Searching journal content for articles similar to Cho et al. 14 (7): 1207.

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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
    ...studies may overlook. On the other hand, analyses of genomic variation frequently reveal a complex interplay among sequence changes, including single-nucleotide polymorphisms (SNPs) and structural variations (SVs), which are associated with altered gene expression and phenotypic traits (Collins et al...
  2. Research: Genetic exchange with an outcrossing sister species causes severe genome-wide dysregulation in a selfing Caenorhabditis nematode
    • Dongying Xie,
    • Pohao Ye,
    • Yiming Ma,
    • Yongbin Li,
    • Xiao Liu,
    • Peter Sarkies,
    • and Zhongying Zhao
    Genome Res. November/December 2022 32: 2015-2027; Published in Advance November 9, 2022, doi:10.1101/gr.277205.122
    ...frequently observed in hybrids (Wei et al. 2014; Lu et al. 2018; Moran et al. 2021). Notably, our previous study of hybrid sterile males between C. briggsae and C. nigoni, resulting from extensive backcrossing with C. nigoni, also revealed the dysregulation of spermatogenesis genes (Li et al. 2016b...
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  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
    ...the gene tree that best represents the underlying alignment. These very solid orthology groups represent a highly useful resource for universal nematode analyses given that our study showed that the frequently used BUSCO set of single-copy orthologs does not really represent the common nematode proteome...
  4. Research: Transposable elements drive the evolution of metazoan zinc finger genes
    • Jonathan N. Wells,
    • Ni-Chen Chang,
    • John McCormick,
    • Caitlyn Coleman,
    • Nathalie Ramos,
    • Bozhou Jin,
    • and Cédric Feschotte
    Genome Res. August 2023 33: 1325-1339; Published in Advance September 15, 2023, doi:10.1101/gr.277966.123
    .... 2019). Furthermore, they are frequently lineage-specific; for example, a survey of three great ape species and rhesus macaque found that ∼10% (213 out of 2253) of predicted KRAB-ZNFs (KZNFs) were species-specific, including seven from humans and 145 from orangutangs (Nowick et al. 2011). This rapid...
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  5. Research: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster
    • Anna Grandchamp,
    • Lucas Kühl,
    • Marie Lebherz,
    • Kathrin Brüggemann,
    • John Parsch,
    • and Erich Bornberg-Bauer
    Genome Res. June 2023 33: 872-890; Published in Advance July 13, 2023, doi:10.1101/gr.277482.122
    ...ORFs shared by lines, suggesting a rapid turnover. Gain and loss of transcription is more frequent than the creation of ORFs, for example, by forming new start and stop codons. Consequently, the gain of ORFs becomes rate limiting and is frequently the initial step in neORFs emergence. Furthermore...
  6. Research: A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes
    • Stefanie Mühlhausen,
    • Peggy Findeisen,
    • Uwe Plessmann,
    • Henning Urlaub,
    • and Martin Kollmar
    Genome Res. July 2016 26: 945-955; Published in Advance May 6, 2016, doi:10.1101/gr.200931.115
    ..., including the branches with altered decoding. The polyphyly of the tRNALeuCAGs is not explained in either of the scenarios. The scenario of two successive CUG-codon reassignments is further weakened by the frequent nature of the CUG codon. Although phylogenetic mapping of variant codes has shown...
  7. Research: Evolution of selenophosphate synthetases: emergence and relocation of function through independent duplications and recurrent subfunctionalization
    • Marco Mariotti,
    • Didac Santesmasses,
    • Salvador Capella-Gutierrez,
    • Andrea Mateo,
    • Carme Arnan,
    • Rory Johnson,
    • Salvatore D'Aniello,
    • Sun Hee Yim,
    • Vadim N. Gladyshev,
    • Florenci Serras,
    • Montserrat Corominas,
    • Toni Gabaldón,
    • and Roderic Guigó
    Genome Res. September 2015 25: 1256-1267; Published in Advance July 20, 2015, doi:10.1101/gr.190538.115
    ...and the SECIS element degenerated. This exemplifies an evolutionary scenario, not frequently reported in the literature, in which alternative transcripts precede gene duplication, providing a possible intermediary step of how a dual-function protein can escape from adaptive conflict (Hittinger and Carroll 2007...
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  8. 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
    ...by homologous recombination (Bernstein et al. 1983; Lewin 1983; Boeke et al. 1985). Since reverse transcription is processed from 39 to 59, and often terminates prematurely, intron losses are expected to occur more frequently in the 39 end of the genes (Fink 1987; Mourier and Jeffares 2003). Nonetheless...
  9. LETTER: Evolutionary dynamics of nematode operons: Easy come, slow go
    • Wenfeng Qian and
    • Jianzhi Zhang
    Genome Res. March 2008 18: 412-421; Published in Advance January 24, 2008, doi:10.1101/gr.7112608
    ...mapped the operon gain and loss events onto the nematode phylogeny ( Fig. 1 ). From the common ancestor of the four Caenorhabditis species to present, 56 operons were formed in the C. elegans lineage. During the same period of time, on average, {[(17 + 12)/2 + 3]+16}/2 = 16.75 operons were broken per...
  10. LETTER: Evolution of Intron/Exon Structure of DEAD Helicase Family Genes in Arabidopsis, Caenorhabditis, and Drosophila
    • Nathalie Boudet,
    • Sébastien Aubourg,
    • Claire Toffano-Nioche,
    • Martin Kreis,
    • and Alain Lecharny
    Genome Res. December 1, 2001 11: 2101-2114; Published in Advance November 12, 2001, doi:10.1101/gr.200801
    ...Evolution of Intron/Exon Structure of DEAD Helicase Family Genes in Arabidopsis , Caenorhabditis , and Drosophila Nathalie Boudet 1 , Sébastien Aubourg 1 , 2 , Claire Toffano-Nioche 1 , Martin Kreis 1 , and Alain Lecharny 1 , 3...
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