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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
...Sbr. The L2 and L3 loci are adjacent to each other in an inverted tandem orientation (i.e., [mSbr][rb′S′m′], where the ′ indicates the opposite orientation) (Supplemental Fig. 21). As a consequence, the Stellate clusters in these loci are separated by ∼24 kb of sequences made up of BATUMI, rDNA, and R1/R2...
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Method: De novo reconstruction of satellite repeat units from sequence data
- Yujie Zhang,
- Justin Chu,
- Haoyu Cheng,
- and Heng Li
Genome Res. November 2023 33: 1994-2001; Published in Advance November 2, 2023, doi:10.1101/gr.278005.123
...long-read HiFi sequencing data for five complex s. Sci Data 7: 399. doi:10.1038/s41597-020-00743-4 ↵Khost DE, Eickbush DG, Larracuente AM. 2017. Single-molecule sequencing resolves the detailed structure of complex satellite DNA loci in Drosophila melanogaster. Genome Res 27: 709–721. doi:10.1101/gr...
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Method: Double insertion of transposable elements provides a substrate for the evolution of satellite DNA
- Michael P. McGurk and
- Daniel A. Barbash
Genome Res. May 2018 28: 714-725; Published in Advance March 27, 2018, doi:10.1101/gr.231472.117
...-element related array in Drosophila guanche is comprised of elements missing ∼100 nt of terminal sequence (Miller et al. 1992), and all elements in the fixed Bari1 tandem array have incomplete TIRs (Marsano et al. 2003). The terminal inverted repeats at the ends of DNA transposons are endonuclease cut sites...
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Resource: The Release 6 reference sequence of the Drosophila melanogaster genome
- Roger A. Hoskins,
- Joseph W. Carlson,
- Kenneth H. Wan,
- Soo Park,
- Ivonne Mendez,
- Samuel E. Galle,
- Benjamin W. Booth,
- Barret D. Pfeiffer,
- Reed A. George,
- Robert Svirskas,
- Martin Krzywinski,
- Jacqueline Schein,
- Maria Carmela Accardo,
- Elisabetta Damia,
- Giovanni Messina,
- María Méndez-Lago,
- Beatriz de Pablos,
- Olga V. Demakova,
- Evgeniya N. Andreyeva,
- Lidiya V. Boldyreva,
- Marco Marra,
- A. Bernardo Carvalho,
- Patrizio Dimitri,
- Alfredo Villasante,
- Igor F. Zhimulev,
- Gerald M. Rubin,
- Gary H. Karpen,
- and Susan E. Celniker
Genome Res. March 2015 25: 445-458; Published in Advance January 14, 2015, doi:10.1101/gr.185579.114
...Resource The Release 6 reference sequence of the Drosophila melanogaster Roger A. Hoskins,1 Joseph W. Carlson,1,10 Kenneth H. Wan,1 Soo Park,1 Ivonne Mendez,1 Samuel E. Galle,1 Benjamin W. Booth,1 Barret D. Pfeiffer,2 Reed A. George,2 Robert Svirskas,2 Martin Krzywinski,3 Jacqueline Schein,3 Maria...
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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
...and Drosophila melanogaster s (Britten and Kohne 1968; International Human Genome Sequencing Consortium 2001; Treangen and Salzberg 2012; Hoskins et al. 2015). These sequences include repeated tandem arrays of noncoding sequences like satellite DNAs, self-replicating selfish elements like transposable elements...
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Method: HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
- Sergey Nurk,
- Brian P. Walenz,
- Arang Rhie,
- Mitchell R. Vollger,
- Glennis A. Logsdon,
- Robert Grothe,
- Karen H. Miga,
- Evan E. Eichler,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. September 2020 30: 1291-1305; Published in Advance August 14, 2020, doi:10.1101/gr.263566.120
...correction, and aggressive false overlap filtering. We benchmark HiCanu with a focus on the recovery of haplotype diversity, major histocompatibility complex (MHC) variants, satellite DNAs, and segmental duplications. For diploid human s sequenced to 30× HiFi coverage, HiCanu achieved superior accuracy...
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Research: Diversification and collapse of a telomere elongation mechanism
- Bastien Saint-Leandre,
- Son C. Nguyen,
- and Mia T. Levine
Genome Res. June 2019 29: 920-931; Published in Advance May 28, 2019, doi:10.1101/gr.245001.118
...; in rare cases, essential host functions rely on retention of the mobilization machinery that promotes recurrent TE insertions into host DNA. The noncanonical telomere elongation mechanism of Drosophila is exemplary (Pardue and DeBaryshe 2003; Casacuberta 2017).In most eukaryotes beyond Drosophila...
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Research: Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications
- Matthias H. Weissensteiner,
- Andy W.C. Pang,
- Ignas Bunikis,
- Ida Höijer,
- Olga Vinnere-Petterson,
- Alexander Suh,
- and Jochen B.W. Wolf
Genome Res. May 2017 27: 697-708; Published in Advance March 30, 2017, doi:10.1101/gr.215095.116
...on the location of DNA sequence associated with heterochromatin is generally absent from assemblies due to its highly repetitive structure. Investigations of the strength and mode of selection shaping genetic variation across s will therefore benefit from detailed information on structure currently inaccessible...
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Research: Accumulation and ineffective silencing of transposable elements on an avian W Chromosome
- Vera M. Warmuth,
- Matthias H. Weissensteiner,
- and Jochen B.W. Wolf
Genome Res. April 2022 32: 671-681; Published in Advance February 11, 2022, doi:10.1101/gr.275465.121
..., satellite DNA, rRNA, and tRNA (Table 1). Repeat content, expressed as the proportion of genomic bases belonging to repeat sequence, varied among chromosome types and was lowest on autosomal sequence (∼6.5%), intermediate on the Z Chromosome (∼11.9%), and highest by far on the W Chromosome (∼84.8%). Genome...
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Research: Genomic architecture constrained placental mammal X Chromosome evolution
- Wesley A. Brashear,
- Kevin R. Bredemeyer,
- and William J. Murphy
Genome Res. August 2021 31: 1353-1365; Published in Advance July 22, 2021, doi:10.1101/gr.275274.121
...sequences (BES) aligned to the domestic cat felCat8.0 assembly. Briefly, clones with both BES mapping to either side of a gap within the assembly, or a single end uniquely mapped adjacent to a gap, were selected for sequencing. Selected clones were cultured and DNA was extracted using standard protocols...

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