The Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins

@article{Dehal2002TheDG,
  title={The Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins},
  author={Paramvir S. Dehal and Y. Satou and R. Campbell and J. Chapman and B. Degnan and A. D. De Tomaso and B. Davidson and A. Di Gregorio and M. Gelpke and D. Goodstein and N. Harafuji and K. Hastings and Isaac Y. Ho and K. Hotta and Wayne Huang and T. Kawashima and P. Lemaire and Diego Martínez and I. Meinertzhagen and Simona Necula and M. Nonaka and N. Putnam and Sam Rash and H. Saiga and M. Satake and A. Terry and L. Yamada and Hong-Gang Wang and S. Awazu and K. Azumi and J. Boore and M. Branno and S. Chin-bow and R. Desantis and S. Doyle and P. Francino and D. Keys and S. Haga and H. Hayashi and K. Hino and K. Imai and K. Inaba and S. Kano and Kenji Kobayashi and Mari Kobayashi and Byung-in Lee and K. Makabe and C. Manohar and G. Matassi and M. Medina and Y. Mochizuki and Steve Mount and T. Morishita and Sachiko Miura and A. Nakayama and Satoko Nishizaka and H. Nomoto and Fumiko Ohta and Kazuko Oishi and I. Rigoutsos and Masako Sano and Akane Sasaki and Y. Sasakura and E. Shoguchi and T. Shin-I and Antoinetta Spagnuolo and D. Stainier and Miho M. Suzuki and Olivier Tassy and N. Takatori and M. Tokuoka and K. Yagi and Fumiko Yoshizaki and S. Wada and Cindy Zhang and P. D. Hyatt and F. Larimer and C. Detter and N. Doggett and T. Glavina and T. Hawkins and P. Richardson and S. Lucas and Y. Kohara and M. Levine and N. Satoh and D. Rokhsar},
  journal={Science},
  year={2002},
  volume={298},
  pages={2157 - 2167}
}
The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. TheCiona genome contains ∼16,000 protein-coding genes, similar to the number in other invertebrates, but only half… Expand
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TLDR
The results show that the genome of Ciona is not representative of the ancestral chordate genome with respect to gene content but rather shows derived features that may reflect adaptation of the specific ecological niche of urochordates. Expand
Phylogenetic Analysis of Ciona intestinalis Gene Superfamilies Supports the Hypothesis of Successive Gene Expansions
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The results support the hypothesis of a gene expansion prior the base of chordate ancestry followed by another gene expansion during vertebrate evolution and indicate that Ciona intestinalis genome will be a very valuable tool for evolutionary analyses. Expand
The Ciona intestinalis genome: when the constraints are off.
  • L. Holland, J. Gibson-Brown
  • Biology, Medicine
  • BioEssays : news and reviews in molecular, cellular and developmental biology
  • 2003
TLDR
Initial analyses of the C. intestinalis genome indicate that it has been evolving rapidly, and that many genes linked together in most other bilaterians have become uncoupled. Expand
How much does the amphioxus genome represent the ancestor of chordates?
TLDR
Whether the amphioxus genome is indeed a good proxy for the genome of the chordate ancestor, with a focus on protein-coding genes is examined, and genome features, such as synteny, gene duplication and gene loss, are investigated. Expand
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TLDR
Whole-genome comparisons illuminate the murky relationships among the three chordate groups (tunicates, lancelets and vertebrates), and allow not only reconstruction of the gene complement of the last common chordate ancestor but also partial reconstruction of its genomic organization. Expand
Ciona intestinalis: an emerging model for whole-genome analyses.
TLDR
Analysis of the Ciona draft genome indicates that the ∼153–159Mb genome contains ∼16 000 protein-coding genes, including a fundamental set of conserved chordate proteins involved in cell signaling and development. Expand
Genomewide surveys of developmentally relevant genes in Ciona intestinalis
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The haploid genome of Ciona intestinalis was previously estimated to be ~160 Mbp in size and to contain 15,500 genes; the draft genome sequence determined showed that this estimate was quite accurate, and should provide insight into the origin and evolution of chordates. Expand
Gene-regulatory networks in the Ciona embryos.
TLDR
In the ascidian Ciona intestinalis, gene-regulatory networks responsible for the embryonic development have been studied on a genome-wide scale and at single-cell resolution, and these simple embryos are now being modeled in the computer, which allows them to be understood very precisely in three dimensions. Expand
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TLDR
The regulatory genes present in the ancestral chordate can be deduced by comparing the extant chordate genomes, crucial to understand the evolution of chordates. Expand
A genomewide survey of developmentally relevant genes in Ciona intestinalis
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The Ciona genome contains orthologous genes of each component of aPKC-Par and PCP pathways and WASP/WAVE/SCAR and ADF/cofilin cascades, with less redundancy than the vertebrate genomes, suggesting that the conserved pathways/cascades function in Ciona development. Expand
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The identification of six FGF genes in a basal chordate gave an insight into the diversification of specific subfamilies of vertebrate FGFs, and it is speculated that three of the other genes are orthologous to vertebrates FGF3/7/10/22, FGF4/5/6 and FGF9/16/20, although the authors cannot assign the sixth member to any of the vertebrates. Expand
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