Searching journal content for articles similar to Brashear et al. 28 (12): 1841.

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  1. Research: Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly
    • Kang Du,
    • Oliver Deusch,
    • Ilja Bezrukov,
    • Christa Lanz,
    • Yann Guiguen,
    • Margarete Hoffmann,
    • Anette Habring,
    • Detlef Weigel,
    • Manfred Schartl,
    • and Christine Dreyer
    Genome Res. March 2025 35: 489-498; Published in Advance March 5, 2025, doi:10.1101/gr.279582.124
    ...possible fidelity of more individuals from different populations and different guppy species to distinguish private SNPs and sequence variation from those that are conserved across all individuals that share the same SD gene and genes encoding sex-linked traits. One possible strategy could be amplicon...
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  2. Mini-Review: Toward telomere-to-telomere cat genomes for precision medicine and conservation biology
    • William J. Murphy and
    • Andrew J. Harris
    Genome Res. May 2024 34: 655-664; Published in Advance June 7, 2024, doi:10.1101/gr.278546.123
    ...(tens of megabases), homologous, gene-rich recombination cold spots shared across the cat family and even with other orders of mammals (Li et al. 2016a,b, 2019; Figueiró et al. 2017, Bredemeyer et al. 2023). A recent study analyzing structural variation from near-gapless single-haplotype s from multiple...
  3. Research: Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages
    • Tracy Jiaye Lee,
    • Yu-Ching Liu,
    • Wei-An Liu,
    • Yu-Fei Lin,
    • Hsin-Han Lee,
    • Huei-Mien Ke,
    • Jen-Pan Huang,
    • Mei-Yeh Jade Lu,
    • Chia-Lun Hsieh,
    • Kuo-Fang Chung,
    • Gianni Liti,
    • and Isheng Jason Tsai
    Genome Res. May 2022 32: 864-877; Published in Advance March 31, 2022, doi:10.1101/gr.276286.121
    ...in the evolution of domesticated S. cerevisiae strains showing more rapid copy number variation than wild strains (Bergström et al. 2014; Yue et al. 2017; Duan et al. 2018). To investigate the extent to which gene families differed between sister natural lineages, we de novo assembled, annotated, and inferred...
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  4. Research: Genomic architecture constrained placental mammal X Chromosome evolution
    • Wesley A. Brashear,
    • Kevin R. Bredemeyer,
    • and William J. Murphy
    Genome Res. August 2021 31: 1353-1365; Published in Advance July 22, 2021, doi:10.1101/gr.275274.121
    ..., and each species possesses one or more members of the same CTA gene family. Ancestral ampliconic genes were also found to be enriched for CTA genes that are expressed in early spermatogenesis and are restricted to the X-conserved region, the portion of the X Chromosome conserved between placental mammals...
  5. Research: The 22q11 low copy repeats are characterized by unprecedented size and structural variability
    • Wolfram Demaerel,
    • Yulia Mostovoy,
    • Feyza Yilmaz,
    • Lisanne Vervoort,
    • Steven Pastor,
    • Matthew S. Hestand,
    • Ann Swillen,
    • Elfi Vergaelen,
    • Elizabeth A. Geiger,
    • Curtis R. Coughlin,
    • Stephen K. Chow,
    • Donna McDonald-McGinn,
    • Bernice Morrow,
    • Pui-Yan Kwok,
    • Ming Xiao,
    • Beverly S. Emanuel,
    • Tamim H. Shaikh,
    • and Joris R. Vermeesch
    Genome Res. September 2019 29: 1389-1401; doi:10.1101/gr.248682.119
    ..., their exact locations have, despite extensive efforts (Guo et al. 2016), remained elusive. We set out to map these repeats to elucidate the LCR22 structures and their variability and to further refine the 22q11DS rearrangement breakpoint regions.ResultsSubunit-resolution LCR assemblies using fiber FISHTo...
  6. Research: Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome
    • Daniela S. Aliaga Goltsman,
    • Christine L. Sun,
    • Diana M. Proctor,
    • Daniel B. DiGiulio,
    • Anna Robaczewska,
    • Brian C. Thomas,
    • Gary M. Shaw,
    • David K. Stevenson,
    • Susan P. Holmes,
    • Jillian F. Banfield,
    • and David A. Relman
    Genome Res. October 2018 28: 1467-1480; Published in Advance September 19, 2018, doi:10.1101/gr.236000.118
    ....Sources of variation in community-wide gene profilesTo gain insights into all potential sources of variation in the patterns of gene abundance across all subjects and samples, nonmetric multidimensional scaling (NMDS) was performed on variance-stabilized abundances of gene families represented in the UniRef90 database...
  7. Resource: Extensive alternative polyadenylation during zebrafish development
    • Igor Ulitsky,
    • Alena Shkumatava,
    • Calvin H. Jan,
    • Alexander O. Subtelny,
    • David Koppstein,
    • George W. Bell,
    • Hazel Sive,
    • and David P. Bartel
    Genome Res. October 2012 22: 2054-2066; Published in Advance June 21, 2012, doi:10.1101/gr.139733.112
    .... elegans sites (Supplemental Fig. S2). Thus, the sequence specificity of the CPA machinery appears to be conserved among fish, mammals, and worms. When related to the annotated gene models (Fig. 1C; Supplemental Fig. S1; Supplemental Table S2), only 19.3% of the poly(A) sites were within 100 bases...
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  8. Research: Great ape Y Chromosome and mitochondrial DNA phylogenies reflect subspecies structure and patterns of mating and dispersal
    • Pille Hallast,
    • Pierpaolo Maisano Delser,
    • Chiara Batini,
    • Daniel Zadik,
    • Mariano Rocchi,
    • Werner Schempp,
    • Chris Tyler-Smith,
    • and Mark A. Jobling
    Genome Res. April 2016 26: 427-439; Published in Advance February 16, 2016, doi:10.1101/gr.198754.115
    ...Great ape Y Chromosome and mitochondrial DNA phylogenies reflect subspecies structure and patterns of mating and dispersal Pille Hallast 1 , 2 , Pierpaolo Maisano Delser 1 , 6 , Chiara Batini 1 , Daniel Zadik 1 , Mariano Rocchi 3...
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  9. LETTER: Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition
    • Keiko Akagi,
    • Jingfeng Li,
    • Robert M. Stephens,
    • Natalia Volfovsky,
    • and David E. Symer
    Genome Res. June 2008 18: 869-880; Published in Advance April 1, 2008, doi:10.1101/gr.075770.107
    ...the , as they are excluded significantly from the X chromosome and from genes associated with the cell cycle, but are enriched in receptor genes. Thus, recent endogenous L1 retrotransposition has diversified genomic structures and transcripts extensively, distinguishing mouse lineages and driving a major portion of natural...
  10. REVIEW: Defensins and the dynamic genome: What we can learn from structural variation at human chromosome band 8p23.1
    • Edward J. Hollox,
    • John C.K. Barber,
    • Anthony J. Brookes,
    • and John A.L. Armour
    Genome Res. November 2008 18: 1686-1697; doi:10.1101/gr.080945.108
    ...Defensins and the dynamic genome: What we can learn from structural variation at human chromosome band 8p23.1 Edward J. Hollox 1 , 4 , John C.K. Barber 2 , Anthony J. Brookes 1 , and John A.L. Armour 3 1 Department of Genetics...
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