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Research: Fragile regions and not functional constraints predominate in shaping gene organization in the genus Drosophila
- Marcin von Grotthuss,
- Michael Ashburner,
- and José M. Ranz
Genome Res. August 2010 20: 1084-1096; Published in Advance July 2, 2010, doi:10.1101/gr.103713.109
...with the largest homologous collinear blocks (HCBs), since regions under no functional constraint would presumably have been disrupted. Likewise, highly rearranged s can show precisely how widespread breakpoint reuse is and to which genomic regions it is associated. The Drosophila is organized into six chromosomal...
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ARTICLE: Fourfold Faster Rate of Genome Rearrangement in Nematodes Than in Drosophila
- Avril Coghlan and
- Kenneth H. Wolfe
Genome Res. June 1, 2002 12: 857-867; doi:10.1101/gr.172702
...–120 million years ago, and that since then there have been 4030 rearrangements between their whole genomes. Our estimate of the rearrangement rate, 0.4–1.0 chromosomal breakages/Mb per Myr, is at least four times that of Drosophila , which was previously reported to be the fastest rate among eukaryotes...
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ARTICLE: Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution
- Stephen Richards,
- Yue Liu,
- Brian R. Bettencourt,
- Pavel Hradecky,
- Stan Letovsky,
- Rasmus Nielsen,
- Kevin Thornton,
- Melissa J. Hubisz,
- Rui Chen,
- Richard P. Meisel,
- Olivier Couronne,
- Sujun Hua,
- Mark A. Smith,
- Peili Zhang,
- Jing Liu,
- Harmen J. Bussemaker,
- Marinus F. van Batenburg,
- Sally L. Howells,
- Steven E. Scherer,
- Erica Sodergren,
- Beverly B. Matthews,
- Madeline A. Crosby,
- Andrew J. Schroeder,
- Daniel Ortiz-Barrientos,
- Catharine M. Rives,
- Michael L. Metzker,
- Donna M. Muzny,
- Graham Scott,
- David Steffen,
- David A. Wheeler,
- Kim C. Worley,
- Paul Havlak,
- K. James Durbin,
- Amy Egan,
- Rachel Gill,
- Jennifer Hume,
- Margaret B. Morgan,
- George Miner,
- Cerissa Hamilton,
- Yanmei Huang,
- Lenée Waldron,
- Daniel Verduzco,
- Kerstin P. Clerc-Blankenburg,
- Inna Dubchak,
- Mohamed A.F. Noor,
- Wyatt Anderson,
- Kevin P. White,
- Andrew G. Clark,
- Stephen W. Schaeffer,
- William Gelbart,
- George M. Weinstock,
- and Richard A. Gibbs
Genome Res. January 2005 15: 1-18; doi:10.1101/gr.3059305
...is flexible. Overall, a pattern of repeat-mediated chromosomal rearrangement, and high coadaptation of both male genes and cis -regulatory sequences emerges as important themes of genome divergence between these species of Drosophila . Footnotes [Supplemental material is available online at www.genome...
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RESOURCE: A BAC-based physical map of the Drosophila buzzatii genome
- Josefa González,
- Michael Nefedov,
- Ian Bosdet,
- Ferran Casals,
- Oriol Calvete,
- Alejandra Delprat,
- Heesun Shin,
- Readman Chiu,
- Carrie Mathewson,
- Natasja Wye,
- Roger A. Hoskins,
- Jacqueline E. Schein,
- Pieter de Jong,
- and Alfredo Ruiz
Genome Res. June 2005 15: 885-892; doi:10.1101/gr.3263105
...: 281 -295. Ranz, J.M., Casals, F., and Ruiz, A. 2001 . How malleable is the eukaryotic ? Extreme rate of chromosomal rearrangements in the genus Drosophila . Genome Res. 11 : 230 -239. Ranz, J.M., González, J., Casals, F., and Ruiz, A. 2003 . Low occurrence of gene transposition events during...
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12 Drosophila Genomes/Letter: Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes
- Andreas Heger and
- Chris P. Ponting
Genome Res. December 2007 17: 1837-1849; Published in Advance November 7, 2007, doi:10.1101/gr.6249707
...Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes Andreas Heger 1 and Chris P. Ponting MRC Functional Genetics Unit, University of Oxford, Department of Physiology, Anatomy and Genetics, Oxford OX1 3QX, United Kingdom...
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PERSPECTIVE: Drosophila melanogaster: A case study of a model genomic sequence and its consequences
- Michael Ashburner and
- Casey M. Bergman
Genome Res. December 2005 15: 1661-1667; doi:10.1101/gr.3726705
...cis -regulatory modules applied to body patterning in the early Drosophila embryo. BMC Bioinformatics 3 : 30 . ↵ Ranz, J.M., Casals, F., and Ruiz, A. 2001 . How malleable is the eukaryotic ? Extreme rate of chromosomal rearrangement in the genus Drosophila. Genome Res. 11 : 230 -239. ↵ Ranz, J...
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ARTICLE: Extensive Exon Reshuffling Over Evolutionary Time Coupled to Trans-Splicing in Drosophila
- Mariano Labrador and
- Victor G. Corces
Genome Res. October 2003 13: 2220-2228; doi:10.1101/gr.1440703
...different insect species is whether the mechanisms responsible for the large amount of local rearrangements observed within the locus are different from those causing rearrangements at the chromosome level. The detailed information obtained from the Drosophila and Anopheles projects provides an exceptional...
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LETTER: Conservation of regulatory sequences and gene expression patterns in the disintegrating Drosophila Hox gene complex
- Bárbara Negre,
- Sònia Casillas,
- Magali Suzanne,
- Ernesto Sánchez-Herrero,
- Michael Akam,
- Michael Nefedov,
- Antonio Barbadilla,
- Pieter de Jong,
- and Alfredo Ruiz
Genome Res. May 2005 15: 692-700; doi:10.1101/gr.3468605
...been rearranged differently in several Drosophila species, producing a striking diversity of Hox gene organizations. We investigated the genomic and functional consequences of the two HOM-C splits present in Drosophila buzzatii . Firstly, we sequenced two regions of the D. buzzatii genome, one...
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LETTER: Genomic Gene Clustering Analysis of Pathways in Eukaryotes
- Jennifer M. Lee and
- Erik L.L. Sonnhammer
Genome Res. May 1, 2003 13: 875-882; Published in Advance April 14, 2003, doi:10.1101/gr.737703
...of chromosomal rearrangement in the genus Drosophila. Genome Res. 11 : 230 – 239 . ↵ Roy P.J. , Stuart J.M. , Lund J. , Kim S.K. ( 2002 ) Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature 418 : 975 – 979 . ↵ Salgado H. , Moreno-Hagelsieb G. , Smith T.F. , Collado-Vides J. ( 2000...
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ARTICLE: Evolution of Gene Order in the Genomes of Two Related Yeast Species
- Gilles Fischer,
- Cécile Neuvéglise,
- Pascal Durrens,
- Claude Gaillardin,
- and Bernard Dujon
Genome Res. December 1, 2001 11: 2009-2019; doi:10.1101/gr.212701
...different synteny breakpoints between neighboring genes and two cases of local gene inversion were characterized in detail. The number and the type of the chromosomal rearrangements that have lead to these differences were identified. We show that evolution of gene order in the genomes of these two yeast...

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