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Research: Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species
- Charles Plessy,
- Michael J. Mansfield,
- Aleksandra Bliznina,
- Aki Masunaga,
- Charlotte West,
- Yongkai Tan,
- Andrew W. Liu,
- Jan Grašič,
- María Sara del Río Pisula,
- Gaspar Sánchez-Serna,
- Marc Fabrega-Torrus,
- Alfonso Ferrández-Roldán,
- Vittoria Roncalli,
- Pavla Navratilova,
- Eric M. Thompson,
- Takeshi Onuma,
- Hiroki Nishida,
- Cristian Cañestro,
- and Nicholas M. Luscombe
Genome Res. March 2024 34: 426-440; Published in Advance April 15, 2024, doi:10.1101/gr.278295.123
...of scrambling than any other group of animals (Fig. 7E).View larger version: In this window In a new window Figure 7. Genome scrambling in 10 × 10-Mbp regions for pairs of s in O. dioica (A), Ciona (B), Drosophila (C), and Caenorhabditis (D). Scaffold names are indicated in gray. (E) The number of breakpoint...
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Research: Topologically associating domains and their role in the evolution of genome structure and function in Drosophila
- Yi Liao,
- Xinwen Zhang,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. March 2021 31: 397-410; Published in Advance February 9, 2021, doi:10.1101/gr.266130.120
...million years of divergence, showed that ∼30%–40% of their s retain conserved TADs. Comparative genomic analysis of 17 Drosophila species revealed that chromosomal rearrangement breakpoints are enriched at TAD boundaries but depleted within TADs. Additionally, genes within conserved TADs show lower...
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Research: Shifts in the intensity of purifying selection: An analysis of genome-wide polymorphism data from two closely related yeast species
- Eyal Elyashiv,
- Kevin Bullaughey,
- Shmuel Sattath,
- Yosef Rinott,
- Molly Przeworski,
- and Guy Sella
Genome Res. November 2010 20: 1558-1573; Published in Advance September 4, 2010, doi:10.1101/gr.108993.110
.... 2005; Keightley and Eyre-Walker 2007). Some studies took a slightly different approach, inferring the DME from multilocus polymorphism data in two closely related species of Drosophila, under the assumption that all changes in f between them reflect differences in their effective population size (Loewe...
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Research: A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility
- Angelo A. Ruggieri,
- Luca Livraghi,
- James J. Lewis,
- Elizabeth Evans,
- Francesco Cicconardi,
- Laura Hebberecht,
- Yadira Ortiz-Ruiz,
- Stephen H. Montgomery,
- Alfredo Ghezzi,
- José Arcadio Rodriguez-Martinez,
- Chris D. Jiggins,
- W. Owen McMillan,
- Brian A. Counterman,
- Riccardo Papa,
- and Steven M. Van Belleghem
Genome Res. October 2022 32: 1862-1875; Published in Advance September 15, 2022, doi:10.1101/gr.276839.122
...factor binding sites with known function in neuron development in Drosophila. We also identified 24 TE insertions with head-specific chromatin accessibility. Our results show high rates of structural evolution that were previously overlooked in comparative genomic studies and suggest a high potential...
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Methods: Regulatory Potential Scores From Genome-Wide Three-Way Alignments of Human, Mouse, and Rat
- Diana Kolbe,
- James Taylor,
- Laura Elnitski,
- Pallavi Eswara,
- Jia Li,
- Webb Miller,
- Ross Hardison,
- and Francesca Chiaromonte
Genome Res. April 2004 14: 700-707; doi:10.1101/gr.1976004
...., Celniker, S.E., Levine, M., Rubin, G.M., and Eisen, M.B. 2002 . Exploiting transcription factor binding site clustering to identify cis -regulatory modules involved in pattern formation in the Drosophila . Proc. Natl. Acad. Sci. 99 : 757 -762. ↵ Biesiada, E., Hamamori, Y., Kedes, L., and Sartorelli, V...
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Methods: Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression
- Mathieu Blanchette,
- Alain R. Bataille,
- Xiaoyu Chen,
- Christian Poitras,
- Josée Laganière,
- Céline Lefèbvre,
- Geneviève Deblois,
- Vincent Giguère,
- Vincent Ferretti,
- Dominique Bergeron,
- Benoit Coulombe,
- and François Robert
Genome Res. May 2006 16: 656-668; Published in Advance April 10, 2006, doi:10.1101/gr.4866006
...Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression Genome-wide cis -regulatory module predictions Mathieu Blanchette 1 , 5 , Alain R. Bataille 2 , Xiaoyu Chen 1 , Christian Poitras 2...
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Research: 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. May 2014 24: 797-808; Published in Advance February 24, 2014, doi:10.1101/gr.163014.113
...); it is essential for organismal form, fitness, and function, and frequently varies within and between species. Comparative studies using genomic surveys of gene expression in yeast (Busby et al. 2011), Drosophila (Rifkin et al. 2003), and mammalian species (Brawand et al. 2011) with a range of divergence times...
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Research: Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints
- Manuel Irimia,
- Juan J. Tena,
- Maria S. Alexis,
- Ana Fernandez-Miñan,
- Ignacio Maeso,
- Ozren Bogdanović,
- Elisa de la Calle-Mustienes,
- Scott W. Roy,
- José L. Gómez-Skarmeta,
- and Hunter B. Fraser
Genome Res. December 2012 22: 2356-2367; Published in Advance June 21, 2012, doi:10.1101/gr.139725.112
..., with evidence for purifying selection on maintaining gene order in hemiascomycetous yeasts (Hurst et al. 2002; Fischer et al. 2006; Poyatos and Hurst 2007), but not in Drosophila (Weber and Hurst 2011), even over short phylogenetic distances. Third, gene order is nearly completely scrambled between humans...
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Resource: Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set
- Joana Damas,
- Rebecca O'Connor,
- Marta Farré,
- Vasileios Panagiotis E. Lenis,
- Henry J. Martell,
- Anjali Mandawala,
- Katie Fowler,
- Sunitha Joseph,
- Martin T. Swain,
- Darren K. Griffin,
- and Denis M. Larkin
Genome Res. May 2017 27: 875-884; Published in Advance November 30, 2016, doi:10.1101/gr.213660.116
..., and reptiles. Genome Biol Evol 8: 2442–2451. Ferguson-Lees J, Christie DA. 2005.Raptors of the world. PrincetonUniversity Press, Princeton, NJ. Fontdevila A, Ruiz A, Ocaña J, Alonso G. 1982. Evolutionary history of Drosophila buzzatii. II. How much has chromosomal polymorphism changed in colonization...
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Research: The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo
- Rahul Satija and
- Robert K. Bradley
Genome Res. April 2012 22: 656-665; Published in Advance January 13, 2012, doi:10.1101/gr.130682.111
...-specific transcription factors active in the Drosophila embryo, we found that binding of all factors exhibits a dose-dependent relationship with “TAGteam” sequence motifs bound by the zinc finger protein Vielfaltig, also known as Zelda, a recently discovered activator of the zygotic genome. TAGteam motifs are present...
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