Searching journal content for articles similar to Thomas et al. 16 (7): 934.

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  1. Research: The impact of widespread regulatory neofunctionalization on homeolog gene evolution following whole-genome duplication in maize
    • Thomas E. Hughes,
    • Jane A. Langdale,
    • and Steven Kelly
    Genome Res. August 2014 24: 1348-1355; Published in Advance April 30, 2014, doi:10.1101/gr.172684.114
    ..., Bennetzen JL, Messing J. 2004b. On the tetraploid origin of the maize . Comp Funct Genomics 5: 281–284. Thomas BC, Pedersen B, Freeling M. 2006. Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Res...
  2. 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
    ...from the most recent paleotetraploidy ( Bowers et al. 2003 ; Thomas et al. 2006 ). Over 80% of the Arabidopsis can be homeologously paired using these α-pairs. Following this tetraploidy, most duplicate (homeologous) genes were fractionated from one or the other, but not both, homeologs, leaving ∼25...
  3. Research: Positionally biased gene loss after whole genome duplication: Evidence from human, yeast, and plant
    • Takashi Makino and
    • Aoife McLysaght
    Genome Res. December 2012 22: 2427-2435; Published in Advance July 26, 2012, doi:10.1101/gr.131953.111
    ...for the clustering of interacting genes such as coexpression or preservation of epistatic interactions. Here we conduct a novel test of a hypothesis that functionally linked genes in the same paralogon are preferentially retained in cis afterWGD.We compare the number of protein–protein interactions (PPIs) between...
  4. Methods: Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps
    • Haibao Tang,
    • Xiyin Wang,
    • John E. Bowers,
    • Ray Ming,
    • Maqsudul Alam,
    • and Andrew H. Paterson
    Genome Res. December 2008 18: 1944-1954; Published in Advance October 2, 2008, doi:10.1101/gr.080978.108
    ...universal common ancestor of angiosperms. Comparative analysis of inferred homologous genes derived from this model shows patterns of preferential gene retention or loss after polyploidy and reveals large variability of nucleotide substitution rates among plant nuclear genomes. Footnotes ↵ 6...
  5. Research: The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible
    • Yue Hao,
    • Makenzie E. Mabry,
    • Patrick P. Edger,
    • Michael Freeling,
    • Chunfang Zheng,
    • Lingling Jin,
    • Robert VanBuren,
    • Marivi Colle,
    • Hong An,
    • R. Shawn Abrahams,
    • Jacob D. Washburn,
    • Xinshuai Qi,
    • Kerrie Barry,
    • Christopher Daum,
    • Shengqiang Shu,
    • Jeremy Schmutz,
    • David Sankoff,
    • Michael S. Barker,
    • Eric Lyons,
    • J. Chris Pires,
    • and Gavin C. Conant
    Genome Res. May 2021 31: 799-810; Published in Advance April 16, 2021, doi:10.1101/gr.270033.120
    ...functioning in DNA repairGO overrepresentation tests were performed with the Arabidopsis orthologs of genes returned to single copy by the end of the root branch from each sub. Similar to previous findings (De Smet et al. 2013), we found that single-copy genes are enriched in biological processes such as DNA...
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  6. Research: Differential retention and divergent resolution of duplicate genes following whole-genome duplication
    • Casey L. McGrath,
    • Jean-Francois Gout,
    • Parul Johri,
    • Thomas G. Doak,
    • and Michael Lynch
    Genome Res. October 2014 24: 1665-1675; Published in Advance August 1, 2014, doi:10.1101/gr.173740.114
    ...the divergence of these two species, making it unlikely that the asymmetry reflects an allopolyploidy event. The small excess of asymmetrical gene loss observed here could have been caused by physical clustering of functional linked genes along chromosomes, as observed inhuman, yeast, and Arabidopsis (Makino...
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