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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
...et al. 1999). Differences in the scale and extent of synteny conservation have led to the concepts of micro- and macrosynteny. Microsynteny (also known as “collinearity” in genomics) refers to the conservation of gene content and order within sets of tightly linked orthologous genes. Generally...
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Research: An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication
- Elise Parey,
- Alexandra Louis,
- Jérôme Montfort,
- Yann Guiguen,
- Hugues Roest Crollius,
- and Camille Berthelot
Genome Res. September 2022 32: 1685-1697; Published in Advance August 12, 2022, doi:10.1101/gr.276953.122
...; Zwaenepoel and Van de Peer 2019; Parey et al. 2020). Previous characterizations of DCS regions in teleosts were therefore limited to regions of highly conserved gene order or small species sets: the largest multispecies data set comprised eight fish species and included ∼29% of all genes in DCS regions...
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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
...). Despite conservation of PCNE order, the neighboring genes are mostly different in each genomic region, indicating that extensive gene rearrangement is possible even when PCNE order is conserved. Nonetheless, there is some evidence of ancient synteny conservation—mouse Sox21, fugu Sox21, and amphioxus Sox...
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LETTER: Genomic Sequence Analysis of Fugu rubripes CFTR and Flanking Genes in a 60 kb Region Conserving Synteny with 800 kb of Human Chromosome 7
- Heather Davidson,
- Martin S. Taylor,
- Ann Doherty,
- A. Christopher Boyd,
- and David J. Porteous
Genome Res. August 1, 2000 10: 1194-1203; doi:10.1101/gr.10.8.1194
...of genomic DNA around the wnt1 locus of Fugu rubripes. Genome Res. 9 : 251 – 258 . ↵ Gilley J. , Armes N. , Fried M. ( 1997 ) Fugu is not a good mammalian model. Nature 385 : 305 – 306 . ↵ Gilley J. , Fried M. ( 1999 ) Extensive gene order differences within regions of conserved synteny between the fugu...
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ARTICLE: Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates
- Hiroshi Kikuta,
- Mary Laplante,
- Pavla Navratilova,
- Anna Z. Komisarczuk,
- Pär G. Engström,
- David Fredman,
- Altuna Akalin,
- Mario Caccamo,
- Ian Sealy,
- Kerstin Howe,
- Julien Ghislain,
- Guillaume Pezeron,
- Philippe Mourrain,
- Staale Ellingsen,
- Andrew C. Oates,
- Christine Thisse,
- Bernard Thisse,
- Isabelle Foucher,
- Birgit Adolf,
- Andrea Geling,
- Boris Lenhard,
- and Thomas S. Becker
Genome Res. May 2007 17: 545-555; Published in Advance March 26, 2007, doi:10.1101/gr.6086307
...in zebrafish/ Tetraodon /fugu rx3 alignments, some of which are within the introns of the neighboring genes (data not shown). These findings suggest that, although several genes are found within this block of conserved synteny, the HCNEs in the region are functional regulatory elements acting on rx3...
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LETTER: Generation and Analysis of 25 Mb of Genomic DNA from the Pufferfish Fugu rubripes by Sequence Scanning
- Greg Elgar,
- Melody S. Clark,
- Stephen Meek,
- Sarah Smith,
- Sarah Warner,
- Yvonne J.K. Edwards,
- Nassima Bouchireb,
- Amanda Cottage,
- Giles S.H. Yeo,
- Yagnesh Umrania,
- Gary Williams,
- and Sydney Brenner
Genome Res. October 1, 1999 9: 960-971; doi:10.1101/gr.9.10.960
..., their order or whether genes d , e, f, g , and h lie between them may not be known. As the amount of genomic sequence increases, the ability to compare gene order at high resolution will improve and it will be more feasible to make estimates of the degree of synteny that Fugu shares with mammalian s. Where...
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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
.... 2006; Brunet et al. 2006). In this study, we performed comparative analyses, including gene order (synteny) and phylogenetic analyses, in D. rerio, T. rubripes, T. nigroviridis, medaka (Oryzias latipes), and stickleback (Gasterosteus aculeatus) to identify gene duplicates retained from the last...
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LETTER: Four-Hundred Million Years of Conserved Synteny of Human Xp and Xq Genes on Three Tetraodon Chromosomes
- Frank Grützner,
- Hugues Roest Crollius,
- Götz Lütjens,
- Olivier Jaillon,
- Jean Weissenbach,
- Hans-Hilger Ropers,
- and Thomas Haaf
Genome Res. September 1, 2002 12: 1316-1322; Published in Advance August 21, 2002, doi:10.1101/gr.222402
.... Life Sci. 55 : 910 – 931 . ↵ Brunner B. , Todt T. , Lenzner S. , Stout K. , Schulz U. , Ropers H.-H. , Kalscheuer V. ( 1999 ) Genomic structure and comparative analysis of nine Fugu genes: Conservation of synteny with human chromosome Xp22.2-p22.1. Genome Res. 9 : 437 – 448 . ↵ Burt D.W. , Bruley C...
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LETTER: Genome Duplication, a Trait Shared by 22,000 Species of Ray-Finned Fish
- John S. Taylor,
- Ingo Braasch,
- Tancred Frickey,
- Axel Meyer,
- and Yves Van de Peer
Genome Res. March 1, 2003 13: 382-390; doi:10.1101/gr.640303
...://www.evolutionsbiologie.uni-konstanz.de/Wanda/ ; WANDA—database of genes duplicated in fish. http://www.jgi.doe.gov/fugu/index.html ; The Fugu rubripes project Web site at the Joint Genome Institute. http://www.ncbi.nlm.nih.gov ; National Center for Biotechnology Information (NCBI). http://zfin.org/ZFIN/ ; The Zebrafish Information Network. http...
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ARTICLE: Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
- Adam Siepel,
- Gill Bejerano,
- Jakob S. Pedersen,
- Angie S. Hinrichs,
- Minmei Hou,
- Kate Rosenbloom,
- Hiram Clawson,
- John Spieth,
- LaDeana W. Hillier,
- Stephen Richards,
- George M. Weinstock,
- Richard K. Wilson,
- Richard A. Gibbs,
- W. James Kent,
- Webb Miller,
- and David Haussler
Genome Res. August 2005 15: 1034-1050; Published in Advance July 15, 2005, doi:10.1101/gr.3715005
..., Houston, Texas 77030, USA Abstract We have conducted a comprehensive search for conserved elements in vertebrate genomes, using genome-wide multiple alignments of five vertebrate species (human, mouse, rat, chicken, and Fugu rubripes ). Parallel searches have been performed with multiple...

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