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
Flagged first, then by citations
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 801–900 of 1,000
Hozumi, A., Horie, T., & Sasakura, Y. (2015) · Developmental Dynamics · doi:10.1002/dvdy.24317 · Cited by 25
Self-citationAase-Remedios, M. E., Coll-Lladó, C., & Ferrier, D. E. K. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa147 · Cited by 27
“2011), and Ciona T-box genes (Dehal et al. 2002), among many others (Minguill on et al.”
BackgroundGilchrist, M. J., Sobral, D., Khoueiry, P., Daian, F., Laporte, B., Patrushev, I., Matsumoto, J., Dewar, K., Hastings, K. E. M., Satou, Y., et al. (2015) · Developmental Biology · doi:10.1016/j.ydbio.2015.05.014 · Cited by 25
Self-citationThe S. purpuratus genome: A comparative perspective
Materna, S. C., Berney, K., & Cameron, R. A. (2006) · Developmental Biology · doi:10.1016/j.ydbio.2006.09.033 · Cited by 25
Anbazhagan, P., Purushottam, M., Kumar, H. B. K., Mukherjee, O., Jain, S., & Sowdhamini, R. (2010) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2010.10508573 · Cited by 25
The tunicateCiona: a model system for understanding the relationship between regeneration and aging
Jeffery, W. R. (2014) · Invertebrate Reproduction & Development · doi:10.1080/07924259.2014.925515 · Cited by 25
“Second, the Ciona genome has been sequenced and annotated (Dehal et al. 2002), potentially permitting numerous genes to be assayed for their involvement in regeneration.”
MethodAbe, Y., Okumura, E., Hosoya, T., Hirota, T., & Kishimoto, T. (2010) · Journal of Cell Science · doi:10.1242/jcs.076315 · Cited by 25
“Ciona intestinalis (ascidian in urochordates) (Dehal et al., 2002) and Branchiostoma floridae (amphioxus in cephalochordates) (Putnam et al.”
BackgroundSatou, Y., & Satoh, N. (2005) · Development Genes and Evolution · doi:10.1007/s00427-005-0016-9 · Cited by 25
“At the top is a depiction of a gene model predicted in the previous study (Dehal et al. 2002) in terms of intron (dashed lines) and exon (black boxes) structures.”
BackgroundInfluentialSelf-citationMizuta, T., Asahina, K., Suzuki, M., & Kubokawa, K. (2008) · Journal of Experimental Zoology Part A Ecological Genetics and Physiology · doi:10.1002/jez.438 · Cited by 25
Self-citationCallahan, A., Deibel, D., McKenzie, C. H., Hall, J. R., & Rise, M. L. (2010) · Aquatic Invasions · doi:10.3391/ai.2010.5.1.5 · Cited by 25
“savignyi from California (Dehal et al. 2002; Vinson et al. 2005). Silva and Smith (2008) reported recently that ten different ascidian species show substantially different levels of genetic polymorphism and exceptions to the assumption that invasive species start with a low level of genetic polymorphism that increases…”
BackgroundInfluentialAzumi, K., Fujie, M., Usami, T., Miki, Y., & Satoh, N. (2004) · Marine Environmental Research · doi:10.1016/j.marenvres.2004.03.042 · Cited by 25
Self-citationBiogenesis and Function of Cellulose in the Tunicates
Kimura, S., & Itoh, T. (2007) · Springer eBooks · doi:10.1007/978-1-4020-5380-1_13 · Cited by 25
Schistosome transcriptome analysis at the cutting edge
McManus, D. P., Hu, W., Brindley, P. J., Feng, Z., & Han, Z. (2004) · Trends in Parasitology · doi:10.1016/j.pt.2004.04.011 · Cited by 25
Turning the clock back on ancient genome duplication
Seoighe, C. (2003) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2003.10.005 · Cited by 25
“If so, the power to finally resolve the 2R debate may lie within the gene orders of invertebrates such as amphioxus and the sea squirt, Ciona intestinalis [18], the genome of which has recently been published in draft form [24].”
BackgroundGenomic, phylogenetic, and cell biological insights into metazoan origins
Nichols, S. A., Dayel, M. J., & King, N. (2009) · Animal Evolution · doi:10.1093/acprof:oso/9780199549429.003.0003 · Cited by 24
Veeman, M. T., & Reeves, W. (2014) · genesis · doi:10.1002/dvg.22828 · Cited by 24
Generation and Use of Transgenic Ascidian Embryos
Zeller, R. W. (2004) · Methods in cell biology · doi:10.1016/s0091-679x(04)74029-7 · Cited by 24
Nishitsuji, K., Horie, T., Ichinose, A., Sasakura, Y., Yasuo, H., & Kusakabe, T. G. (2012) · Development Growth & Differentiation · doi:10.1111/j.1440-169x.2011.01319.x · Cited by 21
“The genomic sequences of C. intestinalis and C. savignyi were obtained from JGI (Dehal et al. 2002; http:// genome.jgi-psf.org/Cioin2/Cioin2.home.html) and from the Broad Institute (http://www.broadinstitute.org/ annotation/ciona/), respectively.”
MethodSelf-citationUsing Ciona to study developmental programmed cell death
Baghdiguian, S., Martinand‐Mari, C., & Mangeat, P. H. (2006) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2006.11.005 · Cited by 24
Transcriptome dynamics in early embryos of the ascidian, Ciona intestinalis
Matsuoka, T., Ikeda, T., Fujimaki, K., & Satou, Y. (2013) · Developmental Biology · doi:10.1016/j.ydbio.2013.10.003 · Cited by 24
Self-citationIn silico identification of the sea squirt selenoproteome
Jiang, L., Liu, Q., & Ni, J. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-289 · Cited by 24
“Abundant sequence data from the sea squirt genome project enable us to investigate selenoprotein distribution in these species, which provides valuable insights into selenium utilization and selenoprotein gene evolution [16,17].”
BackgroundCiona intestinalis and Oxycomanthus japonicus, Representatives of Marine Invertebrates
Sasakura, Y., Inaba, K., Satoh, N., Kondo, M., & Akasaka, K. (2009) · EXPERIMENTAL ANIMALS · doi:10.1538/expanim.58.459 · Cited by 24
“It is supported by the availability of the draft genome sequence that was reported in 2002 [11].”
BackgroundSelf-citationRigon, F., Gasparini, F., Shimeld, S. M., Candiani, S., & Manni, L. (2017) · The Journal of Comparative Neurology · doi:10.1002/cne.24382 · Cited by 23
“…registration, RRID: AB_2314195; Antibody link: http://antibodyregistry.org/ AB_2314195) was prepared and characterized by (Horie et al., 2008), starting from the sequence encoding the vesicular glutamate transporter (Vglut) gene, found in the Ciona genome database (Dehal et al., 2002) (Table 2).”
MethodPark, W., Kim, G. J., Choi, H., Vanacker, J.-M., & Sohn, Y. C. (2008) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2008.08.011 · Cited by 24
Minostransposon causes germline transgenesis of the ascidianCiona savignyi
Matsuoka, T., Awazu, S., Satoh, N., & Sasakura, Y. (2004) · Development Growth & Differentiation · doi:10.1111/j.1440-169x.2004.00742.x · Cited by 24
“The easy generation of enhancer trap lines in Ciona may have been due to the compactness of the Ciona genome comparable to that of Drosophila (Dehal et al. 2002), and Ciona will thus be a suitable chordate for enhancer trapping.”
MethodSelf-citationHopitzan, A. A., Baines, A. J., & Kordeli, E. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msj004 · Cited by 24
Self/nonself discrimination at the basis of chordate evolution: limits on molecular conservation
Khalturin, K., & Bosch, T. C. G. (2006) · Current Opinion in Immunology · doi:10.1016/j.coi.2006.11.001 · Cited by 24
“Comprehensive expressed sequence tag (EST) datasets and genome projects in several taxonomic groups [7–10] indicate that MHC and TCR are not present outside jawed vertebrates.”
BackgroundComputational prediction and experimental validation of Ciona intestinalis microRNA genes
Norden‐Krichmar, T. M., Holtz, J., Pasquinelli, A. E., & Gaasterland, T. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-445 · Cited by 24
“First, as a member of the subphylum Urochordata (also known as Tunicata) whose larval form has a notochord, the sea squirt is situated phylogenetically at the emergence of the vertebrates [13], and therefore can provide information about the evolution of molecular regulators of early development.”
BackgroundDecodingcis-Regulatory Systems in Ascidians
Kusakabe, T. G. (2005) · ZOOLOGICAL SCIENCE · doi:10.2108/zsj.22.129 · Cited by 24
“The genome of C. intestinalis shows a high rate of allelic polymorphism, with an average 1.2% of the nucleotides differing between chromosome pairs of a single individual (Dehal et al., 2002).”
InfluentialUppal, R., Lakshmi, K. V., & Valentine, A. M. (2008) · JBIC Journal of Biological Inorganic Chemistry · doi:10.1007/s00775-008-0375-6 · Cited by 24
Construction and characterization of EST libraries from the porcelain crab, Petrolisthes cinctipes
Stillman, J. H., Teranishi, K. S., Tagmount, A., Lindquist, E., & Brokstein, P. B. (2006) · Integrative and Comparative Biology · doi:10.1093/icb/icl007 · Cited by 24
Lee, Y., Rhee, J., Hwang, D., Kim, I., Raisuddin, S., & Lee, J. (2007) · Molecules and Cells · doi:10.1016/s1016-8478(23)10719-9 · Cited by 24
Wei, J., Wang, G., Li, X., Ren, P., Yu, H., & Dong, B. (2017) · Biology Open · doi:10.1242/bio.026336 · Cited by 23
“The genome of Ciona intestinalis and Ciona savignyi have both been sequenced (Dehal et al., 2002; Small et al., 2007).”
BackgroundMolecular and evolutionary aspects of the protochordate digestive system
Nakayama, S., Sekiguchi, T., & Ogasawara, M. (2019) · Cell and Tissue Research · doi:10.1007/s00441-019-03035-5 · Cited by 23
DeBiasse, M. B., Colgan, W. N., Harris, L., Davidson, B., & Ryan, J. F. (2020) · Genome Biology and Evolution · doi:10.1093/gbe/evaa060 · Cited by 21
“Because they are the closest living relative of vertebrates, comparative studies of tunicate genomes can provide unique insights into vertebrate origins and subsequent genomic changes underlying vertebrate diversification (Delsuc et al. 2006).”
BackgroundSelf-citationChromosomal Inversion Polymorphisms in Two Sympatric Ascidian Lineages
Satou, Y., Sato, A., Yasuo, H., Mihirogi, Y., Bishop, J., Fujie, M., Kawamitsu, M., Hisata, K., & Satoh, N. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab068 · Cited by 21
Self-citationGenome-wide network of regulatory genes for construction of a chordate embryo
Shoguchi, E., Hamaguchi, M., & Satoh, N. (2008) · Developmental Biology · doi:10.1016/j.ydbio.2008.01.009 · Cited by 23
“The complete genome sequence assembly of approximately 160 Mb for C. intestinalis suggests that the ascidian contains the basic ancestral complement of genes involved in development and cell signaling of chordates including vertebrates (Dehal et al., 2002).”
BackgroundInfluentialSelf-citationPrimary Genetic Linkage Maps of the Ascidian, Ciona intestinalis
Kano, S., Satoh, N., & Sordino, P. (2006) · ZOOLOGICAL SCIENCE · doi:10.2108/zsj.23.31 · Cited by 23
“0 by the Joint Genome Institute (JGI; http://genome.jgi-psf.org/ciona4/; Dehal et al., 2002).”
BackgroundMethodInfluentialSelf-citationIrvine, S. Q., Cangiano, M. C., Millette, B. J., & Gutter, E. S. (2007) · Journal of Experimental Zoology Part B Molecular and Developmental Evolution · doi:10.1002/jez.b.21169 · Cited by 23
Nava, G. M., Lee, D. Y., Ospina, J. H., Cai, S., & Gaskins, H. R. (2009) · Physiological Genomics · doi:10.1152/physiolgenomics.00025.2009 · Cited by 23
Regulatory genes in the ancestral chordate genomes
Satou, Y., Wada, S., Sasakura, Y., & Satoh, N. (2008) · Development Genes and Evolution · doi:10.1007/s00427-008-0219-y · Cited by 23
“Vertebrate genomes contain additional regulatory genes not found in the tunicate genome, such as Tbx4/5, Gbx, and wnt11 (Dehal et al. 2002).”
BackgroundSelf-citationAntero-posterior ectoderm patterning by canonical Wnt signaling during ascidian development
Feinberg, S. L., Roure, A., Piron, J., & Darras, S. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008054 · Cited by 20
Regulation of Neurogenesis by FGF Signaling and Neurogenin in the Invertebrate Chordate Ciona
Kim, K., Gibboney, S., Razy‐Krajka, F., Lowe, E. K., Wang, W., & Stolfi, A. (2020) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2020.00477 · Cited by 23
Szydlowski, L., Boschetti, C., Crisp, A., Barbosa, E. G. G., & Tunnacliffe, A. (2015) · Gene · doi:10.1016/j.gene.2015.04.007 · Cited by 24
“As well as being a major component of plant and algal cell walls, cellulose is also synthesized by some bacteria, fungi (Delmer, 1999) and even urochordates (Matthysse et al., 2004).”
BackgroundOrganizing chordates with an organizer
García‐Fernàndez, J., D’Aniello, S., & Escrivá, H. (2007) · BioEssays · doi:10.1002/bies.20596 · Cited by 23
Bullmann, T., Härtig, W., Holzer, M., & Arendt, T. (2010) · The Journal of Comparative Neurology · doi:10.1002/cne.22351 · Cited by 23
“The tau gene of the sea squirt Ciona intestinalis contains three microtubule-binding repeats (transcript Ci0100130712; Ciona intestinalis genome project: Dehal et al., 2002).”
BackgroundMochizuki, Y., Satou, Y., & Satoh, N. (2003) · genesis · doi:10.1002/gene.10199 · Cited by 23
“The whole genome draft sequence of C. intestinalis, which has a compact genome compared to those of vertebrates, has just been completed (Dehal et al., 2002).”
InfluentialSelf-citationPonczek, M. B., Bijak, M., & Nowak, P. (2012) · Journal of Molecular Evolution · doi:10.1007/s00239-012-9509-0 · Cited by 23
“2008) and sea squirt Ciona Intestinalis (Dehal et al. 2002), hemichordates like acorn worm Saccoglossus kowalevskii and echinoderms such as sea urchin Strongylocentrotus purpuratus (Sodergren et al.”
InfluentialJones, T. A., Otto, W., Marz, M., Eddy, S. R., & Stadler, P. F. (2009) · RNA Biology · doi:10.4161/rna.6.1.7634 · Cited by 23
“0, Oct 2002) [19] and Oikopleura dioica (Genoscope, v3.”
BackgroundThe calculation of information and organismal complexity
Jiang, Y., & Xu, C. (2010) · Biology Direct · doi:10.1186/1745-6150-5-59 · Cited by 22
“2e8[45] 69%”
Live imaging and morphometric analysis of embryonic development in the ascidianCiona intestinalis
Rhee, J. M., Oda‐Ishii, I., Passamaneck, Y. J., Hadjantonakis, A., & Gregorio, A. D. (2005) · genesis · doi:10.1002/gene.20164 · Cited by 23
Evolution of Integrin I Domains
Johnson, M. S., & Chouhan, B. S. (2014) · Advances in experimental medicine and biology · doi:10.1007/978-94-017-9153-3_1 · Cited by 22
Zega, G., Pennati, R., Candiani, S., Pestarino, M., & de Bernardi, F. L. (2009) · Invertebrate survival journal · Cited by 23
Meiniel, A., Meiniel, R., Gonçalves-Mendes, N., Creveaux, I., Didier, R., & Dastugue, B. (2003) · International review of cytology · doi:10.1016/s0074-7696(03)30001-4 · Cited by 23
The varied ways of being male and female
Schärer, L. (2016) · Molecular Reproduction and Development · doi:10.1002/mrd.22775 · Cited by 22
Comparative Neurobiology of Biogenic Amines in Animal Models in Deuterostomes
D’Aniello, E., Paganos, P., Anishchenko, E., D’Aniello, S., & Arnone, M. I. (2020) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2020.587036 · Cited by 22
Conservation of peripheral nervous system formation mechanisms in divergent ascidian embryos
Coulcher, J. F., Roure, A., Chowdhury, R., Robert, M., Lescat, L., Bouin, A., Cadavid, J. C., Nishida, H., & Darras, S. (2020) · eLife · doi:10.7554/elife.59157 · Cited by 22
Longo, V., Parrinello, D., Longo, A., Parisi, M. G., Parrinello, N., Colombo, P., & Cammarata, M. (2021) · Fish & Shellfish Immunology · doi:10.1016/j.fsi.2021.10.022 · Cited by 22
Metabolites and metals in Metazoa – what role do phytochelatins play in animals?
Bundy, J. G., & Kille, P. (2014) · Metallomics · doi:10.1039/c4mt00078a · Cited by 22
Proteomic profiling reveals compartment‐specific, novel functions of ascidian sperm proteins
Nakachi, M., Nakajima, A., Nomura, M., Yonezawa, K., Ueno, K., Endo, T., & Inaba, K. (2011) · Molecular Reproduction and Development · doi:10.1002/mrd.21341 · Cited by 22
Self-citationEvolution of Invertebrate Deuterostomes and Hox/ParaHox Genes
Ikuta, T. (2011) · Genomics Proteomics & Bioinformatics · doi:10.1016/s1672-0229(11)60011-9 · Cited by 22
Shenkar, N., Koplovitz, G., Dray, L., Gissi, C., & Huchon, D. (2016) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2016.04.001 · Cited by 22
Behavioral Neurobiology of the Endocannabinoid System
Kendall, D., & Alexander, S. (2009) · Current topics in behavioral neurosciences · doi:10.1007/978-3-540-88955-7 · Cited by 28
Mitochondrial alternative oxidase contributes to successful tardigrade anhydrobiosis
Wojciechowska, D., Karachitos, A., Roszkowska, M., Rzeźniczak, W., Sobkowiak, R., Kaczmarek, Ł., Kosicki, J. Z., & Kmita, H. (2021) · Frontiers in Zoology · doi:10.1186/s12983-021-00400-5 · Cited by 21
“The aligned sequences were as follows: Ciona intestinalis (Linnaeus, 1767), (TIGR genome (Dehal et al., 2002)), Nematostella vectensis Stephenson, 1935 (NCBI; XM 001635879), Lingula anatine Lamarck, 1801 (NCBI; XP_013379624.”
BackgroundBatta‐Lona, P. G., Maas, A. E., O’Neill, R. J., Wiebe, P. H., & Bucklin, A. (2016) · Polar Biology · doi:10.1007/s00300-016-2051-6 · Cited by 22
Phylogeny of NPY-Family Peptides and Their Receptors
Larhammar, D., Fredriksson, R., Larson, E. T., & Salaneck, E. (2004) · Handbook of experimental pharmacology · doi:10.1007/978-3-642-18764-3_4 · Cited by 22
Hotta, K., Takahashi, H., Ueno, N., & Gojobori, T. (2003) · Gene · doi:10.1016/s0378-1119(03)00700-5 · Cited by 22
Self-citationComparative genome analyses of nervous system-specific genes
Noda, A. O., Ikeo, K., & Gojobori, T. (2005) · Gene · doi:10.1016/j.gene.2005.09.001 · Cited by 22
Inferring gene regulatory networks by thermodynamic modeling
Chen, C.-C., & Zhong, S. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-s2-s19 · Cited by 22
“First, they are capable of self-renewal through apparently unlimited, undifferentiated proliferation in cultured cell lines [18-20]; second, they have remarkable pluripotency potentials [21] to give rise to many different cell types in the body, which may contribute to the study of body development and regenerative me…”
BackgroundLiu, L., Xiang, J., Dong, B., Natarajan, P., Yu, K., & Cai, N.-E. (2006) · Journal of Zhejiang University SCIENCE B · doi:10.1631/jzus.2006.b0467 · Cited by 21
“…Voluminous data including hundreds of thousands of ESTs and the whole genome sequences were published, which are free for use in academic research (Dehal et al., 2002; Satoh et al., 2003); (2) The body of C. intestinalis is transparent regardless of its size and the embryos develop quickly; the…”
BackgroundInfluentialKrasovec, G., Robine, K., Quéinnec, É., Karaı̈skou, A., & Chambon, J. (2019) · Developmental Biology · doi:10.1016/j.ydbio.2018.12.010 · Cited by 21
Amphioxus as a model to study the evolution of development in chordates
D’Aniello, S., Bertrand, S., & Escrivá, H. (2023) · eLife · doi:10.7554/elife.87028 · Cited by 21
Yan, Y., Dai, T., Guo, M., Zhao, X., Chen, C., Zhou, Y., Qin, M., Xu, L., & Zhao, J. (2024) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2024.132686 · Cited by 21
Verslycke, T. A., Goldstone, J. V., & Stegeman, J. J. (2006) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2006.04.017 · Cited by 21
Kusakabe, R., Tani-Matsuhana, S., Nishitsuji, K., Shindo, M., Okamura, K., Miyamoto, Y., Nakai, K., Suzuki, Y., Kusakabe, T. G., & Inoue, K. (2012) · Gene Expression Patterns · doi:10.1016/j.gep.2012.11.001 · Cited by 21
Irimia, M., Maeso, I., Burguera, D., Hidalgo‐Sánchez, M., Puelles, L., Roy, S. W., García‐Fernàndez, J., & Ferrán, J. L. (2011) · Genome Biology and Evolution · doi:10.1093/gbe/evr056 · Cited by 22
The Lancelet and Ammocoete Mouths
Yasui, K., & Kaji, T. (2008) · ZOOLOGICAL SCIENCE · doi:10.2108/zsj.25.1012 · Cited by 21
“As to why ascidian phylogeny changes radically among analyses, we may consider the genomic compaction and rapid modification of the mitochondrial and nuclear genomes in urochordates (Seo et al., 2001; Dehal et al., 2002; Winchell et al., 2002).”
An introgression breakthrough left by an anthropogenic contact between two ascidians
Moan, A. L., Roby, C., Fraïssé, C., Daguin‐Thiébaut, C., Bierne, N., & Viard, F. (2021) · Molecular Ecology · doi:10.1111/mec.16189 · Cited by 23
Gibbons, T., Mount, S. M., Cooper, E. D., & Delwiche, C. F. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0625-x · Cited by 21
“The addition of sequences from four other eukaryotes (Anopheles gambiae [23], Ciona intestinalis [24], Chlamydomonas reinhardtii [25], and Toxoplasma gondii [26]), for which the CEGMA developers have provided annotations, led to a test data set we refer to as the Expanded CEGMA KOGs (ECK) database.”
MethodSelf-citationRichter, I., & Fidler, A. E. (2014) · Toxicon · doi:10.1016/j.toxicon.2014.12.011 · Cited by 21
Tissue-Specific Profile of DNA Replication in the Swimming Larvae of Ciona intestinalis
Nakayama, A., Satoh, N., & Sasakura, Y. (2005) · ZOOLOGICAL SCIENCE · doi:10.2108/zsj.22.301 · Cited by 21
“In Ciona intestinalis , the draft genome sequences have been determined (Dehal et al ., 2002), a large EST/cDNA database is available (Satou et al ., 2002), and many genes including genes regulating the cell cycle are annotated (e. g. Kawashima et al ., 2003; Sasakura et al ., 2003c, d; Satou and…”
BackgroundSelf-citationHahn, M. E., Merson, R. R., & Karchner, S. I. (2005) · Biochemistry and molecular biology of fishes · doi:10.1016/s1873-0140(05)80010-4 · Cited by 21
Nitta, K. R., Vincentelli, R., Jacox, E. H., Cimino, A., Ohtsuka, Y., Sobral, D., Satou, Y., Cambillau, C., & Lemaire, P. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9624-7_23 · Cited by 21
Self-citationBlock, W. D., & Lees‐Miller, S. P. (2005) · DNA repair · doi:10.1016/j.dnarep.2005.06.008 · Cited by 20
Sea squirts and immune tolerance
Tomaso, A. W. D. (2009) · Disease Models & Mechanisms · doi:10.1242/dmm.001156 · Cited by 22
A word-oriented approach to alignment validation
Beiko, R. G., Chan, C. X., & Ragan, M. A. (2005) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti335 · Cited by 21
A genomic overview of short genetic variations in a basal chordate, Ciona intestinalis
Satou, Y., Shin‐I, T., Kohara, Y., Satoh, N., & Chiba, S. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-208 · Cited by 21
“Of these ESTs, 73% are derived from animals sampled from Onagawa, Miyagi, Japan, where we sampled the animals for generating the JP dataset.”
BackgroundMethodInfluentialSelf-citationFrom so simple a beginning – what amphioxus can teach us about placode evolution
Schlosser, G. (2017) · The International Journal of Developmental Biology · doi:10.1387/ijdb.170127gs · Cited by 20
“…none of the neuropeptides produced by the vertebrate adenohypophysis (MSH, ACTH) was found in either the amphioxus, ascidian or any other invertebrate genomes suggesting that these are vertebrate innovations (Campbell et al., 2004, Dehal et al., 2002, Holland et al., 2008, Putnam et al., 2008).”
BackgroundEcological Review of the Ciona Species Complex
Wilson, E. R., Murphy, K. J., & Wyeth, R. C. (2022) · Biological Bulletin · doi:10.1086/719476 · Cited by 20
“…the sequencing and manipulation of the genome of each Ciona spp. have shed light on the genetics behind the development and adaptations of the species and other chordates (Simmen and Bird, 2000; Dehal et al., 2002; Satoh, 2003; Nydam and Harrison, 2007; Silva and Smith, 2008; Ni et al., 2018).”
BackgroundCiliary photoreceptors in sea urchin larvae indicate pan-deuterostome cell type conservation
Valencia, J. E., Feuda, R., Mellott, D. O., Burke, R. D., & Peter, I. S. (2021) · BMC Biology · doi:10.1186/s12915-021-01194-y · Cited by 21
Mechanisms of Sperm–Egg Interactions: What Ascidian Fertilization Research Has Taught Us
Sawada, H., & Saitô, T. (2022) · Cells · doi:10.3390/cells11132096 · Cited by 20
“On the other hand, the N-terminal sequence of the 25-kDa CUB1-interacting protein was found at the upstream region of the cDNA of the CT and was identified as a penultimate C-terminal fragment of vitellogenin (Figure 4), referred to as the von Willebrand factor D (vWF-D) region [13].”
BackgroundEliso, M. C., Bergami, E., Bonciani, L., Riccio, R., Belli, G., Belli, M., Corsi, I., & Spagnuolo, A. (2022) · Environmental Pollution · doi:10.1016/j.envpol.2022.120892 · Cited by 20
Self-citationNatural Variation of Model Mutant Phenotypes in Ciona intestinalis
Sordino, P., Andreakis, N., Brown, E. R., Leccia, N. I., Squarzoni, P., Tarallo, R., Alfano, C., Caputi, L., D’Ambrosio, P., Daniele, P., et al. (2008) · PLoS ONE · doi:10.1371/journal.pone.0002344 · Cited by 20
Self-citationOren, M., Douek, J., Fishelson, Z., & Rinkevich, B. (2007) · Developmental & Comparative Immunology · doi:10.1016/j.dci.2006.12.009 · Cited by 20
“This is further supported by the availability of improved research tools, such as the publication of the draft genome from the solitary ascidian Ciona intestinalis [4].”
BackgroundCha, I. S., del Castillo, C. S., Nho, S. W., Hikima, J.-I., Aoki, T., & Jung, T. S. (2011) · Developmental & Comparative Immunology · doi:10.1016/j.dci.2011.01.011 · Cited by 20
Bauermeister, A., Branco, P. C., Furtado, L. C., Jimenez, P. C., Costa-Lotufo, L. V., & Lotufo, T. M. D. C. (2018) · Drug Discovery Today Disease Models · doi:10.1016/j.ddmod.2019.08.008 · Cited by 20
Rosental, B., Raveh, T., Voskoboynik, A., & Weissman, I. L. (2020) · Current Opinion in Immunology · doi:10.1016/j.coi.2019.12.006 · Cited by 19
Mita, K., Kawai, N., Rueckert, S., & Sasakura, Y. (2012) · Diseases of Aquatic Organisms · doi:10.3354/dao02534 · Cited by 20
“In 2002, the draft genome of this species was determined with about 160 mega base pairs (Mbp) per haploid, encoding 15 852 protein-coding genes (Dehal et al. 2002).”
BackgroundSelf-citationStudy of Cis-regulatory Elements in the Ascidian Ciona intestinalis
Irvine, S. Q. (2013) · Current Genomics · doi:10.2174/138920213804999192 · Cited by 19
“The high allelic variation makes genome assembly a difficult task [4, 15].”
BackgroundBartl, S., Miracle, A. L., Rumfelt, L. L., Kepler, T. B., Mochon, E., Litman, G. W., & Flajnik, M. F. (2003) · Immunogenetics · doi:10.1007/s00251-003-0608-3 · Cited by 21
“The combined activities of the RAG proteins and TdT in lymphocyte development result in such high diversity of receptors that only rarely do two B or T cells with Nregion addition have the same receptor on their surfaces (Alt et al. 1992; Chen and Alt 1993; Davis 1990; Lieber et al. 1994; Matis 1988).”
Background
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
