Searching journal content for articles similar to Vakirlis et al. 26 (7): 918.

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  1. Research: Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution
    • Chris Papadopoulos,
    • Isabelle Callebaut,
    • Jean-Christophe Gelly,
    • Isabelle Hatin,
    • Olivier Namy,
    • Maxime Renard,
    • Olivier Lespinet,
    • and Anne Lopes
    Genome Res. December 2021 31: 2303-2315; Published in Advance November 22, 2021, doi:10.1101/gr.275638.121
    ...predicted as foldable. Then, we investigated the early stages of de novo gene birth by reconstructing the ancestral sequences of 70 yeast de novo genes and characterized the sequence and structural properties of intergenic ORFs with a strong translation signal. This enabled us to highlight sequence...
  2. Research: Polymorphic centromere locations in the pathogenic yeast Candida parapsilosis
    • Mihaela Ola,
    • Caoimhe E. O'Brien,
    • Aisling Y. Coughlan,
    • Qinxi Ma,
    • Paul D. Donovan,
    • Kenneth H. Wolfe,
    • and Geraldine Butler
    Genome Res. May 2020 30: 684-696; Published in Advance May 18, 2020, doi:10.1101/gr.257816.119
    ...reconstruction was then compared with the other s using SynChro (delta values one to six), and a second ancestral (A2) was constructed from A1 and C. metapsilosis, with L. elongisporus as an outgroup. The best A2 candidate, with the smallest number of chromosomes (15) and conflicts (one) and the highest number...
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  3. RESOURCE: Initial sequence and comparative analysis of the cat genome
    • Joan U. Pontius,
    • James C. Mullikin,
    • Douglas R. Smith,
    • Agencourt Sequencing Team,
    • Kerstin Lindblad-Toh,
    • Sante Gnerre,
    • Michele Clamp,
    • Jean Chang,
    • Robert Stephens,
    • Beena Neelam,
    • Natalia Volfovsky,
    • Alejandro A. Schäffer,
    • Richa Agarwala,
    • Kristina Narfström,
    • William J. Murphy,
    • Urs Giger,
    • Alfred L. Roca,
    • Agostinho Antunes,
    • Marilyn Menotti-Raymond,
    • Naoya Yuhki,
    • Jill Pecon-Slattery,
    • Warren E. Johnson,
    • Guillaume Bourque,
    • Glenn Tesler,
    • NISC Comparative Sequencing Program,
    • and Stephen J. O’Brien
    Genome Res. November 2007 17: 1675-1689; doi:10.1101/gr.6380007
    ...), suitable for linkage or association studies were characterized in the context of long stretches of chromosome homozygosity. In spite of the light coverage capturing ∼65% of euchromatin sequence from the cat genome, these comparative insights shed new light on the tempo and mode of gene/genome evolution...
  4. Research: Convergent origination of a Drosophila-like dosage compensation mechanism in a reptile lineage
    • Ray Marin,
    • Diego Cortez,
    • Francesco Lamanna,
    • Madapura M. Pradeepa,
    • Evgeny Leushkin,
    • Philippe Julien,
    • Angélica Liechti,
    • Jean Halbert,
    • Thoomke Brüning,
    • Katharina Mössinger,
    • Timo Trefzer,
    • Christian Conrad,
    • Halie N. Kerver,
    • Juli Wade,
    • Patrick Tschopp,
    • and Henrik Kaessmann
    Genome Res. December 2017 27: 1974-1987; Published in Advance November 13, 2017, doi:10.1101/gr.223727.117
    ...resolved in fundamentally different ways.Sex determination in vertebrates is triggered during development by environmental cues or, genotypically, through the activity of master regulator genes on sex chromosomes, which differentiated from ancestral autosomes during evolution through recombination arrests...
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  5. Research: Multiple Pristionchus pacificus genomes reveal distinct evolutionary dynamics between de novo candidates and duplicated genes
    • Neel Prabh and
    • Christian Rödelsperger
    Genome Res. July 2022 32: 1315-1327; Published in Advance May 26, 2022, doi:10.1101/gr.276431.121
    ..., the number of identified de novo genes varied greatly with their definition. The resulting numbers ranged from thousands of species-specific open reading frames with transcriptional activity in yeast to a single gene with evidence of purifying selection and a well-supported noncoding status of the ancestral...
  6. PERSPECTIVE: Comparing the human and chimpanzee genomes: Searching for needles in a haystack
    • Ajit Varki and
    • Tasha K. Altheide
    Genome Res. December 2005 15: 1746-1758; doi:10.1101/gr.3737405
    ...longer time periods and for eliminating false positives. Also, genomic data alone cannot predict epistatic interactions between various loci, nor can it reveal the pleiotropic effects of changes that have occurred in a single gene. Comparative functional studies are necessary to reap the full potential...
  7. LETTER: Comparative Analysis of Apicomplexa and Genomic Diversity in Eukaryotes
    • Thomas J. Templeton,
    • Lakshminarayan M. Iyer,
    • Vivek Anantharaman,
    • Shinichiro Enomoto,
    • Juan E. Abrahante,
    • G.M. Subramanian,
    • Stephen L. Hoffman,
    • Mitchell S. Abrahamsen,
    • and L. Aravind
    Genome Res. September 2004 14: 1686-1695; doi:10.1101/gr.2615304
    ...lineage-specific gene loss is indicated by the absence of widespread eukaryotic proteins specifically in either one of the apicomplexan lineages ( Fig. 4 ), suggesting that the common ancestral apicomplexan possessed a more complex encoding a greater repertoire of biochemical activities. The streamlining...
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