Searching journal content for articles similar to Roy and Hartl 16 (6): 750.

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  1. LETTER: Large-scale intron conservation and order-of-magnitude variation in intron loss/gain rates in apicomplexan evolution
    • Scott William Roy and
    • David Penny
    Genome Res. October 2006 16: 1270-1275; Published in Advance September 8, 2006, doi:10.1101/gr.5410606
    .... Proc. Natl. Acad. Sci. 102 : 5773 – 5778 . ↵ Roy, S.W. , Gilbert, W. ( 2006 ) The evolution of spliceosomal introns: Patterns, puzzles, and progress . Nat. Rev. Genet. 7 : 211 – 221 . ↵ Roy, S.W. , Hartl, D.L. ( 2006 ) Very little intron loss/gain in Plasmodium: Intron loss/gain mutation rates...
  2. LETTER: Characterization of intron loss events in mammals
    • Jasmin Coulombe-Huntington and
    • Jacek Majewski
    Genome Res. January 2007 17: 23-32; Published in Advance November 15, 2006, doi:10.1101/gr.5703406
    ...frequent and recurrent intron loss and a much slower (fivefold to 10-fold) rate of putative intron gain. Roy and Hartl (2006) studied two relatively closely related Plasmodium species and found a very slow rate of intron loss and possibly no gain during ∼100 Myr of evolution. On the other hand...
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  3. Letter: Complex selection on 5′ splice sites in intron-rich organisms
    • Manuel Irimia,
    • Scott William Roy,
    • Daniel E. Neafsey,
    • Josep F. Abril,
    • Jordi Garcia-Fernandez,
    • and Eugene V. Koonin
    Genome Res. November 2009 19: 2021-2027; Published in Advance September 10, 2009, doi:10.1101/gr.089276.108
    ...interkingdomconservationof intronpositionsandmassive, lineage-specific intron loss and gain in eukaryotic evolution. Curr Biol 13: 1512–1517. Roy SW,GilbertW. 2005. Complex early genes. Proc Natl Acad Sci102: 1986– 1991. Roy SW, Hartl DL. 2006. Very little intron loss/gain in Plasmodium: Intron loss/gain mutation rates...
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  4. LETTER: Three distinct modes of intron dynamics in the evolution of eukaryotes
    • Liran Carmel,
    • Yuri I. Wolf,
    • Igor B. Rogozin,
    • and Eugene V. Koonin
    Genome Res. July 2007 17: 1034-1044; Published in Advance May 10, 2007, doi:10.1101/gr.6438607
    ...dynamics of eukaryotic gene structure, which is manifested in intron gain and loss, has been a subject of intense investigation. Generally, the abundance of introns in a is thought to be determined by the effective population size and the characteristic mutation rate of the respective species ( Lynch...
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  5. Research: Genome scanning of Amazonian Plasmodium falciparum shows subtelomeric instability and clindamycin-resistant parasites
    • Neekesh V. Dharia,
    • David Plouffe,
    • Selina E.R. Bopp,
    • Gonzalo E. González-Páez,
    • Carmen Lucas,
    • Carola Salas,
    • Valeria Soberon,
    • Badry Bursulaya,
    • Tadeusz J. Kochel,
    • David J. Bacon,
    • and Elizabeth A. Winzeler
    Genome Res. November 2010 20: 1534-1544; Published in Advance September 9, 2010, doi:10.1101/gr.105163.110
    ...not been reported, but in vitro studies have suggested that mutations in the apicoplast confer resistance to the macrolide antibiotic azithromycin (Sidhu et al. 2007). Tomeasure the conservation of this RNA gene in Plasmodium species, we used publicly available reads from sequencing projects for P...
  6. LETTER: Lymphopenia in the BB Rat Model of Type 1 Diabetes is Due to a Mutation in a Novel Immune-Associated Nucleotide (Ian)-Related Gene
    • Armand J. MacMurray,
    • Daniel H. Moralejo,
    • Anne E. Kwitek,
    • Elizabeth A. Rutledge,
    • Brian Van Yserloo,
    • Paul Gohlke,
    • Sara J. Speros,
    • Ben Snyder,
    • Jonathan Schaefer,
    • Sabine Bieg,
    • Jianjie Jiang,
    • Ruth A. Ettinger,
    • Jessica Fuller,
    • Terri L. Daniels,
    • Anna Pettersson,
    • Kimberly Orlebeke,
    • Bruce Birren,
    • Howard J. Jacob,
    • Eric S. Lander,
    • and Åke Lernmark
    Genome Res. July 1, 2002 12: 1029-1039; doi:10.1101/gr.412702
    ...that Contains a 1-bp Deletion Unique to the DR. lyp  Rat The intron/exon structure of the r Ian5 gene is shown in Figure 1 c in comparison with its mouse and human orthologs, m Ian5 and IAN4L1 ( hIan5 ). The overall genomic structure is similar to that reported previously in this family of genes ( Stamm et al...
  7. Method: Detection of simple and complex de novo mutations with multiple reference sequences
    • Kiran V. Garimella,
    • Zamin Iqbal,
    • Michael A. Krause,
    • Susana Campino,
    • Mihir Kekre,
    • Eleanor Drury,
    • Dominic Kwiatkowski,
    • Juliana M. Sá,
    • Thomas E. Wellems,
    • and Gil McVean
    Genome Res. August 2020 30: 1154-1169; Published in Advance August 19, 2020, doi:10.1101/gr.255505.119
    ...and evaluate the approach using extensive simulations and use it to characterize the rate and spectrum of de novo mutation events in 119 progeny from four Plasmodium falciparum experimental crosses, using long-read data on the parents to inform reconstructions of the progeny and to detect several known...
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  8. LETTER: Evolutionarily conserved genes preferentially accumulate introns
    • Liran Carmel,
    • Igor B. Rogozin,
    • Yuri I. Wolf,
    • and Eugene V. Koonin
    Genome Res. July 2007 17: 1045-1050; Published in Advance May 10, 2007, doi:10.1101/gr.5978207
    ...and in mutation rates ( Lynch 2002 ; Lynch and Conery 2003 ). This population-genetic perspective predicts an inverse correlation between intron gain and loss along lineages, a prediction that was refuted by our observations (see accompanying paper in this issue, Carmel et al. 2007 ). Several recent -wide studies...
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  9. Research: Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control
    • Daniel E. Neafsey,
    • Bridget M. Barker,
    • Thomas J. Sharpton,
    • Jason E. Stajich,
    • Daniel J. Park,
    • Emily Whiston,
    • Chiung-Yu Hung,
    • Cody McMahan,
    • Jared White,
    • Sean Sykes,
    • David Heiman,
    • Sarah Young,
    • Qiandong Zeng,
    • Amr Abouelleil,
    • Lynne Aftuck,
    • Daniel Bessette,
    • Adam Brown,
    • Michael FitzGerald,
    • Annie Lui,
    • J. Pendexter Macdonald,
    • Margaret Priest,
    • Marc J. Orbach,
    • John N. Galgiani,
    • Theo N. Kirkland,
    • Garry T. Cole,
    • Bruce W. Birren,
    • Matthew R. Henn,
    • John W. Taylor,
    • and Steven D. Rounsley
    Genome Res. July 2010 20: 938-946; Published in Advance June 1, 2010, doi:10.1101/gr.103911.109
    ...calling We identified 687,250 SNPs using the C. immitis RS finished assembly as a reference.Of these, 389,250were intergenic, 58,054were intronic, 46,791 were found in untranslated regions (UTRs), 96,505 were synonymous coding, and 95,235 were nonsynonymous coding. Table 2 illustrates further details...
  10. LETTER: Cloning, Characterization, and Mapping of a Murine Promiscuous Chemokine Receptor Gene: Homolog of the Human Duffy Gene
    • Hong Luo,
    • Asok Chaudhuri,
    • Kenneth R. Johnson,
    • Kuldeep Neote,
    • Valerie Zbrzezna,
    • Yu He,
    • and A. Oscar Pogo
    Genome Res. September 1, 1997 7: 932-941; doi:10.1101/gr.7.9.932
    ...in mouse provides a tool to gain further insights into the role of the human Duffy gene FY. RESULTS AND DISCUSSION Sequence Analysis of Dfy and Bone Marrow cDNA Nucleotide analysis of Dfy and bone marrow cDNA indicated that the structure of Dfy consists of two exons and a single intron (Fig. 1 A). Exon 1...
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