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Research: A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility
- Angelo A. Ruggieri,
- Luca Livraghi,
- James J. Lewis,
- Elizabeth Evans,
- Francesco Cicconardi,
- Laura Hebberecht,
- Yadira Ortiz-Ruiz,
- Stephen H. Montgomery,
- Alfredo Ghezzi,
- José Arcadio Rodriguez-Martinez,
- Chris D. Jiggins,
- W. Owen McMillan,
- Brian A. Counterman,
- Riccardo Papa,
- and Steven M. Van Belleghem
Genome Res. October 2022 32: 1862-1875; Published in Advance September 15, 2022, doi:10.1101/gr.276839.122
...(Ebert et al. 2021). Several studies in plants and fungi identified the widespread presence of SVs, often linked to phenotypic variation (Read et al. 2013; Plissonneau et al. 2018; Hübner et al. 2019). Aside from these studies performed on humans and nonmetazoans, a few studies in mollusks have also...
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PERSPECTIVE: Genome-wide analyses of alternative splicing in plants: Opportunities and challenges
- W. Brad Barbazuk,
- Yan Fu,
- and Karen M. McGinnis
Genome Res. September 2008 18: 1381-1392; Published in Advance July 30, 2008, doi:10.1101/gr.053678.106
...in the unicellular ancestor of plants, animals, and fungi ( Irimia et al. 2007 ). Therefore, the prevalence of duplication in the evolutionary history of plant s may have contributed to the lower abundance of AS in plants relative to animals. At least two examples of AS loss following gene duplication have been...
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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
...). However, the SET2 family, responsible for H3K36 methylation, was divided into two subfamilies: Set2 and Ash1.View larger version: In this window In a new window Figure 1. Distribution and phylogeny of SET domain proteins across fungi kingdom. (A) Correlation between SET domain protein number and total...
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Research: Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication
- Andrew J. Heidel,
- Hajara M. Lawal,
- Marius Felder,
- Christina Schilde,
- Nicholas R. Helps,
- Budi Tunggal,
- Francisco Rivero,
- Uwe John,
- Michael Schleicher,
- Ludwig Eichinger,
- Matthias Platzer,
- Angelika A. Noegel,
- Pauline Schaap,
- and Gernot Glöckner
Genome Res. November 2011 21: 1882-1891; Published in Advance July 14, 2011, doi:10.1101/gr.121137.111
...-Nd)/(Sd+Nd) values). Estimates for the timing of divergence from a LCA can be derived from phylogenetic analysis of protein sequences. To avoid errors associated with specific proteins being under selection in some lineages, we randomly selected a total of 33 genes that are well conserved between fungi...
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ARTICLE: Structural Characterization of the Human Proteome
- Arne Müller,
- Robert M. MacCallum,
- and Michael J.E. Sternberg
Genome Res. November 1, 2002 12: 1625-1641; doi:10.1101/gr.221202
...by the dimerization domain of the AraC protein that is involved in the transcription regulation of that operon. Third is the superfamily of the DNA-bending protein. Other potentially specific superfamilies are involved in transport (especially the phosphate transferase system, possibly also present in fungi...
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LETTER: Comparative Analysis of Apicomplexa and Genomic Diversity in Eukaryotes
- Thomas J. Templeton,
- Lakshminarayan M. Iyer,
- Vivek Anantharaman,
- Shinichiro Enomoto,
- Juan E. Abrahante,
- G.M. Subramanian,
- Stephen L. Hoffman,
- Mitchell S. Abrahamsen,
- and L. Aravind
Genome Res. September 2004 14: 1686-1695; doi:10.1101/gr.2615304
...of animals, fungi, and plants ( Fig. 1A ). Giardia occupies a basal position amidst the eukaryotes included in this analysis. This topology is also supported by domain architecture analysis of ∼400 proteins belonging to different functional categories as discrete characters. Previous reports propose a weak...
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LETTER: Gene number expansion and contraction in vertebrate genomes with respect to invertebrate genomes
- Anuphap Prachumwat and
- Wen-Hsiung Li
Genome Res. February 2008 18: 221-232; Published in Advance December 14, 2007, doi:10.1101/gr.7046608
...in determining different gene duplicabilities between vertebrates and invertebrates. Methods Genomic data and annotation Vertebrates, invertebrates, fungi, and prokaryotes (Archaea and Eubacteria) have 12, 8, 11, and 436 completely sequenced s, respectively. Annotated s of 12 vertebrates (eight tetrapods: Homo...

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