Searching journal content for articles similar to Daubin et al. 12 (7): 1080.

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  1. Method: Accurate reconstruction of bacterial pan- and core genomes with PEPPAN
    • Zhemin Zhou,
    • Jane Charlesworth,
    • and Mark Achtman
    Genome Res. November 2020 30: 1667-1679; Published in Advance October 14, 2020, doi:10.1101/gr.260828.120
    ...of these was disrupted in at least one of the 14,115 Streptococcus s in RefSeq. This is a common problem for core analyses, especially because the multiple contigs within draft s can result in the absence of multiple genes from assemblies. Core schemes used for cgMLST are therefore usually based on a relaxed core...
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  2. Resource: The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity
    • Zhemin Zhou,
    • Nabil-Fareed Alikhan,
    • Khaled Mohamed,
    • Yulei Fan,
    • the Agama Study Group,
    • and Mark Achtman
    Genome Res. January 2020 30: 138-152; Published in Advance December 6, 2019, doi:10.1101/gr.251678.119
    ..., Vibrio, and Moraxella and genotyped those assemblies by core multilocus sequence typing (cgMLST). Hierarchical clustering of cgMLST sequence types allows mapping a new bacterial strain to predefined population structures at multiple levels of resolution within a few hours after uploading its short reads...
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  3. Research: Single worm transcriptomics identifies a developmental core network of oscillating genes with deep conservation across nematodes
    • Shuai Sun,
    • Christian Rödelsperger,
    • and Ralf J. Sommer
    Genome Res. September 2021 31: 1590-1601; Published in Advance July 22, 2021, doi:10.1101/gr.275303.121
    ...). Both species reproduce as hermaphrodites, which made them important model organisms with the associated establishment of extensive technology platforms as indicated above. P. pacificus and C. elegans are thought to have shared a last common ancestor ∼100 mya (Prabh et al. 2018; Werner et al. 2018...
  4. LETTER: The Genetic Core of the Universal Ancestor
    • J. Kirk Harris,
    • Scott T. Kelley,
    • George B. Spiegelman,
    • and Norman R. Pace
    Genome Res. March 1, 2003 13: 407-412; Published in Advance February 12, 2003, doi:10.1101/gr.652803
    ...to the last common ancestor (LCA) of life. We used the Clusters of Orthologous Groups of proteins (COG) database ( Tatusov et al. 2001 ) to search for constituents of the genetic core by identifying the universally conserved set of related genes that have the same phylogenetic history as rRNA. If a gene...
  5. LETTER: Computing prokaryotic gene ubiquity: Rescuing the core from extinction
    • Robert L. Charlebois and
    • W. Ford Doolittle
    Genome Res. December 2004 14: 2469-2477; doi:10.1101/gr.3024704
    .... 184 : 2072 -2080. ↵ Daubin, V., Gouy, M., and Perrière, G. 2002 . A phylogenomic approach to bacterial phylogeny: Evidence of a core of genes sharing a common history. Genome Res. 12 : 1080 -1090. ↵ Daubin, V., Moran, N.A., and Ochman, H. 2003 . Phylogenetics and the cohesion of bacterial s. Science...
  6. Letter: Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter
    • Tristan Lefébure and
    • Michael J. Stanhope
    Genome Res. July 2009 19: 1224-1232; Published in Advance March 20, 2009, doi:10.1101/gr.089250.108
    ...University, Ithaca, New York 14853, USA Abstract An open question in bacterial genomics is the role that adaptive evolution of the core genome plays in diversification and adaptation of bacterial species, and how this might differ between groups of bacteria occupying different environmental...
  7. Research: Analyses of 600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges
    • John S. Sproul,
    • Scott Hotaling,
    • Jacqueline Heckenhauer,
    • Ashlyn Powell,
    • Dez Marshall,
    • Amanda M. Larracuente,
    • Joanna L. Kelley,
    • Steffen U. Pauls,
    • and Paul B. Frandsen
    Genome Res. October 2023 33: 1708-1717; Published in Advance September 22, 2023, doi:10.1101/gr.277387.122
    ...in the organization, stability, regulation, and evolution of s (Bourque et al. 2018; Wells and Feschotte 2020). At broad scale, REs shape chromatin domains across chromosomes and impact the three-dimensional organization of DNA (Winter et al. 2018; Sun et al. 2020). Rapidly evolving blocks of REs are common sites...
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  8. Research: Contiguous and complete assemblies of Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology
    • Abigail L. Lind,
    • Nathan A. McDonald,
    • Elias R. Gerrick,
    • Ami S. Bhatt,
    • and Katherine S. Pollard
    Genome Res. June 2025 35: 1377-1390; Published in Advance April 22, 2025, doi:10.1101/gr.279080.124
    ...).Although Blastocystis is widespread across vertebrates, there is limited evidence for co-phylogeny of Blastocystis subtypes with their host (Fig. 1). Instead, the Blastocystis phylogeny more closely resembles that of spore-forming gut bacteria (Moeller et al. 2016), with host switching as a common...
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  9. Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
    • Jacopo Martelossi,
    • Jacopo Vujovic,
    • Yue Huang,
    • Alessia Tatti,
    • Kaiwei Xu,
    • Federico Puliga,
    • Yuanxue Chen,
    • Omar Rota Stabelli,
    • Fabrizio Ghiselli,
    • Xiaoping Zhang,
    • and Alessandra Zambonelli
    Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
    ...lineage-specific activity. Together with the presence of representative elements in several other Pezizales species, this makes Tuberaceae an iconic example of how an apparently common size expansion within a clade can be driven by parallel genomic trajectories, involving the differential lineage...
  10. Method: Memory-bound k-mer selection for large and evolutionarily diverse reference libraries
    • Ali Osman Berk Şapcı and
    • Siavash Mirarab
    Genome Res. September 2024 34: 1455-1467; Published in Advance August 29, 2024, doi:10.1101/gr.279339.124
    ...(default), dividing queries into bins of novelty (d*). (C,D) Evaluation of simple ranking strategies (discriminative, common, random) implemented using species counts R or children counts, R′ and our new weighted-sum, R* heuristic [Equation (11)]. See Supplemental Figure S2 for an illustration of functions...
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