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LETTER: Evolutionary Conservation of Regulatory Elements in Vertebrate Hox Gene Clusters
- Simona Santini,
- Jeffrey L. Boore,
- and Axel Meyer
Genome Res. June 2003 13: 1111-1122; doi:10.1101/gr.700503
...clusters, which are now expected to be found in all (or most) ray-finned fishes. Independent gene losses in Hox clusters have happened in different species of fishes ( Fig. 2 ). The pufferfish Hox Aα cluster was initially thought to lack Hox A7α ( Aparicio et al. 1997 ), and it was hypothesized...
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Letter: Evolution of gene function and regulatory control after whole-genome duplication: Comparative analyses in vertebrates
- Karin S. Kassahn,
- Vinh T. Dang,
- Simon J. Wilkins,
- Andrew C. Perkins,
- and Mark A. Ragan
Genome Res. August 2009 19: 1404-1418; Published in Advance May 13, 2009, doi:10.1101/gr.086827.108
...WGD in the pufferfishes Tetraodon nigroviridis and Takifugu rubripes may be as low as 1%–5% (Aparicio et al. 2002; Jaillon et al. 2004), although there has been debate regarding these estimates (Brunet et al. 2006). Analysis of individual gene families in the zebrafish Danio rerio suggested that up...
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ARTICLE: Regulatory Roles of Conserved Intergenic Domains in Vertebrate Dlx Bigene Clusters
- Noël Ghanem,
- Olga Jarinova,
- Angel Amores,
- Qiaoming Long,
- Gary Hatch,
- Byung Keon Park,
- John L.R. Rubenstein,
- and Marc Ekker
Genome Res. April 1, 2003 13: 533-543; doi:10.1101/gr.716103
...) Generation of a P1 artificial chromosome library of the Southern pufferfish. Gene 272 : 283 – 289 . ↵ Amores A. , Force A. , Yan Y.-L. , Joly L. , Amemiya C. , Fritz A. , Ho R.K. , Langeland J. , Prince V. , Wang Y.-L. , et al. ( 1998 ) Zebrafish hox clusters and vertebrate evolution. Science 282 : 1711...
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Resource: Automated identification of conserved synteny after whole-genome duplication
- Julian M. Catchen,
- John S. Conery,
- and John H. Postlethwait
Genome Res. August 2009 19: 1497-1505; Published in Advance May 22, 2009, doi:10.1101/gr.090480.108
.... Zebrafish hox clusters and vertebrate evolution. Science 282: 1711–1714. Birney E, Andrews TD, Bevan P, Caccamo M, Chen Y, Clarke L, Coates G, Cuff J, Curwen V, Cutts T, et al. 2004. An overview of Ensembl. Genome Res 14: 925–928. Blair JE, Hedges SB. 2005. Molecular phylogeny and divergence times...
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LETTER: Bichir HoxA Cluster Sequence Reveals Surprising Trends in Ray-Finned Fish Genomic Evolution
- Chi-hua Chiu,
- Ken Dewar,
- Günter P. Wagner,
- Kazuhiko Takahashi,
- Frank Ruddle,
- Christina Ledje,
- Peter Bartsch,
- Jean-Luc Scemama,
- Edmund Stellwag,
- Claudia Fried,
- Sonja J. Prohaska,
- Peter F. Stadler,
- and Chris T. Amemiya
Genome Res. January 2004 14: 11-17; doi:10.1101/gr.1712904
...., Yan, Y-L., Pomeroy, J., Singer, A., Amemiya, C.T., and Postlethwait, J.H. 2003 . Developmental roles of pufferfish Hox clusters and evolution in ray-fin fish. Genome Res. (this issue). ↵ Aparicio, S., Chapman, J., Stupka, E., Putnam, N., Chia, J.M., Dehal, P., Christoffels, A., Rash, S., Hoon, S...
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LETTER: Systematic genome-wide annotation of spliceosomal proteins reveals differential gene family expansion
- Nuno L. Barbosa-Morais,
- Maria Carmo-Fonseca,
- and Samuel Aparício
Genome Res. January 2006 16: 66-77; Published in Advance December 12, 2005, doi:10.1101/gr.3936206
...., Myers, E.W., and Lipman, D.J. 1990 . Basic local alignment search tool. J. Mol. Biol. 215 : 403 -410. ↵ Amores, A., Force, A., Yan, Y.L., Joly, L., Amemiya, C., Fritz, A., Ho, R.K., Langeland, J., Prince, V., Wang, Y.L., et al. 1998 . Zebrafish hox clusters and vertebrate evolution. Science 282 : 1711...
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Letter: Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention
- Andrew L. Hufton,
- Susanne Mathia,
- Helene Braun,
- Udo Georgi,
- Hans Lehrach,
- Martin Vingron,
- Albert J. Poustka,
- and Georgia Panopoulou
Genome Res. November 2009 19: 2036-2051; Published in Advance August 24, 2009, doi:10.1101/gr.093237.109
...seem to support recent estimates that there has been increased CNE loss in the teleost—and especially pufferfish—lineages (Stephen et al. 2008; Wang et al. 2009). Table 1. Orthology summary Genesa Gene familiesb Total 51,942 8368 Amphioxus 18,946 8368 Mouse 11,935 7443 Fugu 9612 6518 Zebrafish 11...
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LETTER: Gene number expansion and contraction in vertebrate genomes with respect to invertebrate genomes
- Anuphap Prachumwat and
- Wen-Hsiung Li
Genome Res. February 2008 18: 221-232; Published in Advance December 14, 2007, doi:10.1101/gr.7046608
...to this transition and postulated that two rounds of whole- duplication (WGD) occurred in the early evolution of the vertebrates. The existence of multiple copies for many types of genes in vertebrate s has been taken as evidence for two rounds of WGD (e.g., the HOX gene clusters and genes near the major...
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PERSPECTIVE: Fish genomics and biology
- Hugues Roest Crollius and
- Jean Weissenbach
Genome Res. December 2005 15: 1675-1682; doi:10.1101/gr.3735805
....K., Langeland, J., Prince, V., Wang, Y.L., et al. 1998 . Zebrafish hox clusters and vertebrate evolution. Science 282 : 1711 -1714. ↵ Aparicio, S., Morrison, A., Gould, A., Gilthorpe, J., Chaudhuri, C., Rigby, P., Krumlauf, R., and Brenner, S. 1995 . Detecting conserved regulatory elements with the model...
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ARTICLE: Ancient duplicated conserved noncoding elements in vertebrates: A genomic and functional analysis
- Gayle K. McEwen,
- Adam Woolfe,
- Debbie Goode,
- Tanya Vavouri,
- Heather Callaway,
- and Greg Elgar
Genome Res. April 2006 16: 451-465; Published in Advance March 13, 2006, doi:10.1101/gr.4143406
...(white). Nineteen dCNE families were located in regions containing large clusters of related paralogous trans-dev genes (e.g., HOX and IRX clusters) or in regions containing several unrelated trans-dev paralogs (e.g., LMX1A and PBX1 on Chr1 and LMX1B and PBX3 on Chr9). A further 10 dCNE families were...

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