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

By Paramvir S. Dehal, Y. Satou, R. Campbell, Jarrod Chapman, B. Degnan, A. D. De Tomaso, Brad A. Davidson, Anna Di Gregorio, M. Gelpke, D. Goodstein and 77 more. Science, 2002

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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 that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.

Subfields: Global and Planetary Change, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/8c350b708a537cf7f4f147af6600534364f64a9a

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Citations in the corpus

Deep whole-genome resequencing sheds light on the distribution and effect of amphioxus SNPs (2022, background): “5% in sea squirts (urochordate) [25], 4–5% in sea urchin (echinoderm) [26], 2–2.”
The Repertoire of G-Protein–Coupled Receptors in Fully Sequenced Genomes (2005, background): “The sequence contains 2500 contigs and covers 116 Mbp of nonrepetitive sequence, approximately 90% of the total nonrepetitive material (Dehal et al., 2002), and an annotation project is ongoing at (http://genome.jgi-psf.org).”
Conservation and divergence of methylation patterning in plants and animals (2010, background): “Ciona is a primitive chordate that is distantly related to vertebrates (15), and, like vertebrates, it possesses Dnmt1 and Dnmt3 homologs (8).”
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes (2004, background): “The genomes of the mouse [87], the fugu fish [88], the Anopheles mosquito [89], the urochordate Ciona instestinalis [90] and the malarial parasite Plasmodium falciparum [91] have become available since then but were not included, partly because of problems with protein annotation for some of these g”
Morphological evidence that the molecularly determined Ciona intestinalis type A and type B are different species: Ciona robusta and Ciona intestinalis (2015, neutral): “This promoted the study of this organism and helped to clarify the evolutionary origin of chordate novelties (Dehal et al. 2002).”
The COG database: an updated version includes eukaryotes (2003, background): “Manual correction and annotation of KOGs is a labor-intensive process, which precluded immediate inclusion of the genomes of the mouse [53], fugu fish [54], mosquito [55], the urochordate Ciona instestinalis [56], and the malarial parasite Plasmodium falciparum [57], which have become available sinc”
GeneWise and Genomewise. (2004, background): “…since 1997 (Birney and Durbin 1997) and has been used in numerous genome projects, both as part of the Ensembl pipe-line (The International Human Genome Sequencing Consortium 2001; Aparicio et al. 2002; Waterston et al. 2002) and as a stand-alone tool (Dehal et al. 2002; Galagan et al. 2003).”
Two Rounds of Whole Genome Duplication in the Ancestral Vertebrate (2005, background): “, at least draft quality) genome sequences are available for the tunicate Ciona intestinalis [38] (a basal chordate outgroup) and the vertebrates Takifugu rubripes [39] (a pufferfish ‘‘fugu’’), Mus musculus”
Urochordate βγ-Crystallin and the Evolutionary Origin of the Vertebrate Eye Lens (2005, neutral): “A search of the genome [ 8 ]o fC. intestinalis for βγ-crystallin-like sequences identified one gene coding for a single domain protein with homology to vertebrate βγ-crystallins (for full details of methods, please see the Supplemental Data available with this article online).”
Mechanisms of germ cell specification across the metazoans: epigenesis and preformation (2003, background): “Ctenophores (comb jellies) also probably diverged from other Metazoa before the origin of the Bilateria (Fig.”
Phylogenetic Analysis of the Plant Endo-β-1,4-Glucanase Gene Family (2004, background): “Because ascidians are the only animals known to make cellulose, Dehal et al. (2002) suggested that the genes involved in the metabolism of cellulose in Ciona might be a lineage-specific innovation.”
A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety (2007, background): “Among recently sequenced animal genomes, a high SNP frequency was found in sea urchin [90] and Cyona intestinalis [91].”
The thrombospondins. (2011, background): “Interestingly, although Ciona is considered to have diverged from the ancestral chordate before the whole genome duplications that took place during the evolution of modern vertebrates (Dehal et al., 2002; Panopoulou et al., 2003), not one but two distinct TSP-encoding sequences were identified with”