Searching journal content for articles similar to Hughes and Friedman 13 (5): 794.

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  1. 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...
  2. Method: Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe
    • Arnaud Belcour,
    • Jeanne Got,
    • Méziane Aite,
    • Ludovic Delage,
    • Jonas Collén,
    • Clémence Frioux,
    • Catherine Leblanc,
    • Simon M. Dittami,
    • Samuel Blanquart,
    • Gabriel V. Markov,
    • and Anne Siegel
    Genome Res. June 2023 33: 972-987; Published in Advance July 19, 2023, doi:10.1101/gr.277056.122
    ...that could help detect signals of adaptation in an overall noisy data set. Such models exist, for instance, to detect selective signatures in the evolution of the protein-coding gene (Shapiro and Alm 2008) but, to our knowledge, have not been developed for metabolic networks or presence/absence signatures...
  3. Research: The evolution of duplicate gene expression in mammalian organs
    • Katerina Guschanski,
    • Maria Warnefors,
    • and Henrik Kaessmann
    Genome Res. September 2017 27: 1461-1474; Published in Advance July 25, 2017, doi:10.1101/gr.215566.116
    ...in transcription and regulation of gene Figure 2. Median expression levels for single-copy (yellow) and duplicate genes (shades of blue) across all organs in the mouse . Duplicate genes are grouped into age classes. Expression evolution of mammalian duplicate genes Genome Research 1463 www..org expression...
  4. Research: Intron evolution in Neurospora: the role of mutational bias and selection
    • Yu Sun,
    • Carrie A. Whittle,
    • Pádraic Corcoran,
    • and Hanna Johannesson
    Genome Res. January 2015 25: 100-110; Published in Advance October 23, 2014, doi:10.1101/gr.175653.114
    ...) Intron gain/loss rate ratio. Intron evolution in Neurospora Genome Research 103 www..org with the RT-mRNA as an intron loss mechanism for these particular genes. No statistically significant differences were detected in the number of short direct repeats for the lost introns (inferred by the sequence...
  5. Research: Polygenic cis-regulatory adaptation in the evolution of yeast pathogenicity
    • Hunter B. Fraser,
    • Sasha Levy,
    • Arun Chavan,
    • Hiral B. Shah,
    • J. Christian Perez,
    • Yiqi Zhou,
    • Mark L. Siegal,
    • and Himanshu Sinha
    Genome Res. October 2012 22: 1930-1939; Published in Advance May 29, 2012, doi:10.1101/gr.134080.111
    ...-alleles at 37°C in vitro for 11 of 11 RH strain pairs. Genes are ordered by decreasing significance of the Y-allele advantage. Error bars, 61 SE. Fraser et al. 1934 Genome Research www..org Prud’homme et al. 2007; Wray 2007; Rebeiz et al. 2009, Manceau et al. 2011). Since unicellular species such as yeast...
  6. Review: Origins, evolution, and phenotypic impact of new genes
    • Henrik Kaessmann
    Genome Res. October 2010 20: 1313-1326; Published in Advance July 22, 2010, doi:10.1101/gr.101386.109
    ....e., after the divergence from lineage of egg-layingmonotremes), and hence are younger than previously thought (Potrzebowski et al. 2008). Notably, tracing the evolutionary origin of individual X-derived retrogenes also identified striking cases of independent parallel exports of key housekeeping genes...
  7. RESOURCE: Comparative genome analysis across a kingdom of eukaryotic organisms: Specialization and diversification in the Fungi
    • Michael J. Cornell,
    • Intikhab Alam,
    • Darren M. Soanes,
    • Han Min Wong,
    • Cornelia Hedeler,
    • Norman W. Paton,
    • Magnus Rattray,
    • Simon J. Hubbard,
    • Nicholas J. Talbot,
    • and Stephen G. Oliver
    Genome Res. December 2007 17: 1809-1822; Published in Advance November 5, 2007, doi:10.1101/gr.6531807
    .... This observation has been confirmed by the lack of a homolog of the S. cerevisiae FOX2 gene (which encodes a multifunctional β-oxidation protein) in the s of either of these two fungi. The lack of β-oxidation has been noted before in the case of E. cuniculi and is not surprising, since this unicellular eukaryote...
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  8. Methods: Reconstructing ancestral gene content by coevolution
    • Tamir Tuller,
    • Hadas Birin,
    • Uri Gophna,
    • Martin Kupiec,
    • and Eytan Ruppin
    Genome Res. January 2010 20: 122-132; Published in Advance November 30, 2009, doi:10.1101/gr.096115.109
    .... Abstract Inferring the gene content of ancestral genomes is a fundamental challenge in molecular evolution. Due to the statistical nature of this problem, ancestral genomes inferred by the maximum likelihood (ML) or the maximum-parsimony (MP) methods are prone to considerable error rates. In general...
  9. 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
    ...beyond sequence per se, such as gene composition and gene order, have been used to construct “ trees” that, generally, combine the phylogenetic signal with signals reflecting the lifestyles of the compared organisms, for example, parallel gene loss in parasites ( Snel et al. 1999 , 2005 ; Wolf et al...
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  10. LETTER: The Role of Lineage-Specific Gene Family Expansion in the Evolution of Eukaryotes
    • Olivier Lespinet,
    • Yuri I. Wolf,
    • Eugene V. Koonin,
    • and L. Aravind
    Genome Res. July 1, 2002 12: 1048-1059; doi:10.1101/gr.174302
    ...://ncbi.nlm.nih.gov/pub/aravind/expansions , and http://www..org .] The eukaryotic crown group (the unresolved assemblage of lineages in the eukaryotic tree, which includes plants, animals, fungi, and some protists, as opposed to early branching eukaryotes, which are all unicellular protists), although only representing the proverbial tip...
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