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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
...that challenges our previous vision of speciation in which similar animals always share similar structures.The concept of “reference ” for each species comes from the notion that genomic structural variations and chromosomal rearrangements within species are rare, which is a fundamental aspect sustaining projects...
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Methods: Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi
- Jong Hyun Kim,
- Michael S. Waterman,
- and Lei M. Li
Genome Res. July 2007 17: 1101-1110; Published in Advance June 13, 2007, doi:10.1101/gr.5894107
...analysis with Ciona savignyi , and discover interesting patterns of conserved DNA elements in chordates. Footnotes ↵ 4 Corresponding author. ↵ 4 E-mail jonghkim@usc.edu ; fax (213) 740-2437. [Supplemental material is available at www.genome.org . The diploid genome sequence...
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Resource: The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program
- Olivier Tassy,
- Delphine Dauga,
- Fabrice Daian,
- Daniel Sobral,
- François Robin,
- Pierre Khoueiry,
- David Salgado,
- Vanessa Fox,
- Danièle Caillol,
- Renaud Schiappa,
- Baptiste Laporte,
- Anne Rios,
- Guillaume Luxardi,
- Takehiro Kusakabe,
- Jean-Stéphane Joly,
- Sébastien Darras,
- Lionel Christiaen,
- Magali Contensin,
- Hélène Auger,
- Clément Lamy,
- Clare Hudson,
- Ute Rothbächer,
- Michael J. Gilchrist,
- Kazuhiro W. Makabe,
- Kohji Hotta,
- Shigeki Fujiwara,
- Nori Satoh,
- Yutaka Satou,
- and Patrick Lemaire
Genome Res. October 2010 20: 1459-1468; Published in Advance July 20, 2010, doi:10.1101/gr.108175.110
...Gilchrist, M.J Laporte, Baptiste Magali Contensin Schiappa Fabrice, Daian Robin Danièle J Joly Rios Anne Lemaire genome;gr.108175.110 10.1101/gr.108175.110 1088-9051 The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program Resource The ANISEED database...
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PERSPECTIVE: Unraveling genomic regulatory networks in the simple chordate, Ciona intestinalis
- Weiyang Shi,
- Michael Levine,
- and Brad Davidson
Genome Res. December 2005 15: 1668-1674; doi:10.1101/gr.3768905
..., M.I., Pachter, L., Keys, D.N., and Rubin, E.M. 2004 . Intraspecies sequence comparisons for annotating s. Genome Res. 14 : 2406 -2411. ↵ Canestro, C., Bassham, S., and Postlethwait, J.H. 2003 . Seeing chordate evolution through the Ciona sequence. Genome Biol. 4 : 208 . ↵ Christiaen, L., Bourrat, F...
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ARTICLE: De novo discovery of a tissue-specific gene regulatory module in a chordate
- David S. Johnson,
- Qing Zhou,
- Kasumi Yagi,
- Nori Satoh,
- Wing Wong,
- and Arend Sidow
Genome Res. October 2005 15: 1315-1324; Published in Advance September 16, 2005, doi:10.1101/gr.4062605
...-8502 Japan Abstract We engage the experimental and computational challenges of de novo regulatory module discovery in a complex and largely unstudied metazoan genome. Our analysis is based on the comprehensive characterization of regulatory elements of 20 muscle genes in the chordate, Ciona...
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Resource: HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies
- Shengfeng Huang,
- Zelin Chen,
- Guangrui Huang,
- Ting Yu,
- Ping Yang,
- Jie Li,
- Yonggui Fu,
- Shaochun Yuan,
- Shangwu Chen,
- and Anlong Xu
Genome Res. August 2012 22: 1581-1588; Published in Advance May 3, 2012, doi:10.1101/gr.133652.111
...obligately outcrossing nematodes. Genome Res 19: 470–480. Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein DM, et al. 2002. The draft of Ciona intestinalis: Insights into chordate and vertebrate origins. Science 298: 2157–2167. Denoeud F, Henriet...
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LETTER: Gene Conversion and the Evolution of Protocadherin Gene Cluster Diversity
- James P. Noonan,
- Jane Grimwood,
- Jeremy Schmutz,
- Mark Dickson,
- and Richard M. Myers
Genome Res. March 2004 14: 354-366; doi:10.1101/gr.2133704
..., J Mark, Dickson Noonan James P. JP Noonan Mark Dickson Noonan, James P JamesP Noonan Jeremy, Schmutz Jane, Grimwood James P Noonan R Myers genome;14/3/354 10.1101/gr.2133704 1088-9051 Gene Conversion and the Evolution of Protocadherin Gene Cluster Diversity Gene Conversion and the Evolution...
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RESOURCE: Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis
- Eiichi Shoguchi,
- Takeshi Kawashima,
- Yutaka Satou,
- Makoto Hamaguchi,
- Tadasu Sin-I,
- Yuji Kohara,
- Nik Putnam,
- Daniel S. Rokhsar,
- and Nori Satoh
Genome Res. February 2006 16: 297-303; Published in Advance December 14, 2005, doi:10.1101/gr.4156606
...important insights into the origin and evolution of chordates as well as vertebrates. However, because this genomic data has not yet been mapped onto chromosomes, important biological questions including regulation of gene expression at the -wide level cannot yet be addressed. Here, we report the molecular...
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REVIEW: Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques
- Laura Elnitski,
- Victor X. Jin,
- Peggy J. Farnham,
- and Steven J.M. Jones
Genome Res. December 2006 16: 1455-1464; Published in Advance October 19, 2006, doi:10.1101/gr.4140006
...that generate broad conclusions about binding site preferences and regulation of gene expression, are described below. Protocols for these experimental assays are available in the references and in Supplemental Table 2. DNaseI hypersensitivity DNaseI hypersensitivity provides a method to map changes...
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