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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
...Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi Jong Hyun Kim 1 , 4 , Michael S. Waterman 2 , 3 , and Lei M. Li 2 , 3 1 Department of Computer Science, Yonsei University, Seoul, 120...
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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
..., et al. 2005. Assembly of polymorphic s: Algorithms and application to Ciona savignyi. Genome Res 15: 1127–1135. Walenz B, Florea L. 2011. Sim4db and Leaff: Utilities for fast batch spliced alignment and sequence indexing. Bioinformatics 27: 1869–1870. Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen...
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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
.... 2005 . Assembly of polymorphic s: Algorithms and application to Ciona savignyi. Genome Res. 15 : 1127 -1135. Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis Eiichi Shoguchi 1 , 2 , 6 , 7 , Takeshi Kawashima 1 , 6 , Yutaka Satou 1 , 6 , Makoto Hamaguchi 1 , Tadasu Sin-I 3 , Yuji...
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RESOURCE: The C. savignyi genetic map and its integration with the reference sequence facilitates insights into chordate genome evolution
- Matthew M. Hill,
- Karl W. Broman,
- Elia Stupka,
- William C. Smith,
- Di Jiang,
- and Arend Sidow
Genome Res. August 2008 18: 1369-1379; Published in Advance June 2, 2008, doi:10.1101/gr.078576.108
...for Marine Molecular Biology, N-5008 Bergen, Norway Abstract The urochordate Ciona savignyi is an emerging model organism for the study of chordate evolution, development, and gene regulation. The extreme level of polymorphism in its population has inspired novel approaches in genome assembly...
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Resource: Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads
- Rei Kajitani,
- Kouta Toshimoto,
- Hideki Noguchi,
- Atsushi Toyoda,
- Yoshitoshi Ogura,
- Miki Okuno,
- Mitsuru Yabana,
- Masayuki Harada,
- Eiji Nagayasu,
- Haruhiko Maruyama,
- Yuji Kohara,
- Asao Fujiyama,
- Tetsuya Hayashi,
- and Takehiko Itoh
Genome Res. August 2014 24: 1384-1395; Published in Advance April 22, 2014, doi:10.1101/gr.170720.113
...) (heterozygosity: 1.2%; scaffold N50: 37.9 kbp) and Ciona savignyi (Vinson et al. 2005; Small et al. 2007) (heterozygosity: 4.6%; scaffold N50: 496 kbp) (note that both projects used the Sanger sequencingmethod). These results suggest that longer haplotype sequences are constructed for higher variant densities...
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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
..., N., Satou, Y., Nusbaum, C., et al. 2005 . Assembly of polymorphic s: Algorithms and application to Ciona savignyi. Genome Res. 15 : 1127 -1135. ↵ Wada, S., Tokuoka, M., Shoguchi, E., Kobayashi, K., Di Gregorio, A., Spagnuolo, A., Branno, M., Kohara, Y., Rokhsar, D., Levine, M., et al. 2003 . A wide...
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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
...years (Fig. 7A,E). To better contextualize this result, we estimated the same value for comparisons of ascidian tunicates using two isolates of Ciona intestinalis, Ciona robusta (differing only by pigmentation) (Caputi et al. 2007) and Ciona savignyi (a known example of scrambling on a long divergence...
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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
...to amplify C. savignyi genomic DNA ( http://www.broad.mit.edu/annotation/ciona/ ) for our initial functional regulatory constructs. We used the djmcs.lacZ plasmid for all native fusion constructs ( Johnson et al. 2004 ), and either pCES ( Harafuji et al. 2002 ) or a Brachyury ( Bra ) basal promoter plasmid...
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Method: metaSPAdes: a new versatile metagenomic assembler
- Sergey Nurk,
- Dmitry Meleshko,
- Anton Korobeynikov,
- and Pavel A. Pevzner
Genome Res. May 2017 27: 824-834; Published in Advance March 15, 2017, doi:10.1101/gr.213959.116
...classification algorithm. PLoS One 9: e93269. 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. Dick GJ, Andersson AF, Baker BJ...
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Method: HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
- Sergey Nurk,
- Brian P. Walenz,
- Arang Rhie,
- Mitchell R. Vollger,
- Glennis A. Logsdon,
- Robert Grothe,
- Karen H. Miga,
- Evan E. Eichler,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. September 2020 30: 1291-1305; Published in Advance August 14, 2020, doi:10.1101/gr.263566.120
...Sergey Nurk1,6, Brian P. Walenz1,6, Arang Rhie1, Mitchell R. Vollger2, Glennis A. Logsdon2, Robert Grothe3, Karen H. Miga4, Evan E. Eichler2,5, Adam M. Phillippy1 and Sergey Koren1 1Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute...
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