Searching journal content for articles similar to Garrigan et al. 22 (8): 1499.

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  1. Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
    • Harsh G. Shukla,
    • Mahul Chakraborty,
    • and J.J. Emerson
    Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
    ...on mutational processes shaping two functionally important tandem arrays in the Drosophila .ResultsGenome assembliesThe strains selected include the Drosophila community's reference strain (iso-1) (Adams et al. 2000) and two strains from the Drosophila Synthetic Population Resource (A3 and A4) (King et al. 2012...
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  2. Research: Evolution of genome structure in the Drosophila simulans species complex
    • Mahul Chakraborty,
    • Ching-Ho Chang,
    • Danielle E. Khost,
    • Jeffrey Vedanayagam,
    • Jeffrey R. Adrion,
    • Yi Liao,
    • Kristi L. Montooth,
    • Colin D. Meiklejohn,
    • Amanda M. Larracuente,
    • and J.J. Emerson
    Genome Res. March 2021 31: 380-396; Published in Advance February 9, 2021, doi:10.1101/gr.263442.120
    ...total TE sequence in D. simulans than in D. melanogaster, which is substantially lower than previously reported (Young and Schwartz 1981; Dowsett and Young 1982; Nuzhdin 1995; Vieira et al. 1999; Vieira and Biémont 2004; Drosophila 12 Genomes Consortium 2007).Intron size evolution may also be modulated...
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  3. Research: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster
    • Anna Grandchamp,
    • Lucas Kühl,
    • Marie Lebherz,
    • Kathrin Brüggemann,
    • John Parsch,
    • and Erich Bornberg-Bauer
    Genome Res. June 2023 33: 872-890; Published in Advance July 13, 2023, doi:10.1101/gr.277482.122
    ...of de novo genes that emerged within a single species. We sequenced and assembled s with long-read technology and the corresponding transcriptomes from inbred lines of Drosophila melanogaster, derived from seven geographically diverse populations. We found line-specific neORFs in abundance but few ne...
  4. Research: Topologically associating domains and their role in the evolution of genome structure and function in Drosophila
    • Yi Liao,
    • Xinwen Zhang,
    • Mahul Chakraborty,
    • and J.J. Emerson
    Genome Res. March 2021 31: 397-410; Published in Advance February 9, 2021, doi:10.1101/gr.266130.120
    ...million years of divergence, showed that ∼30%–40% of their s retain conserved TADs. Comparative genomic analysis of 17 Drosophila species revealed that chromosomal rearrangement breakpoints are enriched at TAD boundaries but depleted within TADs. Additionally, genes within conserved TADs show lower...
  5. Research: Single-molecule sequencing resolves the detailed structure of complex satellite DNA loci in Drosophila melanogaster
    • Daniel E. Khost,
    • Danna G. Eickbush,
    • and Amanda M. Larracuente
    Genome Res. May 2017 27: 709-721; Published in Advance April 3, 2017, doi:10.1101/gr.213512.116
    ...of these assemblies (Supplemental Fig. S15). To detect patterns of concerted evolution, we constructed a neighbor-joining tree using monomers from the 260-bp locus, the five contigs containing 353/356-bp repeats, an X-linked 1.688 repeat (359-bp), and a related repeat (360-bp) fromDrosophila simulans (Fig. 6). We...
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  6. Research: Genome-wide evidence for speciation with gene flow in Heliconius butterflies
    • Simon H. Martin,
    • Kanchon K. Dasmahapatra,
    • Nicola J. Nadeau,
    • Camilo Salazar,
    • James R. Walters,
    • Fraser Simpson,
    • Mark Blaxter,
    • Andrea Manica,
    • James Mallet,
    • and Chris D. Jiggins
    Genome Res. November 2013 23: 1817-1828; Published in Advance September 17, 2013, doi:10.1101/gr.159426.113
    ...result in reduced differentiation and an excess of shared variation between sympatric populations comparedwith allopatric populations. This logic has been applied on a genomic scale to test for gene flow in Drosophila (Kulathinal et al. 2009) andhominids (Green et al. 2010). However, this approach does...
  7. Research: Tempo and mode of regulatory evolution in Drosophila
    • Joseph D. Coolon,
    • C. Joel McManus,
    • Kraig R. Stevenson,
    • Brenton R. Graveley,
    • and Patricia J. Wittkopp
    Genome Res. May 2014 24: 797-808; Published in Advance February 24, 2014, doi:10.1101/gr.163014.113
    ...); it is essential for organismal form, fitness, and function, and frequently varies within and between species. Comparative studies using genomic surveys of gene expression in yeast (Busby et al. 2011), Drosophila (Rifkin et al. 2003), and mammalian species (Brawand et al. 2011) with a range of divergence times...
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  8. Research: Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana
    • Viola Nolte,
    • Ram Vinay Pandey,
    • Robert Kofler,
    • and Christian Schlötterer
    Genome Res. January 2013 23: 99-110; Published in Advance October 10, 2012, doi:10.1101/gr.139873.112
    ...Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana Viola Nolte , Ram Vinay Pandey , Robert Kofler and Christian Schlötterer 1 Institut für Populationsgenetik...
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  9. Research: Evolution of splicing regulatory networks in Drosophila
    • C. Joel McManus,
    • Joseph D. Coolon,
    • Jodi Eipper-Mains,
    • Patricia J. Wittkopp,
    • and Brenton R. Graveley
    Genome Res. May 2014 24: 786-796; Published in Advance February 10, 2014, doi:10.1101/gr.161521.113
    ...). The publicly available assemblies of these species are of vastly different quality. The s of D.melanogaster,D. sechellia, andD. simulanswere originally sequenced to ;12-, five-, and threefold coverage, respectively (Drosophila 12 Genomes Consortium 2007). In addition, the strains used in our study likely...
  10. Research: Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis
    • Cristel G. Thomas,
    • Wei Wang,
    • Richard Jovelin,
    • Rajarshi Ghosh,
    • Tatiana Lomasko,
    • Quang Trinh,
    • Leonid Kruglyak,
    • Lincoln D. Stein,
    • and Asher D. Cutter
    Genome Res. May 2015 25: 667-678; Published in Advance March 17, 2015, doi:10.1101/gr.187237.114
    ....0001) (Fig. 6D). Moreover, PSCmutations are nonuniformly distributed along coding sequences (χ2 = 92.37, P < 0.0001), being more prevalent in the last 10% of coding sequences (Fig. 6C) as seen in Drosophila (Hoehn et al. 2012; Lee and Reinhardt 2012). However, unlike in D. melanogaster (Lee and Reinhardt...
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