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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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Research: Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine
- Sarah M. Leichter,
- Kami Ahmad,
- and Steven Henikoff
Genome Res. January 2026 36: 102-114; Published in Advance November 17, 2025, doi:10.1101/gr.281058.125
...tissues because the epithelium undergoes continuous cell turnover, with a median cellular life span for differentiated cells of 4 days (Liang et al. 2017). This rapid turnover ensures that both young and aged intestines maintain similar cellular age distributions. Despite this, the Drosophila intestine...
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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
...developed. Most SV callers perform similarly, so differences are often based on runtime or additional features. For example, SVision Pro can detect more complex SVs, while Sniffles2 allows rapid comparison of multiple samples. Of note, there are also cancer-specific variant callers that streamline...
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Perspective: Functional assays in Drosophila facilitate classification of variants of uncertain significance associated with rare diseases
- Jung-Wan Mok,
- Shelley B. Gibson,
- Haley A. Dostalik,
- and Shinya Yamamoto
Genome Res. July 2025 35: 1473-1484; Published in Advance June 4, 2025, doi:10.1101/gr.278291.123
...research pioneered by Seymour Benzer indicated that complex traits such as behavior are also under the tight regulation of genetic factors. The sequencing of the euchromatic portion of the Drosophila melanogaster (Adams et al. 2000) accelerated the utilization of fruit flies in human disease studies...
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Research: Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotypes and phenotypes in chronic lymphocytic leukemia
- Gage S. Black,
- Xiaomeng Huang,
- Yi Qiao,
- Philip Moos,
- Deepa Sampath,
- Deborah M. Stephens,
- Jennifer A. Woyach,
- and Gabor T. Marth
Genome Res. April 2025 35: 686-697; Published in Advance February 18, 2025, doi:10.1101/gr.279049.124
...with ibrutinib in relapsed chronic lymphocytic leukemia. N Engl J Med 369: 32–42. doi:10.1056/NEJMoa1215637 ↵Cingolani P, Patel VM, Coon M, Nguyen T, Land SJ, Ruden DM, Lu X. 2012. Using Drosophila melanogaster as a model for genotoxic chemical...
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Research: Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations
- Zoe June Assaf,
- Susanne Tilk,
- Jane Park,
- Mark L. Siegal,
- and Dmitri A. Petrov
Genome Res. December 2017 27: 1988-2000; Published in Advance October 27, 2017, doi:10.1101/gr.219956.116
...Figure 3. Pipeline for identification and validation of rare polymorphisms. Step 1 data set is from the Drosophila Genome Nexus (DGN) (Lack et al. 2015) which represent predominantly monoallelic s (i.e., either haploid or inbred) from 35 populations across three continents that were sequenced to high...
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Research: Evolution and genomic signatures of spontaneous somatic mutation in Drosophila intestinal stem cells
- Nick Riddiford,
- Katarzyna Siudeja,
- Marius van den Beek,
- Benjamin Boumard,
- and Allison J. Bardin
Genome Res. August 2021 31: 1419-1432; Published in Advance June 24, 2021, doi:10.1101/gr.268441.120
...of SNVs, indels, and additional structural variants. Our data show a rapid accumulation of mutations over a short evolutionary time span during the adult life of D. melanogaster.DiscussionWe have applied whole- sequencing to interrogate how spontaneous tumors arise from stem cells in the Drosophila...
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Research: Rates and spectra of de novo structural mutations in Chlamydomonas reinhardtii
- Eugenio López-Cortegano,
- Rory J. Craig,
- Jobran Chebib,
- Eniolaye J. Balogun,
- and Peter D. Keightley
Genome Res. January 2023 33: 45-60; Published in Advance December 12, 2022, doi:10.1101/gr.276957.122
...research because its relatively large (∼111 Mb) and short generation time (∼2.5 generations per day) enable the rapid accumulation of large numbers of new mutations in a short time, and the species has been used to explore diverse genomic properties of mutations (Ness et al. 2012; Sung et al. 2012; López...
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Research: A-to-I RNA editing contributes to the persistence of predicted damaging mutations in populations
- Te-Lun Mai and
- Trees-Juen Chuang
Genome Res. November 2019 29: 1766-1776; Published in Advance September 12, 2019, doi:10.1101/gr.246033.118
...is particularly strong when editing sites are located in highly important genes/loci. Examinations of deleterious missense variants from the 1000 Genomes Project further show a significantly higher proportion of rare missense mutations for G-to-A changes than for other types of changes. The proportion for G...
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Resource: The genomic architecture and molecular evolution of ant odorant receptors
- Sean K. McKenzie and
- Daniel J.C. Kronauer
Genome Res. November 2018 28: 1757-1765; Published in Advance September 24, 2018, doi:10.1101/gr.237123.118
...mg of ants using the Qiagen MagAttract HMW DNA kit, and libraries were prepared for Nanopore sequencing using the Rapid Sequencing kit (SQK-RAD002) and sequenced on two MinION SpotON flow cells (R9.4). Hi-C sequencing was performed by Phase Genomics (Seattle, WA). Genomic DNA for Illumina sequencing...

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