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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
...with D. mojavensis (Table 1).View this table: In this window In a new window Table 1. Total number of genes annotated in the six cactophilic Drosophila species sequenced in this workMinor effects of positive selection in HLAU genesThe use of Opuntia sp. has been proposed as the ancestral state...
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Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
- A. Bernardo Carvalho,
- Bernard Y. Kim,
- and Fabiana Uno
Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
...(Fingerhut et al. 2024). A complete assembly of the Drosophila Y is bound to shed light on some of these mysteries.The phenomenon of missing exons has obvious relevance for genomics and sequence technology; it most likely is not unique to Drosophila, and it is probably a matter of time before other cases...
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Research: microRNA target prediction programs predict many false positives
- Natalia Pinzón,
- Blaise Li,
- Laura Martinez,
- Anna Sergeeva,
- Jessy Presumey,
- Florence Apparailly,
- and Hervé Seitz
Genome Res. February 2017 27: 234-245; Published in Advance November 15, 2016, doi:10.1101/gr.205146.116
...two individuals in the human population (Cheung et al. 2003), two pools of individuals from a genetically homogenized Drosophila population (Laurie-Ahlberg et al. 1982), or two phenotypically identical mouse neural stem cells (Subkhankulova et al. 2008). Natural polymorphism in cis...
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Method: GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes
- Tomáš Brůna,
- Alexandre Lomsadze,
- and Mark Borodovsky
Genome Res. May 2024 34: 757-768; Published in Advance June 12, 2024, doi:10.1101/gr.278373.123
....For benchmarking, we selected seven eukaryotic s, both GC-homogeneous and GC-inhomogeneous: Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Solanum lycopersicum, Danio rerio, Gallus gallus, and Mus musculus. Along with GeneMark-ETP we tested GeneMark-ET; GeneMark-EP+; the pipelines BRAKER1...
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Research: Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary
- Satyam P. Srivastav,
- Cédric Feschotte,
- and Andrew G. Clark
Genome Res. May 2024 34: 711-724; Published in Advance May 15, 2024, doi:10.1101/gr.278062.123
...in Drosophila melanogaster, much less is known about the origin and evolution of piCs in this or any other species. To investigate piC origin and evolution, we use a population genomic approach to compare piC activity and sequence composition across eight geographically distant strains of D. melanogaster...
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Research: Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles
- Xuejing Wang and
- Gerald Heckel
Genome Res. June 2024 34: 851-862; Published in Advance July 2, 2024, doi:10.1101/gr.278487.123
....1086/418744 ↵Aguilar A, Roemer G, Debenham S, Binns M, Garcelon D, Wayne RK. 2004. High MHC diversity maintained by balancing selection in an otherwise genetically monomorphic mammal. Proc Natl Acad Sci 101: 3490–3494. doi:10.1073/pnas.0306582101 ↵Andolfatto P. 2005. Adaptive evolution of non-coding DNA in Drosophila...
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Research: Variation in mutation, recombination, and transposition rates in Drosophila melanogaster and Drosophila simulans
- Yiguan Wang,
- Paul McNeil,
- Rashidatu Abdulazeez,
- Marta Pascual,
- Susan E. Johnston,
- Peter D. Keightley,
- and Darren J. Obbard
Genome Res. April 2023 33: 587-598; Published in Advance April 10, 2023, doi:10.1101/gr.277383.122
...to ongoing selection, and levels of genetic load. However, even for key evolutionary model species such as Drosophila melanogaster and Drosophila simulans, few estimates of these parameters are available, and we have little idea of how rates vary between individuals, sexes, or populations. Knowledge...
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Method: Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe
- Arnaud Belcour,
- Jeanne Got,
- Méziane Aite,
- Ludovic Delage,
- Jonas Collén,
- Clémence Frioux,
- Catherine Leblanc,
- Simon M. Dittami,
- Samuel Blanquart,
- Gabriel V. Markov,
- and Anne Siegel
Genome Res. June 2023 33: 972-987; Published in Advance July 19, 2023, doi:10.1101/gr.277056.122
...).The fungal data set includes 74 fungal s which were selected according to the method of Wang et al. (2009) as representative of the fungal diversity, together with three outgroup s: Caenorhabditis elegans, Drosophila melanogaster, and Monosiga brevicollis. All proteomes and s were downloaded from...
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Research: High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis
- Yuan Lu,
- Edward Rice,
- Kang Du,
- Susanne Kneitz,
- Magali Naville,
- Corentin Dechaud,
- Jean-Nicolas Volff,
- Mikki Boswell,
- William Boswell,
- LaDeana Hillier,
- Chad Tomlinson,
- Kremitzki Milin,
- Ronald B. Walter,
- Manfred Schartl,
- and Wesley C. Warren
Genome Res. April 2023 33: 557-571; Published in Advance May 5, 2023, doi:10.1101/gr.277434.122
...of Xiphophorus, in particular viviparity, may have required changes in protein structures and should be visible as signatures of positive selection. To uncover such genomic traces of natural selection, 8492 one-to-one orthologs from the three Xiphophorus species and seven other teleost species were collected...
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Research: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster
- Anna Grandchamp,
- Lucas Kühl,
- Marie Lebherz,
- Kathrin Brüggemann,
- John Parsch,
- and Erich Bornberg-Bauer
Genome Res. June 2023 33: 872-890; Published in Advance July 13, 2023, doi:10.1101/gr.277482.122
...means that the neORF is found only in one line. The y-axis represents the neORFs length. The four boxes on the right represent the average lengths of de novo genes found in Drosophila with different ages. (B) Number of exons in neORFs. The x-axis shows the genomic position of neORFs. The y-axis shows...

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