Searching journal content for articles similar to Copley et al. 17 (9): 1327.

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  1. Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
    • Daniel Siqueira de Oliveira,
    • Anaïs Larue,
    • William Vilas Boas Nunes,
    • Francois Sabot,
    • Alejandra Bodelón,
    • María Pilar García Guerreiro,
    • Cristina Vieira,
    • and Claudia Marcia Aparecida Carareto
    Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
    ...relative to total gene expression (x-axis). Chimeric transcripts without assembled sequence or contribution <25% were removed (gray bars). (C) Number of common and unique chimeric transcripts from HLAU genes detected in heads and larvae. (D) The Eato/LOC6578120 (ABC transporter) gene has a conserved TE...
  2. 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
    ...@tamu.edu, jje@uci.eduAbstractMany essential functions of organisms are encoded in highly repetitive genomic regions, including histones involved in DNA packaging, centromeres that are core components of chromosome segregation, ribosomal RNA comprising the protein translation machinery, telomeres that ensure...
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  3. Research: Experimentally evolving Drosophila erecta populations may fail to establish an effective piRNA-based host defense against invading P-elements
    • Divya Selvaraju,
    • Filip Wierzbicki,
    • and Robert Kofler
    Genome Res. March 2024 34: 410-425; Published in Advance March 15, 2024, doi:10.1101/gr.278706.123
    ...eukaryotic transposons, into naive lines of Drosophila erecta. We monitored the invasion in three replicates for more than 50 generations by sequencing the genomic DNA (using short and long reads), the small RNAs, and the transcriptome at regular intervals. A piRNA-based host defense was rapidly established...
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  4. Resource: A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons
    • Qicheng Ma,
    • Satyam P. Srivastav,
    • Stephanie Gamez,
    • Gargi Dayama,
    • Fabiana Feitosa-Suntheimer,
    • Edward I. Patterson,
    • Rebecca M. Johnson,
    • Erik M. Matson,
    • Alexander S. Gold,
    • Douglas E. Brackney,
    • John H. Connor,
    • Tonya M. Colpitts,
    • Grant L. Hughes,
    • Jason L. Rasgon,
    • Tony Nolan,
    • Omar S. Akbari,
    • and Nelson C. Lau
    Genome Res. March 2021 31: 512-528; Published in Advance January 8, 2021, doi:10.1101/gr.265157.120
    ...-Hösle and Förstemann 2014; Wen et al. 2014, 2015). Last, arbovirus-specific siRNAs and piRNAs persist in Dmel cell cultures (Flynt et al. 2009; Wu et al. 2010; Vodovar et al. 2011; Goic et al. 2013; Wen et al. 2014; Palmer et al. 2018).Culicidae mosquitoes are relatives of Drosophilid fruit flies as members...
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  5. Research: Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F1 hybrids
    • Carina F. Mugal,
    • Mi Wang,
    • Niclas Backström,
    • David Wheatcroft,
    • Murielle Ålund,
    • Marie Sémon,
    • S. Eryn McFarlane,
    • Ludovic Dutoit,
    • Anna Qvarnström,
    • and Hans Ellegren
    Genome Res. December 2020 30: 1727-1739; Published in Advance November 3, 2020, doi:10.1101/gr.254508.119
    ...the same six candidate explanatory variables largely confirmed the GLM results (Supplemental Table S2), but MLR suggests stronger significance for determinants of gene expression evolution, while GLM appears to be more conservative.Gene expression in naturally occurring hybridsTo visualize the relative...
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  6. Research: Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus
    • Jaaved Mohammed,
    • Alex S. Flynt,
    • Alexandra M. Panzarino,
    • Md Mosharrof Hossain Mondal,
    • Matthew DeCruz,
    • Adam Siepel,
    • and Eric C. Lai
    Genome Res. January 2018 28: 52-65; Published in Advance December 12, 2017, doi:10.1101/gr.226068.117
    ...not previously been explicitly identified. This served as an initial check on the overall quality of the data sets, since genomic conservation of a miRNA is usually taken to imply processing into mature small RNAs. Our data support the first cloning evidence for 592 unannotated homologs of conserved Drosophilid...
  7. Research: MicroRNA evolution, expression, and function during short germband development in Tribolium castaneum
    • Maria Ninova,
    • Matthew Ronshaugen,
    • and Sam Griffiths-Jones
    Genome Res. January 2016 26: 85-96; Published in Advance October 30, 2015, doi:10.1101/gr.193367.115
    ...addition of nucleotides different from the ones at the genomic position immediately after the microRNA 3′ end cleavage site, our estimates of the extent of microRNA modifications in insect oocytes are likely to be conservative. Results showed at least 20% of the maternally deposited microRNAs in T...
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  8. Research: High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation
    • Anil Ozdemir,
    • Katherine I. Fisher-Aylor,
    • Shirley Pepke,
    • Manoj Samanta,
    • Leslie Dunipace,
    • Kenneth McCue,
    • Lucy Zeng,
    • Nobuo Ogawa,
    • Barbara J. Wold,
    • and Angelike Stathopoulos
    Genome Res. April 2011 21: 566-577; Published in Advance March 7, 2011, doi:10.1101/gr.104018.109
    ...is a signature of many biologically-significant regulatory regions and sequence motif instances. On average, our Twist-occupied regions were more conserved over a sequence domain of ;300 bp compared to random genomic background conservation (blue versus red trace, Fig. 7A). Figure 3. Motif composition of Twist...
  9. Research: A long-term demasculinization of X-linked intergenic noncoding RNAs in Drosophila melanogaster
    • Ge Gao,
    • Maria D. Vibranovski,
    • Li Zhang,
    • Zheng Li,
    • Ming Liu,
    • Yong E. Zhang,
    • Xinmin Li,
    • Wenxia Zhang,
    • Qichang Fan,
    • Nicholas W. VanKuren,
    • Manyuan Long,
    • and Liping Wei
    Genome Res. April 2014 24: 629-638; Published in Advance January 9, 2014, doi:10.1101/gr.165837.113
    ...with all 12 sequenced Drosophila s similar to the procedure reported by Sturgill et al. (2007). We ran NCBI BLAST against genomic DNA of each species. To handle the relatively low sequence conservation of noncoding genes, optimized BLAST parameters were employed as suggested in previous literatures (Korf...
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  10. PERSPECTIVE: Qualifying the relationship between sequence conservation and molecular function
    • Gregory M. Cooper and
    • Christopher D. Brown
    Genome Res. February 2008 18: 201-205; doi:10.1101/gr.7205808
    ...Qualifying the relationship between sequence conservation and molecular function Gregory M. Cooper 1 , 3 , 4 and Christopher D. Brown 2 , 3 1 Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; 2...
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