tobacco (Nicotiana tabacum), maize (Zea mays), and wheat (Triticum aestivum) that efficiently enhances translation (Akbergenov et al. 2004). These results provide experimental evidence that CU-rich elements enhance translation initiation in plant m...
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Research: Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements
- Yuyun Zhang,
- Zijuan Li,
- Yu'e Zhang,
- Kande Lin,
- Yuan Peng,
- Luhuan Ye,
- Yili Zhuang,
- Meiyue Wang,
- Yilin Xie,
- Jingyu Guo,
- Wan Teng,
- Yiping Tong,
- Wenli Zhang,
- Yongbiao Xue,
- Zhaobo Lang,
- and Yijing Zhang
Genome Res. December 2021 31: 2276-2289; Published in Advance September 9, 2021, doi:10.1101/gr.275658.121
...vacuum-infiltrated with a formaldehyde cross-linking solution for use in the ChIP-seq and DHS assay.DAP-seq assayDAP-seq was performed as previously described (Bartlett et al. 2017). Genomic DNA was extracted from wheat leaves using Plant DNAzol Reagent) and fragmented. DNA was then end-repaired using...
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Method: CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant genomes
- Marzia Rossato,
- Luca Marcolungo,
- Luca De Antoni,
- Giulia Lopatriello,
- Elisa Bellucci,
- Gaia Cortinovis,
- Giulia Frascarelli,
- Laura Nanni,
- Elena Bitocchi,
- Valerio Di Vittori,
- Leonardo Vincenzi,
- Filippo Lucchini,
- Kirstin E. Bett,
- Larissa Ramsay,
- David James Konkin,
- Massimo Delledonne,
- and Roberto Papa
Genome Res. May 2023 33: 787-797; Published in Advance May 1, 2023, doi:10.1101/gr.277628.122
...-quality alignments that hinder the calling of accurate genotypes, which is a consistent challenge particularly for those plant species with large s, in which repetitive elements account for up to 90% of the total DNA. This includes many domesticated crops such as corn (Zea mays), wheat (Triticum spp.), lentil (Lens...
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