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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
...-derived sequences (Lipatov et al. 2005). A recent transcriptome-wide study identified 327 genes in Drosophila melanogaster that generate chimeric transcripts across different populations (Oliveira et al. 2023). Among all genes, 76 generate chimeric transcripts from TE insertions that were present in one strain...
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Resource: The developmental proteome of Drosophila melanogaster
- Nuria Casas-Vila,
- Alina Bluhm,
- Sergi Sayols,
- Nadja Dinges,
- Mario Dejung,
- Tina Altenhein,
- Dennis Kappei,
- Benjamin Altenhein,
- Jean-Yves Roignant,
- and Falk Butter
Genome Res. July 2017 27: 1273-1285; Published in Advance April 5, 2017, doi:10.1101/gr.213694.116
...including embryo, larva, pupa, and adult, undergoing a complete phenotypic metamorphosis (Lawrence 1992). These transitions are based on tightly regulated gene expression at the transcriptional, epigenetic, and translational level. Currently, most developmental gene expression studies in Drosophila rely...
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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
...differences in these host defenses may contribute to the TE abundance differences between the sim-complex and D. melanogaster. TE insertions also alter local chromatin state in Drosophila, which can spread and suppress the expression of adjacent genes, with potentially deleterious consequences (Lee and Karpen...
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LETTER: Function and evolution of a gene family encoding odorant binding-like proteins in a social insect, the honey bee (Apis mellifera)
- Sylvain Forêt and
- Ryszard Maleszka
Genome Res. November 2006 16: 1404-1413; Published in Advance October 25, 2006, doi:10.1101/gr.5075706
...and gene models . Nucleic Acids Res. 33 : D390 – D395 . ↵ Felsenstein, J. ( 2005 ) PHYLIP (Phylogeny Inference Package) version 3.5 ( Department of Genome Sciences, University of Washington , Seattle, WA ). ↵ Galindo, K. , Smith, D. ( 2001 ) A large family of divergent Drosophila odorant-binding proteins...
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Research: High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes
- Penka Markova-Raina and
- Dmitri Petrov
Genome Res. June 2011 21: 863-874; Published in Advance March 10, 2011, doi:10.1101/gr.115949.110
...-coding genes in 12 Drosophila genomes annotated in either all 12 species (∼6690 genes) or in the six melanogaster group species. We compare six popular aligners: PRANK, T-Coffee, ClustalW, ProbCons, AMAP, and MUSCLE, and find that the aligner choice strongly influences the estimates of positive selection...
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Research: The genomic basis of evolutionary differentiation among honey bees
- Bertrand Fouks,
- Philipp Brand,
- Hung N. Nguyen,
- Jacob Herman,
- Francisco Camara,
- Daniel Ence,
- Darren E. Hagen,
- Katharina J. Hoff,
- Stefanie Nachweide,
- Lars Romoth,
- Kimberly K.O. Walden,
- Roderic Guigo,
- Mario Stanke,
- Giuseppe Narzisi,
- Mark Yandell,
- Hugh M. Robertson,
- Nikolaus Koeniger,
- Panuwan Chantawannakul,
- Michael C. Schatz,
- Kim C. Worley,
- Gene E. Robinson,
- Christine G. Elsik,
- and Olav Rueppell
Genome Res. July 2021 31: 1203-1215; Published in Advance May 4, 2021, doi:10.1101/gr.272310.120
...and Lipman 1988) with an E-value threshold of 1 × 10−6 to compute reciprocal alignments between Apis comparative proteins and a Drosophila melanogaster protein set consisting of the longest protein isoform of each gene (annotation version r6.14). We identified reciprocal best hits (RBH) and transferred GO...
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Method: Joint genotyping on the fly: Identifying variation among a sequenced panel of inbred lines
- Eric A. Stone
Genome Res. May 2012 22: 966-974; Published in Advance February 23, 2012, doi:10.1101/gr.129122.111
..., Negron YL, Mackay TF, Anholt RR. 2010. Natural variation, functional pleiotropy and transcriptional contexts of odorant binding protein genes in Drosophila melanogaster. Genetics 186: 1475–1485. ↵ Aylor DL, Valdar W, Foulds-Mathes W, Buus RJ, Verdugo RA, Baric RS, Ferris MT, Frelinger JA, Heise M...
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12 Drosophila Genomes/Letter: Genomic regulatory blocks underlie extensive microsynteny conservation in insects
- Pär G. Engström,
- Shannan J. Ho Sui,
- Øyvind Drivenes,
- Thomas S. Becker,
- and Boris Lenhard
Genome Res. December 2007 17: 1898-1908; Published in Advance November 7, 2007, doi:10.1101/gr.6669607
.... These arrays span key developmental regulatory genes, forming genomic regulatory blocks (GRBs). We recently described GRBs in vertebrates, where most HCNEs function as enhancers and HCNE arrays specify complex expression programs of their target genes. Here we present a comparison of five Drosophila genomes...
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Research: Phenotypically distinct female castes in honey bees are defined by alternative chromatin states during larval development
- Marek Wojciechowski,
- Robert Lowe,
- Joanna Maleszka,
- Danyal Conn,
- Ryszard Maleszka,
- and Paul J. Hurd
Genome Res. October 2018 28: 1532-1542; Published in Advance August 22, 2018, doi:10.1101/gr.236497.118
...uses a likelihood ratio test, and hence we tested for those genes whose abundance is significantly better explained when caste is included in the model compared to a reduced model in which a single parameter is fitted for each gene.Gene Ontology analysisDrosophila melanogaster GO terms were downloaded...
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LETTER: Evolution of the Yellow/Major Royal Jelly Protein family and the emergence of social behavior in honey bees
- Mark David Drapeau,
- Stefan Albert,
- Robert Kucharski,
- Carsten Prusko,
- and Ryszard Maleszka
Genome Res. November 2006 16: 1385-1394; Published in Advance October 25, 2006, doi:10.1101/gr.5012006
....D. , Radovic, A. , Wittkopp, P.J. , Long, A.D. ( 2003 ) A gene necessary for normal male courtship, yellow , acts downstream of fruitless in the Drosophila melanogaster larval brain . J. Neurobiol. 55 : 53 – 72 . ↵ Drapeau, M.D. , Cyran, S.A. , Viering, M.M. , Geyer, P.K. , Long, A.D. ( 2005 ) A cis...
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