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Research: Semiconservative transmission of DNA N⁶-adenine methylation in a unicellular eukaryote
- Yalan Sheng,
- Yuanyuan Wang,
- Wentao Yang,
- Xue Qing Wang,
- Jiuwei Lu,
- Bo Pan,
- Bei Nan,
- Yongqiang Liu,
- Fei Ye,
- Chun Li,
- Jikui Song,
- Yali Dou,
- Shan Gao,
- and Yifan Liu
Genome Res. May 2024 34: 740-756; Published in Advance May 14, 2024, doi:10.1101/gr.277843.123
...; Bochtler and Fernandes 2021). 6mA studies in eukaryotes are complicated by varying abundance and divergent functions across species. In protists, green algae, and basal fungi, 6mA is abundant, enriched at the ApT dinucleotide, and associated with genes, all of which are consistent with its role...
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Research: A low-abundance class of Dicer-dependent siRNAs produced from a variety of features in C. elegans
- Thiago L. Knittel,
- Brooke E. Montgomery,
- Alex J. Tate,
- Ennis W. Deihl,
- Anastasia S. Nawrocki,
- Frederic J. Hoerndli,
- and Taiowa A. Montgomery
Genome Res. December 2024 34: 2203-2216; Published in Advance December 2, 2024, doi:10.1101/gr.279083.124
...from siRNAs in mice and flies, but is a common feature of most siRNAs in plants and fungi (Cogoni and Macino 1999; Dalmay et al. 2000; Mourrain et al. 2000; Smardon et al. 2000; Sijen et al. 2001; Volpe et al. 2002; Aoki et al. 2007; Pak and Fire 2007; Gent et al. 2009, 2010; Gu et al. 2009; Han et al...
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Research: Historical RNA expression profiles from the extinct Tasmanian tiger
- Emilio Mármol-Sánchez,
- Bastian Fromm,
- Nikolay Oskolkov,
- Zoé Pochon,
- Panagiotis Kalogeropoulos,
- Eli Eriksson,
- Inna Biryukova,
- Vaishnovi Sekar,
- Erik Ersmark,
- Björn Andersson,
- Love Dalén,
- and Marc R. Friedländer
Genome Res. August 2023 33: 1299-1316; Published in Advance July 18, 2023, doi:10.1101/gr.277663.123
...the thylacine in our data is relatively low. The remaining assigned reads corresponded to human (7%), mouse (5%), undetermined fungi (4%), other eukaryotes (1%), and zebrafish (8%) and other related fish species (4%). These findings were consistent with those obtained for untrimmed skeletal muscle reads (Fig. 3...
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Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
- Ezequiel Calvo-Roitberg,
- Rachel F. Daniels,
- and Athma A. Pai
Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
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Research: Hybridization drives mitochondrial DNA degeneration and metabolic shift in a species with biparental mitochondrial inheritance
- Mathieu Hénault,
- Souhir Marsit,
- Guillaume Charron,
- and Christian R. Landry
Genome Res. November/December 2022 32: 2043-2056; Published in Advance November 9, 2022, doi:10.1101/gr.276885.122
...remains largely unknown. Here, we use Saccharomyces yeasts, fungi with constitutive biparental mtDNA inheritance, to investigate the resolution of mtDNA heteroplasmy in a variety of hybrid genotypes. We previously designed 11 crosses along a gradient of parental evolutionary divergence using...
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Research: Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules
- Jonathon L. Baker,
- James T. Morton,
- Márcia Dinis,
- Ruth Alvarez,
- Nini C. Tran,
- Rob Knight,
- and Anna Edlund
Genome Res. January 2021 31: 64-74; Published in Advance November 25, 2020, doi:10.1101/gr.265645.120
...to be associated with changes in the oral microbiome independent of caries, as EBV positive subjects were broadly distributed through ordination space in the PCA analysis. The role of viruses and fungi in dental caries is likely to be of significance; however, the amount of research examining these relationships...
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PERSPECTIVE: Genomics of the fungal kingdom: Insights into eukaryotic biology
- James E. Galagan,
- Matthew R. Henn,
- Li-Jun Ma,
- Christina A. Cuomo,
- and Bruce Birren
Genome Res. December 2005 15: 1620-1631; doi:10.1101/gr.3767105
...between fungi and man. The future of fungal genomics The growing number of complete fungal s provides an unprecedented opportunity to study the biology and evolution of an entire eukaryotic kingdom. However, sequence is only the tip of the iceberg for fungal genomics. The availability of sequence has...
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Resource: Organ-level protein networks as a reference for the host effects of the microbiome
- Robert H. Mills,
- Jacob M. Wozniak,
- Alison Vrbanac,
- Anaamika Campeau,
- Benoit Chassaing,
- Andrew Gewirtz,
- Rob Knight,
- and David J. Gonzalez
Genome Res. February 2020 30: 276-286; Published in Advance January 28, 2020, doi:10.1101/gr.256875.119
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Method: System-wide analyses of the fission yeast poly(A)⁺ RNA interactome reveal insights into organization and function of RNA–protein complexes
- Cornelia Kilchert,
- Tea Kecman,
- Emily Priest,
- Svenja Hester,
- Ebru Aydin,
- Krzysztof Kus,
- Oliver Rossbach,
- Alfredo Castello,
- Shabaz Mohammed,
- and Lidia Vasiljeva
Genome Res. July 2020 30: 1012-1026; Published in Advance June 18, 2020, doi:10.1101/gr.257006.119
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LETTER: Evolution of protein domain promiscuity in eukaryotes
- Malay Kumar Basu,
- Liran Carmel,
- Igor B. Rogozin,
- and Eugene V. Koonin
Genome Res. March 2008 18: 449-461; Published in Advance January 29, 2008, doi:10.1101/gr.6943508
...eukaryotes. Altogether, 215 domains are identified as strongly promiscuous. The fraction of promiscuous domains in animals is shown to be significantly greater than that in fungi or plants. Evolutionary reconstructions indicate that domain promiscuity is a volatile, relatively fast-changing feature...
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