Searching journal content for articles similar to Boeke 13 (9): 1975.

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  1. Research: Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits
    • Elise Parey,
    • Diego Fernandez-Aroca,
    • Stephanie Frost,
    • Ainhoa Uribarren,
    • Thomas J. Park,
    • Markus Zöttl,
    • Ewan St. John Smith,
    • Camille Berthelot,
    • and Diego Villar
    Genome Res. September 2023 33: 1513-1526; Published in Advance August 25, 2023, doi:10.1101/gr.277715.123
    .... First, we adapted and applied a phylogenetic modeling approach to quantitatively compare epigenomic signals at orthologous regulatory elements and identified thousands of promoter and enhancer regions with differential epigenomic activity in mole-rats. These elements associate with known mole...
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  2. 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
    ...,675 for C. nigoni and from 22,830 to 23,282 for C. briggsae isolates (Fig. 1A,B; Supplemental Table S1).View larger version: In this window In a new window Figure 1. Comparative analysis reveals larger sizes and higher gene numbers in C. nigoni strains relative to C. briggsae strains. (Left) Phylogenetic...
  3. Research: Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species
    • Damira Veseljak,
    • Evelin Despot-Slade,
    • Marin Volarić,
    • Lucija Horvat,
    • Tanja Vojvoda Zeljko,
    • Nevenka Meštrović,
    • and Brankica Mravinac
    Genome Res. November 2025 35: 2445-2460; Published in Advance September 16, 2025, doi:10.1101/gr.280516.125
    ...Fig. S11A). We found this transposon-like element scattered on all chromosomes in both species, except for the T. castaneum X Chromosome (Supplemental Fig. S11B). Phylogenetic analysis showed that copies from T. castaneum and T. freemani generally separated in species-specific groups (Supplemental Fig...
  4. Letter: Unusual composition of a yeast chromosome arm is associated with its delayed replication
    • Célia Payen,
    • Gilles Fischer,
    • Christian Marck,
    • Caroline Proux,
    • David James Sherman,
    • Jean-Yves Coppée,
    • Mark Johnston,
    • Bernard Dujon,
    • and Cécile Neuvéglise
    Genome Res. October 2009 19: 1710-1721; Published in Advance July 10, 2009, doi:10.1101/gr.090605.108
    ...Unusual composition of a yeast chromosome arm is associated with its delayed replication Célia Payen 1 , Gilles Fischer 1 , Christian Marck 2 , Caroline Proux 3 , David James Sherman 4 , Jean-Yves Coppée 3 , Mark Johnston 5...
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  5. 12 Drosophila Genomes/Letter: Drosophila telomeric retrotransposons derived from an ancestral element that was recruited to replace telomerase
    • Alfredo Villasante,
    • José P. Abad,
    • Rosario Planelló,
    • María Méndez-Lago,
    • Susan E. Celniker,
    • and Beatriz de Pablos
    Genome Res. December 2007 17: 1909-1918; Published in Advance November 7, 2007, doi:10.1101/gr.6365107
    ...). The phylogenetic relationship among these telomeric elements is congruent with the phylogeny of the species, suggesting that they have been vertically inherited from a common ancestor. Our results suggest that an existing non-LTR retrotransposon was recruited to perform the cellular function of telomere...
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  6. Research: The rate and spectrum of new mutations in mice inferred by long-read sequencing
    • Eugenio López-Cortegano,
    • Jobran Chebib,
    • Anika Jonas,
    • Anastasia Vock,
    • Sven Künzel,
    • Peter D. Keightley,
    • and Diethard Tautz
    Genome Res. January 2025 35: 43-54; Published in Advance December 2, 2024, doi:10.1101/gr.279982.124
    ...or directly as a consequence of transposition. For example, LINE retrotransposons occasionally promote large deletions upon aberrant insertion into the (Rodriguez-Martin et al. 2020) and can act as substrate for ectopic recombination, resulting in diverse types of SM (Balachandran et al. 2022).SMs have been...
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  7. Research: Diversification and collapse of a telomere elongation mechanism
    • Bastien Saint-Leandre,
    • Son C. Nguyen,
    • and Mia T. Levine
    Genome Res. June 2019 29: 920-931; Published in Advance May 28, 2019, doi:10.1101/gr.245001.118
    ...consistent with both predictions. Searching the raw reads of the 15-Myr-old melanogaster species group, we generated de novo jockey retrotransposon consensus sequences and used phylogenetic tree-building to delineate four distinct telomere-associated lineages. Recurrent gains, losses, and replacements...
  8. Research: Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza
    • Rodolphe Dombey,
    • Daniel Buendía-Ávila,
    • Verónica Barragán-Borrero,
    • Laura Diezma-Navas,
    • Arturo Ponce-Mañe,
    • José Mario Vargas-Guerrero,
    • Rana Elias,
    • and Arturo Marí-Ordóñez
    Genome Res. March 2025 35: 522-544; Published in Advance March 4, 2025, doi:10.1101/gr.279532.124
    ...RdDM targets such as 5S rDNA repeats and further strengthens the hypothesis that such silencing mechanisms only apply to long, complete TEs. Indeed, increased H3K9me2 and DNA methylation at long TEs hints that their self-reinforcement is focused at potentially functional or recently active ones...
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  9. Resource: The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals
    • Christine E. Schnitzler,
    • E. Sally Chang,
    • Justin Waletich,
    • Gonzalo Quiroga-Artigas,
    • Wai Yee Wong,
    • Anh-Dao Nguyen,
    • Sofia N. Barreira,
    • Liam B. Doonan,
    • Paul Gonzalez,
    • Sergey Koren,
    • James M. Gahan,
    • Steven M. Sanders,
    • Brian Bradshaw,
    • Timothy Q. DuBuc,
    • Febrimarsa,
    • Danielle de Jong,
    • Eric P. Nawrocki,
    • Alexandra Larson,
    • Samantha Klasfeld,
    • Sebastian G. Gornik,
    • R. Travis Moreland,
    • Tyra G. Wolfsberg,
    • Adam M. Phillippy,
    • James C. Mullikin,
    • Oleg Simakov,
    • Paulyn Cartwright,
    • Matthew Nicotra,
    • Uri Frank,
    • and Andreas D. Baxevanis
    Genome Res. March 2024 34: 498-513; Published in Advance March 20, 2024, doi:10.1101/gr.278382.123
    ...development with no larval stage. These differences between the two lineages are unsurprising given that they diverged at least 500 million years ago (MYA) (Steele et al. 2011).View larger version: In this window In a new window Figure 1. Overview of Hydractinia, phylogenetic analysis, synteny analysis...
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  10. Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
    • Xinghua Li,
    • Judith E. Mank,
    • and Liping Ban
    Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
    ...of the X Chromosome to test for temporal dynamics to Fast-X evolution, and find evidence of a recent burst evolution for new X-linked genes in contrast to slow evolution of X-conserved genes.Grasshoppers (order Orthoptera, suborder Caelifera) represent an important phylogenetic and developmental comparison...
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