Searching journal content for articles similar to Thomas 16 (8): 1017.

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  1. 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
    ...in nematodes (Thomas 2006). These findings suggest that C. nigoni populations are likely to experience some stronger selection pressures such as pathogen exposure compared with C. briggsae, driving the species-specific expansion and evolution of the ubiquitin-ligase-adaptor genes.View larger version...
  2. 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
    ...cerevisiae and Schizosaccharomyces pombe , the nematode Caenorhabditis elegans , the fruit fly Drosophila melanogaster , and the green plant Arabidopsis thaliana . A significant fraction of the proteins encoded in each of these s, up to 80% in A. thaliana , belong to LSEs. Many paralogous gene families...
  3. Method: Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis
    • Alejandro Ceron-Noriega,
    • Miguel V. Almeida,
    • Michal Levin,
    • and Falk Butter
    Genome Res. January 2023 33: 112-128; Published in Advance January 18, 2023, doi:10.1101/gr.277070.122
    ...positive selection across the studied nematode species. As expected, the majority of genes show genetic drift: 45.3% for Caenorhabditis, 56.4% for Eurhabditis, and 63.2% for Rhabditida (Fig. 5C). As we were mostly interested in signals of positive (adaptive) evolution, we evaluated branch-site models...
  4. LETTER: Many or most genes in Arabidopsis transposed after the origin of the order Brassicales
    • Michael Freeling,
    • Eric Lyons,
    • Brent Pedersen,
    • Maqsudul Alam,
    • Ray Ming,
    • and Damon Lisch
    Genome Res. December 2008 18: 1924-1937; Published in Advance October 3, 2008, doi:10.1101/gr.081026.108
    ...that plant disease-resistance gene clusters might generate diversity under extreme stress ( Friedman and Baker 2007 ). Here we present evidence that NB-LRR genes, and many others, are particularly prone to have become transposed. In contrast, genes in other gene families, like those encoding most sorts...
  5. Methods: Efficient high-resolution deletion discovery in Caenorhabditis elegans by array comparative genomic hybridization
    • Jason S. Maydan,
    • Stephane Flibotte,
    • Mark L. Edgley,
    • Joanne Lau,
    • Rebecca R. Selzer,
    • Todd A. Richmond,
    • Nathan J. Pofahl,
    • James H. Thomas,
    • and Donald G. Moerman
    Genome Res. March 2007 17: 337-347; Published in Advance January 31, 2007, doi:10.1101/gr.5690307
    ...of indel differences observed among the Bristol, Hawaiian, and Madeiran nematode strains points to the dynamic nature of s and the flux of many of the gene families within this organism. Results Oligonucleotide probe quality and detection of homozygous 50-kb and 1-kb deletions We designed a pilot...
  6. Methods: Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays
    • Georg Zeller,
    • Richard M. Clark,
    • Korbinian Schneeberger,
    • Anja Bohlen,
    • Detlef Weigel,
    • and Gunnar Rätsch
    Genome Res. June 2008 18: 918-929; Published in Advance March 6, 2008, doi:10.1101/gr.070169.107
    ...plant with a sequenced (Supplemental Fig. S9; Tuskan et al. 2006 ). Among large gene families within A. thaliana ( n > 125) ( Clark et al. 2007 ), variation in PR content was readily apparent ( Fig. 7A,B ; Supplemental Fig. S10). Transcription factors, for which MBML2 SNP data suggested strong...
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