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Corrigendum: Corrigendum: Tempo and mode of regulatory evolution in Drosophila
- Joseph D. Coolon,
- C. Joel McManus,
- Kraig R. Stevenson,
- Brenton R. Graveley,
- and Patricia J. Wittkopp
Genome Res. November 2018 28: 1766; doi:10.1101/gr.244087.118
...Research Genome Res. Genome Res 1088-9051 1549-5469 Cold Spring Harbor Laboratory Press 9509184 10.1101/gr.244087.118 ;28/11/1766 ;gr.244087.118 1766 gr.244087.118 Corrigendum Corrigendum Corrigenda Corrigendum: Tempo and mode of regulatory evolution in Drosophila Coolon Joseph D. McManus C. Joel Stevenson...
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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: The mode of expression divergence in Drosophila fat body is infection-specific
- Bryan A. Ramirez-Corona,
- Stephanie Fruth,
- Oluchi Ofoegbu,
- and Zeba Wunderlich
Genome Res. June 2021 31: 1024-1034; Published in Advance April 15, 2021, doi:10.1101/gr.269597.120
...the two primary signaling pathways in the Drosophila innate immune response. The mode of expression divergence strongly depends on the condition, with trans-acting effects dominating in response to Gram-negative infection and cis-acting effects dominating in Gram-positive and preinfection conditions...
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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
...Evolution of structure in the Drosophila simulans species complex Mahul Chakraborty1,7, Ching-Ho Chang2,7,8, Danielle E. Khost2,3, Jeffrey Vedanayagam4, Jeffrey R. Adrion5, Yi Liao1, Kristi L. Montooth6, Colin D. Meiklejohn6, Amanda M. Larracuente2 and J.J. Emerson1 1Department of Ecology...
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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
...of de novo genes that emerged within a single species. We sequenced and assembled s with long-read technology and the corresponding transcriptomes from inbred lines of Drosophila melanogaster, derived from seven geographically diverse populations. We found line-specific neORFs in abundance but few ne...
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Research: Evolution of splicing regulatory networks in Drosophila
- C. Joel McManus,
- Joseph D. Coolon,
- Jodi Eipper-Mains,
- Patricia J. Wittkopp,
- and Brenton R. Graveley
Genome Res. May 2014 24: 786-796; Published in Advance February 10, 2014, doi:10.1101/gr.161521.113
...Evolution of splicing regulatory networks in Drosophila C. Joel McManus 1 , 2 , 4 , Joseph D. Coolon 3 , Jodi Eipper-Mains 1 , Patricia J. Wittkopp 3 and Brenton R. Graveley 1 , 4 1 Department of Genetics...
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Resource: A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes
- Jing Liu,
- Zongji Wang,
- Jing Li,
- Luohao Xu,
- Jiaqi Liu,
- Shaohong Feng,
- Chunxue Guo,
- Shengchan Chen,
- Zhanjun Ren,
- Jinpeng Rao,
- Kai Wei,
- Yuezhou Chen,
- Erich D. Jarvis,
- Guojie Zhang,
- and Qi Zhou
Genome Res. March 2021 31: 497-511; Published in Advance January 6, 2021, doi:10.1101/gr.271569.120
...or vertebrate karyotype because of their much slower rate of evolution. Here, we generated a new chromosome-level assembly of a female emu, and estimated the tempo of chromosome evolution across major avian phylogenetic branches, by comparing it to chromosome-level assemblies of 11 other bird and one turtle...
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Research: Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F₁ hybrids
- Carina F. Mugal,
- Mi Wang,
- Niclas Backström,
- David Wheatcroft,
- Murielle Ålund,
- Marie Sémon,
- S. Eryn McFarlane,
- Ludovic Dutoit,
- Anna Qvarnström,
- and Hans Ellegren
Genome Res. December 2020 30: 1727-1739; Published in Advance November 3, 2020, doi:10.1101/gr.254508.119
...-factors (Carroll 2005; Wray 2007). This has recently been exemplified for single traits, such as pigmentation in Drosophila (Hollocher et al. 2000; Kopp et al. 2000; Kopp and True 2002; Gompel and Carroll 2003; Gompel et al. 2005) and pelvic reduction in sticklebacks (Cresko et al. 2004; Shapiro et al. 2004...
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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
...constitute a principal driver of evolution, shaping its architecture and regulatory networks. In this context, Tuberaceae can become an important model system to study their genomic impact; however, the family lacks high-quality assemblies. Here, we investigate the interplay between TEs and Tuberaceae...
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Research: Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution
- Amit Blumberg,
- Edward J. Rice,
- Anshul Kundaje,
- Charles G. Danko,
- and Dan Mishmar
Genome Res. March 2017 27: 362-373; Published in Advance January 3, 2017, doi:10.1101/gr.209924.116
...bacterial ancestor (Zollo et al. 2012). However, as mtDNA transcription was mostly studied in vitro, little remains known about the mode and tempo of in vivo OXPHOS genes’ transcription residing on the mtDNA.During the early 1980s, human mtDNA transcription initiation sites (TISs) were identified...

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