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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
..., and A3The histone locus in Drosophila melanogaster is present at the 39DE region of Chromosome 2L, bordering the pericentromeric heterochromatin. The highly homogeneous nature of this locus has impeded its resolution to the base pair level. The current reference iso-1 Rel6 has only ∼69 kb (12 units...
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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
...regions of the in unprecedented detail. We show here that some complex satDNA loci are tractable models for determining tandem repeat organization in pericentric heterochromatin. These assemblies provide a platform for evolutionary and functional genomic studies of satDNA in Drosophila. Methods Assemblies...
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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
..., University of California, Berkeley, California 94720, USA Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference sequence reported more than a decade ago had a profound impact...
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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
...for two large (>100-kb) inversions within pericentromeric heterochromatin on Chromosomes 3 and X (Fig. 2; Supplemental Fig. S11A–D). Because Drosophila erecta shares the same configuration as the sim-complex species, the pericentric inversion on Chromosome 3 likely occurred in the D. melanogaster lineage...
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Research: Loss of HP1 causes depletion of H3K27me3 from facultative heterochromatin and gain of H3K27me2 at constitutive heterochromatin
- Kirsty Jamieson,
- Elizabeth T. Wiles,
- Kevin J. McNaught,
- Simone Sidoli,
- Neena Leggett,
- Yanchun Shao,
- Benjamin A. Garcia,
- and Eric U. Selker
Genome Res. January 2016 26: 97-107; Published in Advance November 4, 2015, doi:10.1101/gr.194555.115
...relationships between marks of constitutive and facultative heterochromatin. Specifically, we used the filamentous fungus Neurospora crassa, which unlike many other simple model eukaryotes (e.g., budding and fission yeasts,Drosophila and Caenorhabditis elegans) has both DNA methylation and H3K27me (Aramayo...
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Research: Defining heterochromatin in C. elegans through genome-wide analysis of the heterochromatin protein 1 homolog HPL-2
- Jacob M. Garrigues,
- Simone Sidoli,
- Benjamin A. Garcia,
- and Susan Strome
Genome Res. January 2015 25: 76-88; Published in Advance December 2, 2014, doi:10.1101/gr.180489.114
...of heterochromatin protein 1 (HP1), a highly conserved, small nonhistone protein first identified in Drosophila (James and Elgin 1986). Heterochromatin is typically concentrated at pericentric and subtelomeric regions. How heterochromatin is distributed in an organismwithnumerous centromeres distributed along...
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Resource: Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines
- Wen Huang,
- Andreas Massouras,
- Yutaka Inoue,
- Jason Peiffer,
- Miquel Ràmia,
- Aaron M. Tarone,
- Lavanya Turlapati,
- Thomas Zichner,
- Dianhui Zhu,
- Richard F. Lyman,
- Michael M. Magwire,
- Kerstin Blankenburg,
- Mary Anna Carbone,
- Kyle Chang,
- Lisa L. Ellis,
- Sonia Fernandez,
- Yi Han,
- Gareth Highnam,
- Carl E. Hjelmen,
- John R. Jack,
- Mehwish Javaid,
- Joy Jayaseelan,
- Divya Kalra,
- Sandy Lee,
- Lora Lewis,
- Mala Munidasa,
- Fiona Ongeri,
- Shohba Patel,
- Lora Perales,
- Agapito Perez,
- LingLing Pu,
- Stephanie M. Rollmann,
- Robert Ruth,
- Nehad Saada,
- Crystal Warner,
- Aneisa Williams,
- Yuan-Qing Wu,
- Akihiko Yamamoto,
- Yiqing Zhang,
- Yiming Zhu,
- Robert R.H. Anholt,
- Jan O. Korbel,
- David Mittelman,
- Donna M. Muzny,
- Richard A. Gibbs,
- Antonio Barbadilla,
- J. Spencer Johnston,
- Eric A. Stone,
- Stephen Richards,
- Bart Deplancke,
- and Trudy F.C. Mackay
Genome Res. July 2014 24: 1193-1208; Published in Advance April 8, 2014, doi:10.1101/gr.171546.113
...Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines Wen Huang 1 , 10 , Andreas Massouras 2 , 3 , 10 , Yutaka Inoue 4 , Jason Peiffer 1 , Miquel Ràmia 5 , Aaron M. Tarone 6...
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Method: Efficient identification of Y chromosome sequences in the human and Drosophila genomes
- Antonio Bernardo Carvalho and
- Andrew G. Clark
Genome Res. November 2013 23: 1894-1907; Published in Advance August 6, 2013, doi:10.1101/gr.156034.113
...Identification of Y-linked scaffolds in Drosophila virilis The Drosophila virilis was sequenced in 2007 using unsexed embryos (Drosophila 12 Genomes Consortium 2007). A previous search of the orthologs of the D. melanogaster Y-linked genes identified six genes on the D. virilis Y chromosome (Koerich et al. 2008...
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Research: Heterochromatin protein 1 (HP1) modulates replication timing of the Drosophila genome
- Michaela Schwaiger,
- Hubertus Kohler,
- Edward J. Oakeley,
- Michael B. Stadler,
- and Dirk Schübeler
Genome Res. June 2010 20: 771-780; Published in Advance April 30, 2010, doi:10.1101/gr.101790.109
...–4984. Belyaeva ES, Zhimulev IF, Volkova EI, Alekseyenko AA, Moshkin YM, Koryakov DE. 1998. Su(UR)ES: A gene suppressing DNA underreplication in intercalary and pericentric heterochromatin of Drosophila melanogaster polytene chromosomes. Proc Natl Acad Sci 95: 7532–7537. Caizzi R, Caggese C, Pimpinelli S. 1993...
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LETTER: Genomic organization of the Drosophila telomere retrotransposable elements
- Janet A. George,
- P. Gregory DeBaryshe,
- Karen L. Traverse,
- Susan E. Celniker,
- and Mary-Lou Pardue
Genome Res. October 2006 16: 1231-1240; Published in Advance September 8, 2006, doi:10.1101/gr.5348806
...of the Drosophila melanogaster genome, with the most recent update of euchromatic sequence, gives the first genome-wide view of the chromosomal distribution of the telomeric retrotransposons, HeT-A , TART , and Tahre . As expected, these elements are entirely excluded from euchromatin, although sequence...

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