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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...catalyzing DNA demethylation (erasers). Investigation of DNA methyltransferases in Arabidopsis thaliana has revealed sequence context-specific activity for these enzymes: MET1 is responsible for maintaining mCG, being recruited to hemimethylated sites after replication (Finnegan et al. 1996; Ronemus et al...
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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
...reference, we compared it to the mitochondrial assembly of Oryza minuta (BBCC , NCBI GenBank: NC_029816.1), a closely related species, using whole- alignment (NUCmer). The comparison revealed 97% sequence identity and 83.1% coverage, supporting the use of O. sativa mtDNA for NUMT detection in closely...
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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
...al. 2016. The pan of an agronomically important crop plant Brassica oleracea. Nat Commun 7: 13390. doi:10.1038/ncomms13390 ↵Hardwick SA, Chen WY, Wong T, Deveson IW, Blackburn J, Andersen SB, Nielsen LK, Mattick JS, Mercer TR. 2016. Spliced synthetic genes as internal controls in RNA sequencing...
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Method: Combining DNA and protein alignments to improve genome annotation with LiftOn
- Kuan-Hao Chao,
- Jakob M. Heinz,
- Celine Hoh,
- Alan Mao,
- Alaina Shumate,
- Mihaela Pertea,
- and Steven L. Salzberg
Genome Res. February 2025 35: 311-325; Published in Advance December 27, 2024, doi:10.1101/gr.279620.124
...al. 2023), and RefSeq (Pruitt et al. 2007). Additionally, we show that LiftOn is effective for mapping annotation between members of nonhuman species, including Mus musculus (mouse), Apis mellifera (honey bee), Arabidopsis thaliana (thale cress), and Oryza sativa (rice). To demonstrate Lift...
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Method: Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq
- Alejandro Paniagua,
- Cristina Agustín-García,
- Francisco J. Pardo-Palacios,
- Thomas Brown,
- Maite De Maria,
- Nancy D. Denslow,
- Camila J. Mazzoni,
- and Ana Conesa
Genome Res. April 2025 35: 1053-1064; Published in Advance December 23, 2024, doi:10.1101/gr.279864.124
...-read-based manatee annotation with the NCBI annotationWe compared our LRB annotation to the available NCBI T. manatus latirostris Annotation Release 102, obtained using short reads and the NCBI Eukaryotic Genome Annotation Pipeline, to evaluate any gain or loss of information. We first determined the number...
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Research: Thermal stress accelerates Arabidopsis thaliana mutation rate
- Eric J. Belfield,
- Carly Brown,
- Zhong Jie Ding,
- Lottie Chapman,
- Mengqian Luo,
- Eleanor Hinde,
- Sam W. van Es,
- Sophie Johnson,
- Youzheng Ning,
- Shao Jian Zheng,
- Aziz Mithani,
- and Nicholas P. Harberd
Genome Res. January 2021 31: 40-50; Published in Advance December 17, 2020, doi:10.1101/gr.259853.119
...(Belfield et al. 2012); A. thaliana - Saline – ST (Jiang et al. 2014); Oryza sativa – ST (Yang et al. 2015); Escherichia coli – ST (Chu et al. 2018); E. coli – CT (28°C) (Chu et al. 2018); E. coli – CT (25°C) (Chu et al. 2018); A. thaliana A – ST (Ossowski et al. 2010); A. thaliana B – ST (Jiang et al. 2014...
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Method: Robust and efficient annotation of cell states through gene signature scoring
- Laure Ciernik,
- Agnieszka Kraft,
- Florian Barkmann,
- Josephine Yates,
- and Valentina Boeva
Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
..., particularly for unsupervised cellular state annotation based on maximum signature score values. However, this application requires robust and comparable score distributions across diverse signatures and experimental conditions. Our systematic evaluation of established scoring methodologies—Seurat, SCANPY...
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Method: Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS
- Qunlun Shen,
- Shuqin Zhang,
- and Shihua Zhang
Genome Res. November 2025 35: 2527-2538; Published in Advance October 1, 2025, doi:10.1101/gr.280821.125
...in accuracy, a 49.4% increase in macro F1 score, and a 57.3% increase in weighted F1 score compared with the random selection (Fig. 3C).View larger version: In this window In a new window Figure 3. Application of CAMUS for method selection in 672 pairs of cross-species cell type annotations. (A) Dot plot...
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Resource: Genome-scale targeted mutagenesis in Brassica napus using a pooled CRISPR library
- Jianjie He,
- Kai Zhang,
- Shuxiang Yan,
- Mi Tang,
- Weixian Zhou,
- Yongtai Yin,
- Kang Chen,
- Chunyu Zhang,
- and Maoteng Li
Genome Res. May 2023 33: 798-809; Published in Advance June 8, 2023, doi:10.1101/gr.277650.123
..., there has yet to be a report about creating a mutant collection in plants with complex polyploid s using targeted mutagenesis.Rapeseed (Brassica napus, AACC; 2n = 38), a typical polyploid and hybridized from Brassica rapa (AA; 2n = 20) and Brassica oleracea (CC; 2n = 18) ∼7500 years ago, is a vital oil crop...
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Resource: Building better genome annotations across the tree of life
- Adam H. Freedman and
- Timothy B. Sackton
Genome Res. May 2025 35: 1261-1276; Published in Advance April 15, 2025, doi:10.1101/gr.280377.124
...methods to recover fewer BUSCOs with increasing divergence from the reference species. The greater evolutionary distances of Oryza sativa and Brachypodium distachyon from Z. mays (i.e., the annotation used as the source to be lifted over) than between Z. mays and Setaria italica (each the other's source...

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