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Research: Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species
- Damira Veseljak,
- Evelin Despot-Slade,
- Marin Volarić,
- Lucija Horvat,
- Tanja Vojvoda Zeljko,
- Nevenka Meštrović,
- and Brankica Mravinac
Genome Res. November 2025 35: 2445-2460; Published in Advance September 16, 2025, doi:10.1101/gr.280516.125
...Dynamic evolution of satellite DNAs drastically differentiates the s of Tribolium sibling species Damira Veseljak, Evelin Despot-Slade, Marin Volarić, Lucija Horvat, Tanja Vojvoda Zeljko, Nevenka Meštrović and Brankica Mravinac Ruđer Bošković Institute, Division of Molecular Biology, HR-10000...
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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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Review: Recent advances in methods to characterize archaic introgression in modern humans
- David Peede,
- Mayra M. Bañuelos,
- Jazeps Medina Tretmanis,
- Miriam Miyagi,
- and Emilia Huerta-Sánchez
Genome Res. February 2026 36: 239-256; Published in Advance January 16, 2026, doi:10.1101/gr.278993.124
...increased, opening exciting new avenues for studying human evolution. Here, we review recent methodological advances in the study of archaic introgression. We begin by providing an overview of the genealogical and genomic signatures left behind by introgression events before reviewing recent methods...
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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: 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
...identified in a West African and a European population of Drosophila melanogaster, and a European population of Drosophila simulans. (A) The genomic positions of the SNMs on chromosomes. Each gray bar represents the of one offspring. Point color represents mutation type and point shape represents...
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Research: Experimentally evolving Drosophila erecta populations may fail to establish an effective piRNA-based host defense against invading P-elements
- Divya Selvaraju,
- Filip Wierzbicki,
- and Robert Kofler
Genome Res. March 2024 34: 410-425; Published in Advance March 15, 2024, doi:10.1101/gr.278706.123
...eukaryotic transposons, into naive lines of Drosophila erecta. We monitored the invasion in three replicates for more than 50 generations by sequencing the genomic DNA (using short and long reads), the small RNAs, and the transcriptome at regular intervals. A piRNA-based host defense was rapidly established...
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Research: Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events
- Marin Volarić,
- Evelin Despot-Slade,
- Damira Veseljak,
- Brankica Mravinac,
- and Nevenka Meštrović
Genome Res. November 2024 34: 1878-1894; Published in Advance October 22, 2024, doi:10.1101/gr.279225.124
...of the most species-rich animal order on Earth, the coleopterans. T. castaneum has become one of the most important models in the field of the evolution, physiology, and development of insects because its development is more representative for insects compared with Drosophila (Campbell et al. 2022; Klingler...
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Research: tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis
- Junling Shi,
- Jiaqi Xu,
- Jun Ma,
- and Feng He
Genome Res. December 2023 33: 2119-2132; Published in Advance November 16, 2023, doi:10.1101/gr.278128.123
...simulans and Drosophila yakuba (Supplemental Fig. S5D). Altogether, these results suggested that 5′-tsRNA accumulation during the larva-to-pupa transition in Drosophila is a developmentally controlled and evolutionarily conserved event.5′-tsRNAs exert regulatory activities through target site recognition...
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Research: Transposons contribute to the functional diversification of the head, gut, and ovary transcriptomes across Drosophila natural strains
- Marta Coronado-Zamora and
- Josefa González
Genome Res. September 2023 33: 1541-1553; Published in Advance October 4, 2023, doi:10.1101/gr.277565.122
...insertion in the top five hits, suggesting that indeed some of these sequences have a clear roo origin (Supplemental Table S5F). Furthermore, we also tested whether this low-complexity region was present in the roo consensus sequence from a closely related species, Drosophila simulans, and found...
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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
...nucleotide diversity on the X Chromosome compared to the autosomes. These results were also observed in Drosophila simulans (Begun et al. 2007). Our results show exactly the same pattern, with reduced nucleotide diversity π between lines in telomeres and centromeres. Moreover, the average and median...

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