The DOI matches its Crossref record; 81 of the 81 references it cites were found in a registry or an index.
The Draft Genome of Ciona intestinalis : Insights into Chordate and Vertebrate Origins
Open accessAbstract
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 . The Ciona 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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“The difference is consistent with the lower gene number and reduced genome size in the urochordates (4).”
From The Genome of the Sea Urchin Strongylocentrotus purpuratus (2006) · cites this paper as [4]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216
Self-citationThe sequence of the human genome
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) · Science · doi:10.1126/science.1058040 · Cited by 13,909
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
The Genome Sequence of Drosophila melanogaster
Adams, M. D., Celniker, S., Holt, R. A., Evans, C. A., Gocayne, J. D., Amanatides, P. G., Scherer, S. E., Li, P. W., Hoskins, R. A., Galle, R. F., et al. (2000) · Science · doi:10.1126/science.287.5461.2185 · Cited by 5,902
Genome Sequence of the Nematode C. elegans : A Platform for Investigating Biology
Berg, J. (1998) · Science · doi:10.1126/science.282.5396.2012 · Cited by 4,458
InterProScan – an integration platform for the signature-recognition methods in InterPro
Zdobnov, E. M., & Apweiler, R. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.9.847 · Cited by 2,915
Multifunctional strands in tight junctions
Tsukita, S., Furuse, M., & Itoh, M. (2001) · Nature reviews. Molecular cell biology · doi:10.1038/35067088 · Cited by 2,578
Phylogenetic Perspectives in Innate Immunity
Hoffmann, J. A., Kafatos, F. C., Janeway, C. A., & Ezekowitz, R. A. B. (1999) · Science · doi:10.1126/science.284.5418.1313 · Cited by 2,524
Caspases: Intracellular Signaling by Proteolysis
Salvesen, G. S., & Dixit, V. M. (1997) · Cell · doi:10.1016/s0092-8674(00)80430-4 · Cited by 2,118
Research works printed but not linked: 10
- Kowalevsky A., Mem. Acad. St. Petersbourg Ser. 7 10, 1 (1866).
- Nishida H., Int. Rev. Cytol. 176, 24 (1997).
- Conklin E. G., J. Acad. Nat. Sci. (Philadelphia) 13, 1 (1905).
- 10.1016/S0022-2836(05)80360-2 · DOI · Paper page
- C. K. Weichert Elements of Chordate Anatomy (McGraw-Hill New York 1953).
- P. Joost A. Methner Genome Biol. in press.
- Ulrich H. D., Curr. Top. Microbiol. Immunol. 268, 137 (2002).
- Tomarev S. I., Int. J. Dev. Biol. 41, 835 (1997).
- Krishnan G., Indian J. Exp. Biol. 13, 172 (1975).
- Zuo J., et al., Plant Cell 12, 1137 (2000).
Cited by
Sorted by citations
Items 301–400 of 1,000
Mitogenomics reveals two cryptic species in Ciona intestinalis
Iannelli, F., Pesole, G., Sordino, P., & Gissi, C. (2007) · Trends in Genetics · doi:10.1016/j.tig.2007.07.001 · Cited by 86
The Evolution and Variety of RFamide-Type Neuropeptides: Insights from Deuterostomian Invertebrates
Elphick, M. R., & Mirabeau, O. (2014) · Frontiers in Endocrinology · doi:10.3389/fendo.2014.00093 · Cited by 97
Mutalipassi, M., Riccio, G., Mazzella, V., Galasso, C., Somma, E., Chiarore, A., de Pascale, D., & Zupo, V. (2021) · Marine Drugs · doi:10.3390/md19040227 · Cited by 97
Zhao, L., Gao, F., Gao, S., Liang, Y., Long, H., Lv, Z., Su, Y., Ye, N., Zhang, L., Zhao, C., et al. (2021) · Science China Life Sciences · doi:10.1007/s11427-020-1915-y · Cited by 83
Voltage‐sensing phosphatase: actions and potentials
Okamura, Y., Murata, Y., & Iwasaki, H. (2008) · The Journal of Physiology · doi:10.1113/jphysiol.2008.163097 · Cited by 86
“Two voltage-sensitive probes have been designed by fusing the VSD of Ci-VSP with the fluorescence resonance energy transfer (FRET) pair cyan and yellow fluorescent proteins (CFP–YFP: VSFP) (Dimitrov et al. 2007; Lundby et al. 2008).”
BackgroundMethodThe evolutionary history of vertebrate cranial placodes – I: Cell type evolution
Patthey, C., Schlosser, G., & Shimeld, S. M. (2014) · Developmental Biology · doi:10.1016/j.ydbio.2014.01.017 · Cited by 84
Tachykinin and Tachykinin Receptor of an Ascidian, Ciona intestinalis
Satake, H., Ogasawara, M., Kawada, T., Masuda, K., Aoyama, M., Minakata, H., Chiba, T., Metoki, H., Satou, Y., & Satoh, N. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m408161200 · Cited by 86
Self-citationInsights from human/mouse genome comparisons
Pennacchio, L. A. (2003) · Mammalian Genome · doi:10.1007/s00335-002-4001-1 · Cited by 86
“The recent explosion of genomic sequence availability from higher eukaryotes has sparked new strategies to uncover functional regions of the mammalian genome (Aparicio et al. 2002; Dehal et al. 2002; Lander et al. 2001; Venter et al. 2001; Waterston et al. 2002).”
BackgroundEvolution of the Animal Apoptosis NetworkPreprint
Zmasek, C. M., & Godzik, A. (2013) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a008649 · Cited by 88
“This observation is based on analyzing the genomic contents of three tunicates for apoptotic domains—Ciona intestinalis (Dehal et al. 2002), Ciona savignyi, and Oikopleura dioica.”
BackgroundIntrinsically disordered regions of p53 family are highly diversified in evolution
Xue, B., Brown, C. J., Dunker, A. K., & Uversky, V. N. (2013) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2013.01.012 · Cited by 86
“Importantly, these proteins were found in many taxa beyond vertebrates, such as ascidians (sea squirts) [68], cnidarians [69, 70], platyhelminths and others [67].”
BackgroundTreen, N., Yoshida, K., Sakuma, T., Sasaki, H., Kawai, N., Yamamoto, T., & Sasakura, Y. (2013) · Development · doi:10.1242/dev.099572 · Cited by 85
“The Ciona genome was sequenced in 2002 (Dehal et al., 2002), has been well annotated and a range of web-based tools are available.”
Self-citationImmunity in Protochordates: The Tunicate Perspective
Franchi, N., & Ballarin, L. (2017) · Frontiers in Immunology · doi:10.3389/fimmu.2017.00674 · Cited by 85
“In addition, Ciona also possesses a rich repertoire of transcripts of genes involved in signal transduction, including those for proteins with immunoreceptor tyrosine-based inhibition motifs and ITAMs, MyD88, IL1 receptor-associated kinase, TNF receptor-associated factor, nuclear factor κ B (NF-κ B), and inhibitor of…”
InfluentialEvolutionary Genomics of Fast Evolving Tunicates
Berná, L., & Álvarez-Valín, F. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu122 · Cited by 84
“Key words: positive selection, genome plasticity, Oikopleura dioica, Ciona.”
BackgroundFormation and Evolution of the Chordate Neurotrophin and Trk Receptor Genes
Hallböök, F., Wilson, K., Thorndyke, M. C., & Olinski, R. P. (2006) · Brain Behavior and Evolution · doi:10.1159/000094083 · Cited by 85
Wada, H., Okuyama, M., Satoh, N., & Zhang, S. (2006) · Evolution & Development · doi:10.1111/j.1525-142x.2006.00109.x · Cited by 84
Self-citationSNAREing the Basis of Multicellularity: Consequences of Protein Family Expansion during Evolution
Kloepper, T. H., Kienle, C. N., & Fasshauer, D. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn151 · Cited by 85
“This can even be seen for the SNAREs from the faster evolving urochordates (Dehal et al. 2002), which, together with cephalochordates and vertebrates, make up the chordates.”
BackgroundEvolution of melanocortin receptors in teleost fish: The melanocortin type 1 receptor
Selz, Y., Braasch, I., Hoffmann, C., Schmidt, C., Schultheis, C., Schartl, M., & Volff, J. (2007) · Gene · doi:10.1016/j.gene.2007.07.005 · Cited by 84
Loss of ancestral genes in the genomic evolution of Ciona intestinalis
Hughes, A. L., & Friedman, R. (2005) · Evolution & Development · doi:10.1111/j.1525-142x.2005.05022.x · Cited by 86
Brown, J. H., Bihoreau, M., Hoffmann, S., Diaeresis]nzlin, B. K., Tychinskaya, I., Diaeresis]ller, N. O., Podlich, D., Boehn, S. N., Kaisaki, P. J., Megel, N., et al. (2005) · Journal of the American Society of Nephrology · doi:10.1681/asn.2005060601 · Cited by 83
CRISPR / C as9‐mediated gene knockout in the ascidian C iona intestinalis
Sasaki, H., Yoshida, K., Hozumi, A., & Sasakura, Y. (2014) · Development Growth & Differentiation · doi:10.1111/dgd.12149 · Cited by 81
Self-citationNFAT and NF-κB factors—the distant relatives
Serfling, E., Berberich‐Siebelt, F., Avots, A., Chuvpilo, S. A., Klein‐Hessling, S., Jha, M. K., Kondo, E., Pagel, P., Schulze‐Luehrmann, J., & Palmetshofer, A. (2003) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2003.07.002 · Cited by 82
Cooper, E. C. (2010) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2010.10.001 · Cited by 92
“The genomes of a model cephalochordate (amphioxus, Branchiostoma floridae) and several urochordates (including the tunicate, Ciona intestinalis) have been cloned [71,72], allowing the sequences of their NaV channels to be deduced [73,74].”
BackgroundFedders, H., Michalek, M., Grötzinger, J., & Leippe, M. (2008) · Biochemical Journal · doi:10.1042/bj20080398 · Cited by 82
The Evolution of Thrombospondins and Their Ligand-Binding Activities
Bentley, A. A., & Adams, J. C. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq107 · Cited by 82
“I v1, Ciona intestinalis v2 (Dehal et al. 2002), Daphnia pulex v1 (Bauer 2007), Dictyostelium purpureum QSDP1; Helobdella robusta v1, Lottia gigantea v1,Monosiga brevicollis v1 (King et al.”
BackgroundEvidence for the regulation of left‐right asymmetry in Ciona intestinalis by ion flux
Shimeld, S. M., & Levin, M. G. (2006) · Developmental Dynamics · doi:10.1002/dvdy.20792 · Cited by 80
“We searched Ciona cDNA and genomic resources (Dehal et al., 2002; Satou et al., 2002) for genes with similar sequence to both subunits from both H K ATPase and the Na K ATPases.”
BackgroundMethodInfluentialOrigins, Lineage-Specific Expansions, and Multiple Losses of Tyrosine Kinases in Eukaryotes
Shiu, S., & Li, W. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh077 · Cited by 85
“Most subfamilies shared among chordates are larger in Tagifugu, mouse, and human than in Ciona, which diverged from the three other chordates analyzed ;550 MYA (Dehal et al. 2002).”
BackgroundMolecular Evolution and Structure of α-Actinin
Virel, A., & Backman, L. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh094 · Cited by 82
“Ana Virel & Lars Backman 5 at Pennsylvania State U niversity on February 21, 2013 http://m be.oxfordjournals.org/ D ow nloaded from Molecular evolution of the spectrin family”
BackgroundMethodInfluentialEstablishment of animal–vegetal polarity during maturation in ascidian oocytes
Prodon, F., Chenevert, J. M., & Sardet, C. (2006) · Developmental Biology · doi:10.1016/j.ydbio.2005.11.025 · Cited by 81
“The ability to study maturation in vitro and the powerful tools made increasingly available in Ciona (Dehal et al., 2002; Sasakura et al., 2003; Deschet et al., 2003) make this emerging model particularly attractive for the study of mRNA and cortical domain localization from maturation and fertilization through to the…”
Neurons of the ascidian larval nervous system in Ciona intestinalis: I. Central nervous system
Imai, J. H., & Meinertzhagen, I. A. (2007) · The Journal of Comparative Neurology · doi:10.1002/cne.21246 · Cited by 81
“…previously a rival view held that cephalochordates are closer to the ancestral chordate condition (Holland and Holland, 2001; Lacalli, 2004), a recent analysis of nuclear gene sequences indicates that tunicates lie closest to chordate, and thus vertebrate, ancestral forms (Delsuc et al., 2006).”
BackgroundSelf-citationKrasowski, M. D., Yasuda, K., Hagey, L. R., & Schuetz, E. G. (2005) · Nuclear Receptor · doi:10.1186/1478-1336-3-2 · Cited by 84
The Phylogenetic Distribution and Evolutionary Origins of Endocannabinoid Signalling
Elphick, M. R., & Egertová, M. (2005) · Springer eBooks · doi:10.1007/3-540-26573-2_9 · Cited by 80
Thyroid hormone metabolism and peroxidase function in two non‐chordate animals
Heyland, A., Price, D. A., Bodnárová, M., & Moroz, L. L. (2006) · Journal of Experimental Zoology Part B Molecular and Developmental Evolution · doi:10.1002/jez.b.21113 · Cited by 80
Evolution of gap junctions: the missing link?
Alexopoulos, H., Böttger, A., Fischer, S., Levin, A., Wolf, A., Fujisawa, T., Hayakawa, S., Gojobori, T., Davies, J. A., David, C. N., et al. (2004) · Current Biology · doi:10.1016/j.cub.2004.09.067 · Cited by 80
“Recently, 17 connexin homologs and two presumptive innexin-like homologs were identified in the protochordate Ciona intestinalis [7,8].”
Genomic Approaches Reveal Unexpected Genetic Divergence Within Ciona intestinalis
Suzuki, M. M., Nishikawa, T., & Bird, A. P. (2005) · Journal of Molecular Evolution · doi:10.1007/s00239-005-0009-3 · Cited by 80
Self-citationCiC3-1a-Mediated Chemotaxis in the Deuterostome Invertebrate Ciona intestinalis (Urochordata)
Pinto, M. R., Chinnici, C. M., Kimura, Y., Melillo, D., Marino, R., Spruce, L. A., Santis, R. D., Parrinello, N., & Lambris, J. D. (2003) · The Journal of Immunology · doi:10.4049/jimmunol.171.10.5521 · Cited by 80
“Recent reports of multiple complement components in ascidians (14, 19, 20) had prompted us to investigate the presence of complement-mediated chemotaxis in the ascidian C.”
BackgroundThe Insect Chemoreceptor Superfamily Is Ancient in Animals
Robertson, H. M. (2015) · Chemical Senses · doi:10.1093/chemse/bjv046 · Cited by 80
“2001), Ciona intestinalis (Dehal et al. 2002; Satou et al. 2008), and Botryllus schlosseri (Voskoboynik et al.”
BackgroundAnalysis and Interpretation of the Impact of Missense Variants in Cancer
Petrosino, M., Novak, L., Pasquo, A., Chiaraluce, R., Turina, P., Capriotti, E., & Consalvi, V. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22115416 · Cited by 81
“This percentage is mostly covered by mutations that occur in the active sites of enzymes or in the binding pockets of receptors [110,111].”
BackgroundTello, J. A., Rivier, J., & Sherwood, N. M. (2005) · Endocrinology · doi:10.1210/en.2004-1558 · Cited by 79
The Repertoires of Ubiquitinating and Deubiquitinating Enzymes in Eukaryotic Genomes
Hutchins, A. P., Liu, S., Díez, D., & Miranda‐Saavedra, D. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst022 · Cited by 79
“2004), Ciona intestinalis (Dehal et al. 2002), Cryptococcus neoformans (Loftus et al.”
BackgroundWong, G. W., Zhuo, L., Kimata, K., LAM, B. K., Satoh, N., & Stevens, R. L. (2014) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2014.07.124 · Cited by 79
“intestinalis genome [38].”
Self-citationImmesberger, A., & Burmester, T. (2004) · Journal of Comparative Physiology B · doi:10.1007/s00360-003-0402-4 · Cited by 79
Large-Scale Trends in the Evolution of Gene Structures within 11 Animal Genomes
Yandell, M. D., Mungall, C., Smith, C., Prochnik, S. E., Kaminker, J. S., Hartzell, G., Lewis, S., & Rubin, G. M. (2006) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020015 · Cited by 81
An Atypical CNG Channel Activated by a Single cGMP Molecule Controls Sperm Chemotaxis
Bönigk, W., Loogen, A., Seifert, R., Kashikar, N. D., Klemm, C., Krause, E., Hagen, V., Kremmer, E., Strünker, T., & Kaupp, U. B. (2009) · Science Signaling · doi:10.1126/scisignal.2000516 · Cited by 78
Sequence Similarity Network Reveals Common Ancestry of Multidomain Proteins
Song, N., Joseph, J. M., Davis, G. B., & Durand, D. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000063 · Cited by 82
Takahashi, T., & Holland, P. W. H. (2004) · Development · doi:10.1242/dev.01201 · Cited by 78
“0 (Dehal et al., 2002), accessed at the Joint Genome Institute server (http://genome.”
BackgroundMethodInfluentialLaurén, J., Airaksinen, M. S., Saarma, M., & Timmusk, T. (2003) · Molecular and Cellular Neuroscience · doi:10.1016/s1044-7431(03)00199-4 · Cited by 78
Rho, M., & Tang, H. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp752 · Cited by 77
“The genomic sequences of Drosophila melanogaster (BDGP Release 5, dm3) (21), Ciona intestinalis (ci2) (22) and Strongylocentrotus purpuratus (strPur2) (23) were downloaded from the UCSC Genome Browser web site (http://genome.”
MethodPolymorphic adaptations in metazoans to establish and maintain photosymbioses
Clavijo, J. M., Donath, A., Serôdio, J., & Christa, G. (2018) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/brv.12430 · Cited by 77
“Ciona intestinalis (Dehal et al., 2002), Ciona savignyi (Small et al.”
BackgroundOhdera, A. H., Ames, C. L., Dikow, R. B., Kayal, E., Chiodin, M., Busby, B., La, S., Pirro, S., Collins, A. G., Medina, M., et al. (2019) · GigaScience · doi:10.1093/gigascience/giz069 · Cited by 77
“(Cephalopoda) [107], Mizuhopecten yessoensis (Bivalvia) [108], and Ciona intestinalis (Ascidiacea) [109] that were not available at the time of the original study.”
Self-citationGuidelines for the nomenclature of genetic elements in tunicate genomes
Stolfi, A., Sasakura, Y., Chalopin, D., Satou, Y., Christiaen, L., Dantec, C., Endo, T., Naville, M., Nishida, H., Swalla, B. J., et al. (2014) · genesis · doi:10.1002/dvg.22822 · Cited by 77
“The genomes of two solitary species of the genus Ciona, Ciona intestinalis (Dehal et al., 2002) and Ciona savignyi (Small et al., 2007), were sequenced in the early 2000s, followed by the genome of the appendicularian Oikopleura dioica (Denoeud et al., 2010).”
BackgroundSelf-citationKawada, T., Ogasawara, M., Sekiguchi, T., Aoyama, M., Hotta, K., Oka, K., & Satake, H. (2011) · Endocrinology · doi:10.1210/en.2010-1348 · Cited by 77
Self-citationMolecular hyperdiversity and evolution in very large populations
Cutter, A. D., Jovelin, R., & Dey, A. (2013) · Molecular Ecology · doi:10.1111/mec.12281 · Cited by 76
“126 after correcting for multiple hits and codon bias; Figs 1 and 2), and the related species Ciona intestinalis also appears to have very high diversity (Dehal et al. 2002; Nydam & Harrison 2010; Tsagkogeorga et al. 2012).”
BackgroundInfluentialA genomewide survey of developmentally relevant genes in Ciona intestinalis
Satou, Y., Sasakura, Y., Yamada, L., Imai, K. S., Satoh, N., & Degnan, B. M. (2003) · Development Genes and Evolution · doi:10.1007/s00427-003-0317-9 · Cited by 77
“Here we determine how many molecular components of this and other RTK signaling pathways are encoded in the draft Ciona intestinalis genome (Dehal et al. 2002).”
Self-citationBenito‐Gutiérrez, È., Näke, C., Llovera, M., Comella, J. X., & García‐Fernàndez, J. (2005) · Development · doi:10.1242/dev.01803 · Cited by 77
“Nevertheless, assembly of the central core most probably occurred just predating the cephalochordate/ vertebrate split, as the genome of the lower chordate Ciona intestinalis does not contains a Trk-like gene (Dehal et al., 2002).”
BackgroundGuardians of the actin monomer
Xue, B., & Robinson, R. C. (2013) · European Journal of Cell Biology · doi:10.1016/j.ejcb.2013.10.012 · Cited by 84
Ancestry of neuronal monoamine transporters in the Metazoa
Caveney, S., Cladman, W., Verellen, L., & Donly, C. (2006) · Journal of Experimental Biology · doi:10.1242/jeb.02607 · Cited by 78
Robinson‐Rechavi, M., Boussau, B., & Laudet, V. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh046 · Cited by 80
“It is indeed noticeable that there has been no report of genome duplications ancestral to sarcopterygians (Pennisi 2001; Wolfe 2001; Durand 2003) or to any of the wellstudied groups therein (e.g., tetrapodes, mammals, or sauropsids).”
BackgroundDopazo, H., Santoyo‐López, J., & Dopazo, J. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth902 · Cited by 76
Field identification of ‘types’ A and B of the ascidian Ciona intestinalis in a region of sympatry
Sato, A., Satoh, N., & Bishop, J. (2012) · Marine Biology · doi:10.1007/s00227-012-1898-5 · Cited by 75
“While the adult forms bear little obvious resemblance to vertebrates, the anatomy of their tadpole-like larvae and molecular evidence indicate that they are the sister group of the vertebrates (Dehal et al. 2002; Putnam et al. 2008).”
BackgroundSelf-citationA cis-Regulatory Signature in Ascidians and Flies, Independent of Transcription Factor Binding Sites
Khoueiry, P., Rothbächer, U., Ohtsuka, Y., Daian, F., Frangulian, E., Roure, A., Dubchak, I. L., & Lemaire, P. (2010) · Current Biology · doi:10.1016/j.cub.2010.03.063 · Cited by 75
“chordates with compact genomes [13, 14] that fulfill these two requirements.”
Self-citationProdon, F., Yamada, L., Shirae‐Kurabayashi, M., Nakamura, Y. T., & Sasakura, Y. (2007) · Developmental Dynamics · doi:10.1002/dvdy.21109 · Cited by 75
Self-citationA genomewide survey of developmentally relevant genes in Ciona intestinalis
Yamada, L., Kobayashi, K., Degnan, B. M., Satoh, N., & Satou, Y. (2003) · Development Genes and Evolution · doi:10.1007/s00427-003-0316-x · Cited by 75
“In the present study, members of both the SOX/TCF/MATA group and the HMG/UBF group were surveyed in the completely determined Ciona intestinalis genome (Dehal et al. 2002) and a cDNA/EST database (Satou et al.”
BackgroundSelf-citationClemens, S., & Simm, C. (2003) · New Phytologist · doi:10.1046/j.1469-8137.2003.00811.x · Cited by 74
Chakravarti, R., & Adams, J. C. (2006) · BMC Genomics · doi:10.1186/1471-2164-7-83 · Cited by 75
“intestinalis genome and EST database [54,76] were also accessed.”
Gene expression profile during the life cycle of the urochordate Ciona intestinalis
Azumi, K., Sabău, S. V., Fujie, M., Usami, T., Koyanagi, R., Kawashima, T., Fujiwara, S., Ogasawara, M., Satake, M., Nonaka, M., et al. (2007) · Developmental Biology · doi:10.1016/j.ydbio.2007.05.022 · Cited by 74
“intestinalis has been published (Dehal et al., 2002), and its ~160 Mbp genome is estimated to contain 15,852 protein-coding genes, similar to the number in other invertebrates, but only half of that found in vertebrates.”
BackgroundSelf-citationNeuronal subtype specification in the spinal cord of a protovertebrate
Stolfi, A., & Levine, M. (2011) · Development · doi:10.1242/dev.061507 · Cited by 74
“Their small size, rapid development and deterministic cell lineages have long been appreciated by classical embryologists (Chabry, 1887; Conklin, 1905), while their compact genome and suitability to molecular perturbation and imaging have propelled them into the post-genome era (Dehal et al., 2002).”
Self-citationMicroalgal nanocellulose – opportunities for a circular bioeconomy
Ross, I. L., Shah, S., Hankamer, B. D., & Amiralian, N. (2021) · Trends in Plant Science · doi:10.1016/j.tplants.2021.05.004 · Cited by 78
Olinski, R. P., Lundin, L., & Hallböök, F. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msj002 · Cited by 74
“Ciona represents a branch of chordates that diverged from the main chordate lineage before the postulated genome duplications and should therefore have a nonduplicated genome (Dehal et al. 2002; Yoshizaki et al. 2005).”
BackgroundResultFeschotte, C. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh188 · Cited by 73
“…in the Sea Squirt Ciona intestinalis TBlastN searches that used Merlin_Cb1p against the WGS assembly of the chordate species Ciona intestinalis (Dehal et al. 2002; see Methods) revealed at least three distinct ORFs with similarity to the putative transposase from the nematode (e-values ,…”
BackgroundYagi, K., Takatori, N., Satou, Y., & Satoh, N. (2005) · Developmental Biology · doi:10.1016/j.ydbio.2005.03.029 · Cited by 73
Self-citationPolyploidy in vertebrate ancestry: Ohno and beyond
Furlong, R. F., & Holland, P. W. H. (2004) · Biological Journal of the Linnean Society · doi:10.1111/j.1095-8312.2004.00329.x · Cited by 73
ANISEED 2015: a digital framework for the comparative developmental biology of ascidians
Brozovic, M., Martin, C., Dantec, C., Dauga, D., Mendez, M., Simion, P., Percher, M., Laporte, B., Scornavacca, C., Gregorio, A. D., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv966 · Cited by 72
“intestinalis type A individual (8) and a set of gene models built by integrating transcript models of various sources (48).”
BackgroundSelf-citationDetermining the native region of the putatively invasive ascidian Didemnum vexillum Kott, 2002
Stefaniak, L. M., Zhang, H., Gittenberger, A., Smith, K. F., Holsinger, K. E., Lin, S., & Whitlatch, R. B. (2012) · Journal of Experimental Marine Biology and Ecology · doi:10.1016/j.jembe.2012.04.012 · Cited by 72
Evolutionary History of the Vertebrate Mitogen Activated Protein Kinases Family
Li, M., Liu, J., & Zhang, C. (2011) · PLoS ONE · doi:10.1371/journal.pone.0026999 · Cited by 76
“HMMsearch were also performed on the genome assemblies of Ciona intestinalis [31], Ciona savignyi and Strongylocentrotus purpuratus [51].”
BackgroundMethodSelf-citationEvolution of Sarcomeric Myosin Heavy Chain Genes: Evidence from Fish
McGuigan, K. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh103 · Cited by 72
Biodiversity of voltage sensor domain proteins
Okamura, Y. (2007) · Pflügers Archiv - European Journal of Physiology · doi:10.1007/s00424-007-0222-6 · Cited by 71
“Recent genome sequencing of an ascidian, the basal group of chordates [11], provided us with a list of candidates genes of ion channels and allowed gain insights into evolution of ion channel genes [49].”
BackgroundLimited functions of Hox genes in the larval development of the ascidian Ciona intestinalis
Ikuta, T., Satoh, N., & Saiga, H. (2010) · Development · doi:10.1242/dev.046938 · Cited by 74
“In the ascidian species Ciona intestinalis, nine Hox genes have been identified (Dehal et al., 2002).”
BackgroundSelf-citationThe repertoire of solute carriers of family 6: Identification of new human and rodent genes
Höglund, P. J., Adzic, D., Scicluna, S. J., Lindblom, J., & Fredriksson, R. (2005) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2005.08.048 · Cited by 70
Genomic overview of mRNA 5'-leader trans-splicing in the ascidian Ciona intestinalis
Satou, Y. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl418 · Cited by 71
“Because 15 852 genes are predicted in the Ciona draft genome sequence (7), the number of genes covered by the full-length ESTs corresponds to 4.”
BackgroundInfluentialSelf-citationHosono, K., Noda, S., Shimizu, A., Nakanishi, N., Ohtsubo, M., Shimizu, N., & Minoshima, S. (2010) · Genomics · doi:10.1016/j.ygeno.2010.05.003 · Cited by 70
Fascin Protrusions in Cell Interactions
Adams, J. C. (2004) · Trends in Cardiovascular Medicine · doi:10.1016/j.tcm.2004.06.002 · Cited by 71
Moret, F., Christiaen, L., Deyts, C., Blin, M., Joly, J., & Vernier, P. (2005) · European Journal of Neuroscience · doi:10.1111/j.1460-9568.2005.04147.x · Cited by 71
“neurons in Ciona larva through a likely conserved enzymatic pathway Our survey of the Ciona genome (Dehal et al., 2002) revealed that urochordates may be endowed with homologous molecular components recruited in vertebrate ancestors to build diverse catecholaminesynthesizing systems, namely the TH,…”
BackgroundGenetic and Genomic Toolbox of the Chordate Ciona intestinalis
Stolfi, A., & Christiaen, L. (2012) · Genetics · doi:10.1534/genetics.112.140590 · Cited by 71
Evolutionary crossroads in developmental biology
Patel, N. H. (2012) · Development · doi:10.1242/dev.085464 · Cited by 77
A glycine receptor is involved in the organization of swimming movements in an invertebrate chordate
Nishino, A., Okamura, Y., Piscopo, S., & Brown, E. R. (2010) · BMC Neuroscience · doi:10.1186/1471-2202-11-6 · Cited by 70
“With the recent sequencing of the genome of Ciona intestinalis [3], there has been an increase in interest in ascidians as useful models to study the evolution of chordates.”
BackgrounddipSPAdes: Assembler for Highly Polymorphic Diploid Genomes
Safonova, Y., Bankevich, A., & Pevzner, P. A. (2015) · Journal of Computational Biology · doi:10.1089/cmb.2014.0153 · Cited by 70
“A similar approach was applied to genome assembly of the sea squirt S. intestinalis (Dehal et al., 2002).”
Embryological Methods in Ascidians: The Villefranche-sur-Mer Protocols
Sardet, C., McDougall, A., Yasuo, H., Chenevert, J. M., Prulière, G., Dumollard, R., Hudson, C., Hebras, C., Nguyen, N. L., & Paix, A. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-210-6_14 · Cited by 70
Comparative genomic tools and databases: providing insights into the human genome
Pennacchio, L. A., & Rubin, E. M. (2003) · Journal of Clinical Investigation · doi:10.1172/jci17842 · Cited by 70
Johnson, D. S., Davidson, B., Brown, C. D., Smith, W. C., & Sidow, A. (2004) · Genome Research · doi:10.1101/gr.2964504 · Cited by 70
“Third, ascidians have attractive embryological and experimental features that facilitate studies of gene regulation during development, including production of large quantities of embryos, development from egg to larva in 18 h, an invariant cell lineage (Nishida 1987), and the ability of embryos to express genes from…”
BackgroundMethodInfluentialSelf-citationCommon and divergent pathways in alternative developmental processes of ascidians
Manni, L., & Burighel, P. (2006) · BioEssays · doi:10.1002/bies.20462 · Cited by 69
“In this respect, we can refer to two emerging model systems investigated from various points of view, the simple larva of Ciona intestinalis, the solitary species whose genome was recently sequenced,((8)) and the more complex larva of Botryllus schlosseri,((3)) a species whose genome is not yet sequenced although mole…”
ResultDietz, M. L., Bernaciak, T. M., Vendetti, F. P., Kielec, J. M., & Hildebrand, J. D. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m512463200 · Cited by 69
Separating the Nature and Nurture of the Allocation of Energy in Response to Global Change
Applebaum, S. L., Pan, T.-C., Hedgecock, D., & Manahan, D. T. (2014) · Integrative and Comparative Biology · doi:10.1093/icb/icu062 · Cited by 69
“For example, genomes are available for two species of the sea squirt Ciona (Dehal et al. 2002; Vinson et al. 2005), the Fig.”
BackgroundBioinformatics for personal genome interpretation
Capriotti, E., Nehrt, N. L., Kann, M. G., & Bromberg, Y. (2012) · Briefings in Bioinformatics · doi:10.1093/bib/bbr070 · Cited by 68
Transcriptional regulation of the peripheral nervous system in Ciona intestinalis
Tang, W. J., Chen, J. S., & Zeller, R. W. (2013) · Developmental Biology · doi:10.1016/j.ydbio.2013.03.016 · Cited by 67
Yue, J., Yu, J., Putnam, N. H., & Holland, L. Z. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu212 · Cited by 69
Self-citationInosine released after hypoxia activates hepatic glucose liberation through A3adenosine receptors
Guinzberg, R., Cortés, D., Díaz‐Cruz, A., Riveros‐Rosas, H., Villalobos‐Molina, R., & Piña, E. (2005) · American Journal of Physiology-Endocrinology and Metabolism · doi:10.1152/ajpendo.00173.2005 · Cited by 68
Genomic cis-regulatory networks in the early Ciona intestinalis embryo
Kubo, A., Suzuki, N., Yuan, X., Nakai, K., Satoh, N., Imai, K. S., & Satou, Y. (2010) · Development · doi:10.1242/dev.046789 · Cited by 68
“Each of these two sets of arrays covers the entire euchromatic region of the Ciona genome (Dehal et al., 2002) (GEO accession numbers for the array design: GPL6555/GPL6556 for the version 1 array; GPL8993 for the version 2 array).”
BackgroundSelf-citationAn Introduction to the Diversity, Ecology, and Conservation of Saproxylic Insects
Ulyshen, M. D., & Šobotník, J. (2018) · Zoological monographs · doi:10.1007/978-3-319-75937-1_1 · Cited by 78
Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyiPreprint
Kim, J. H., Waterman, M. S., & Li, L. M. (2007) · Genome Research · doi:10.1101/gr.5894107 · Cited by 68
“…and assembly strategy, also influence assembly continuity (Vinson et al. 2005), the problem is highlighted when we compare the N50 scaffold length of the human genome with the N50 scaffold length of the Ciona intestinalis genome (2.7 Mb vs. 190 kb) (Dehal et al. 2002; Istrail et al. 2004).”
BackgroundMethodResultInfluentialMolecular signatures for sex in the Placozoa
Signorovitch, A. Y., Dellaporta, S. L., & Buss, L. W. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504031102 · Cited by 66
Metadata
- Authors
- Dehal, P., Satou, Y., Campbell, R. K., Chapman, J., Degnan, B., De Tomaso, A., Davidson, B., Di Gregorio, A., Gelpke, M., Goodstein, D. M., Harafuji, N., Hastings, K. E. M., Ho, I., Hotta, K., Huang, W., Kawashima, T., Lemaire, P., Martinez, D., Meinertzhagen, I. A., Necula, S., Nonaka, M., Putnam, N., Rash, S., Saiga, H., Satake, M., Terry, A., Yamada, L., Wang, H.-G., Awazu, S., Azumi, K., Boore, J., Branno, M., Chin-bow, S., DeSantis, R., Doyle, S., Francino, P., Keys, D. N., Haga, S., Hayashi, H., Hino, K., Imai, K. S., Inaba, K., Kano, S., Kobayashi, K., Kobayashi, M., Lee, B.-I., Makabe, K. W., Manohar, C., Matassi, G., Medina, M., Mochizuki, Y., Mount, S., Morishita, T., Miura, S., Nakayama, A., Nishizaka, S., Nomoto, H., Ohta, F., Oishi, K., Rigoutsos, I., Sano, M., Sasaki, A., Sasakura, Y., Shoguchi, E., Shin-i, T., Spagnuolo, A., Stainier, D., Suzuki, M. M., Tassy, O., Takatori, N., Tokuoka, M., Yagi, K., Yoshizaki, F., Wada, S., Zhang, C., Hyatt, P. D., Larimer, F., Detter, C., Doggett, N., Glavina, T., Hawkins, T., Richardson, P., Lucas, S., Kohara, Y., Levine, M., Satoh, N., & Rokhsar, D. S.
- Affiliations
- Joint Genome Institute (US)
- Kyoto University (JP)
- Marine Biological Laboratory (US)
- The University of Queensland (AU)
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 93950, USA.
- University of California, Berkeley (US)
- Department of Molecular and Cellular Biology, Division of Genetics, 401 Barker Hall, University of California, Berkeley, CA 94720, USA.
- McGill University (CA)
- National Institute of Genetics (JP)
- Institut de Biologie du Développement Marseille (FR)
- Dalhousie University (CA)
- The University of Tokyo (JP)
- U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.
- Tokyo Metropolitan University (JP)
- Tohoku University (JP)
- Moffitt Cancer Center (US)
- Hokkaido University (JP)
- Stazione Zoologica Anton Dohrn (IT)
- IBM (United States) (US)
- University of Maryland, College Park, MD 20742, USA.
- National Institute of Genetics, Mishima 411-8540, Japan.
- Stazione Zoologica “Anton Dohrn,” Villa Comunale, 80121 Napoli, Italy.
- University of California, San Francisco (US)
- Wellcome Centre for Cell Biology (GB)
- Oak Ridge National Laboratory, Post Office Box 2008, Oak Ridge, TN 37831, USA.
- Oak Ridge National Laboratory (US)
- Los Alamos National Laboratory (US)
- Corresponding author
- Dehal, Paramvir
- Satou, Yutaka
- Kohara, Yuji
- Levine, Michael
- Satoh, Nori
- Rokhsar, Daniel S.
- ORCID
- Dehal, Paramvir
- Satou, Yutaka
- Degnan, Bernard
- Davidson, Brad
- Goodstein, David M.
- Harafuji, Naoe
- Hotta, Kohji
- Kawashima, Takeshi
- Lemaire, Patrick
- Martinez, Diego
- Meinertzhagen, Ian A.
- Saiga, Hidetoshi
- Terry, Astrid
- Wang, Hong-Gang
- Boore, Jeffrey
- Hino, Kyosuke
- Imai, Kaoru S.
- Inaba, Kazuo
- Kobayashi, Kenji
- Lee, Byung-In
- Manohar, Chitra
- Matassi, Giorgio
- Rigoutsos, Isidore
- Sasakura, Yasunori
- Shoguchi, Eiichi
- Stainier, Didier
- Suzuki, Miho M.
- Tassy, Olivier
- Tokuoka, Miki
- Doggett, Norman
- Kohara, Yuji
- Levine, Michael
- Rokhsar, Daniel S.
- Venue
- Science
- Published
- 2002-12-13
- Volume
- 298
- Issue
- 5601
- Pages
- 2157-2167
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2170258388
- Cited by
- 1,641
- References
- 81
- Citations by year
- 2026: 20 · 2025: 15 · 2024: 41 · 2023: 26 · 2022: 27 · 2021: 36 · 2020: 41 · 2019: 29 · 2018: 51 · 2017: 49 · 2016: 43 · 2015: 46 · 2014: 62 · 2013: 62 · 2012: 74
- FWCI
- 49.61
- Type
- journal article
- Language
- en
- Open access
- green
- hal.science
- Licence
- cc-by-nc
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- HAL AMU (submittedVersion, cc-by-nc)
- Tokyo Tech Research Repository (Tokyo Institute of Technology) (submittedVersion)
- Funders
- National Institutes of Health (5p01hd037105-20)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (HD37105)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Marine Invertebrate Physiology and Ecology
- Keywords
- Ciona intestinalis, chordate evolution, vertebrate origin, gene family evolution, protein-coding genes, gene loss, developmental genes, Cambrian explosion
- MeSH terms
- Alleles, Animals, Base Sequence, Cellulose, Central Nervous System, Ciona intestinalis, Endocrine System, Genes, Genes, Homeobox, Multigene Family, Heart, Immunity, Molecular Sequence Data, Muscle Proteins, Phylogeny, Polymorphism, Genetic, Proteins, Sequence Homology, Nucleic Acid, Species Specificity, Thyroid Gland, Urochordata, Vertebrates, Genome, Apoptosis, Sequence Analysis, DNA, Gene Dosage, Computational Biology, Gene Duplication, Organizers, Embryonic
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
