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 601–700 of 1,000
Requirements and Standards for Organelle Genome Databases
Boore, J. L. (2006) · OMICS A Journal of Integrative Biology · doi:10.1089/omi.2006.10.119 · Cited by 43
Self-citationBallarin, L., Burighel, P., & Cima, F. (2008) · Current Pharmaceutical Design · doi:10.2174/138161208783378798 · Cited by 42
“Solitary ascidian species (Ciona intestinalis, Ciona savignyi, Halocynthia roretzi) have recently introduced as model organisms for studying the molecular control of embryogenesis and cell differentiation [2-8], and their genome has been partially or fully sequenced [9-10].”
BackgroundInitial characterization of a protochordate histocompatibility locus
Tomaso, A. W. D., & Weissman, I. L. (2003) · Immunogenetics · doi:10.1007/s00251-003-0612-7 · Cited by 42
Origins of lymphocyte developmental programs: transcription factor evidence
Rothenberg, E. V., & Pant, R. (2004) · Seminars in Immunology · doi:10.1016/j.smim.2004.08.002 · Cited by 42
Horie, T., Orii, H., & Nakagawa, M. (2005) · Journal of Neurobiology · doi:10.1002/neu.20197 · Cited by 41
Accelerated Evolutionary Rate of Housekeeping Genes in Tunicates
Tsagkogeorga, G., Turón, X., Galtier, N., Douzery, E., & Delsuc, F. (2010) · Journal of Molecular Evolution · doi:10.1007/s00239-010-9372-9 · Cited by 43
Takahashi, T., McDougall, C., Troscianko, J. T., Chen, W.-C., Jayaraman-Nagarajan, A., Shimeld, S. M., & Ferrier, D. E. K. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-240 · Cited by 41
“It was originally thought to be a unique system in chordates as the genes related to this system had not been found elsewhere [34].”
BackgroundPhotoreceptive Systems in Ascidians†
Kusakabe, T. G., & Tsuda, M. (2007) · Photochemistry and Photobiology · doi:10.1562/2006-07-11-ir-965 · Cited by 42
Zega, G., Biggiogero, M., Groppelli, S., Candiani, S., Oliveri, D., Parodi, M., Pestarino, M., de Bernardi, F. L., & Pennati, R. (2007) · The Journal of Comparative Neurology · doi:10.1002/cne.21565 · Cited by 41
“Since the release of the complete genome of C. intestinalis (Dehal et al., 2002), several studies have focused on the expression patterns of nervous-system-specific genes to investigate neural induction, differentiation, and function (Mochizuki et al., 2003; Yoshida et al., 2004; Meinertzhagen et…”
BackgroundCaterpillars evolved from onychophorans by hybridogenesis
Williamson, D. I. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0908357106 · Cited by 41
“The genome of the larvacean Oikopleura dioica is about one-third that of the tunicate Ciona intestinalis, consistent with my thesis (22, 23).”
BackgroundMolecular Evolution of the Ankyrin Gene Family
Cai, X., & Zhang, Y. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msj056 · Cited by 42
Metazoans and Intrinsic Apoptosis: An Evolutionary Analysis of the Bcl-2 Family
Suraweera, C. D., Banjara, S., Hinds, M. G., & Kvansakul, M. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23073691 · Cited by 44
“The tunicates Ciona intestinalis [60] and Botryllus schlosseri [61] contain multi-motif Bcl-2 proteins.”
BackgroundEfficient targeted mutagenesis of the chordate C iona intestinalis genome with zinc‐finger nucleases
Kawai, N., Ochiai, H., Sakuma, T., Yamada, L., Sawada, H., Yamamoto, T., & Sasakura, Y. (2012) · Development Growth & Differentiation · doi:10.1111/j.1440-169x.2012.01355.x · Cited by 40
“The draft genome sequence of C. intestinalis has already been determined, and largescale expressed sequence tag (EST) information has been obtained (Dehal et al. 2002; Satou et al. 2002).”
BackgroundSelf-citationThe C- and G-value paradox with polyploidy, repeatomes, introns, phenomes and cell economy
Choi, I., Kwon, E., & Kim, N. (2020) · Genes & Genomics · doi:10.1007/s13258-020-00941-9 · Cited by 46
Immunobiology of compound ascidians, with particular reference to Botryllus schlosseri: state of art
Ballarin, L. (2008) · Invertebrate survival journal · Cited by 40
Zeller, R. W., Weldon, D. S., Pellatiro, M. A., & Cone, A. C. (2005) · Developmental Dynamics · doi:10.1002/dvdy.20644 · Cited by 40
“…GFP and wild-type DsRed (all abbreviations are listed in Table 1) with the predicted codon usage for the ascidian Ciona intestinalis, generated using the program CodonW (Peden, 1999) based on all of the predicted genes present in Release 1 of the C. intestinalis genome (Dehal et al., 2002).”
BackgroundMethodPoliakov, E., Gubin, A. N., Stearn, O., Li, Y., Campos, M. M., Gentleman, S., Rogozin, I. B., & Redmond, T. M. (2012) · PLoS ONE · doi:10.1371/journal.pone.0049975 · Cited by 41
“The branch A corresponds to approximately 50 million years, whereas the branch B corresponds to 500 million years [19,20,21,22].”
BackgroundFunctional Characterization of a Ficolin-mediated Complement Pathway in Amphioxus
Huang, H., Huang, S., Yu, Y., Yuan, S., Li, R., Wang, X., Zhao, H., Yu, Y., Li, J., Yang, M., et al. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.245944 · Cited by 40
Distribution and structural diversity of cilia in tadpole larvae of the ascidian Ciona intestinalis
Konno, A., Kaizu, M., Hotta, K., Horie, T., Sasakura, Y., Ikeo, K., & Inaba, K. (2009) · Developmental Biology · doi:10.1016/j.ydbio.2009.10.012 · Cited by 40
“Furthermore, sequence information, including genome and cDNA/expressed sequence tag data, is readily available for the ascidian Ciona intestinalis (Dehal et al., 2002; Satou et al., 2002).”
Self-citationSeeing chordate evolution through the Ciona genome sequence.
Cañestro, C., Bassham, S., & Postlethwait, J. H. (2003) · Genome biology · doi:10.1186/gb-2003-4-3-208 · Cited by 40
“The team [2] identified 15,852 gene models in Ciona, a number comparable to other protostomes (there are 13,639 and 19,518 currently identified in D.”
InfluentialThomas, D. J., Nava, G. M., Cai, S., Boyer, J. L., Hernández‐Zavala, A., & Gaskins, H. R. (2009) · Toxicological Sciences · doi:10.1093/toxsci/kfp250 · Cited by 40
Targeted knockdown of an opsin gene inhibits the swimming behaviour photoresponse of ascidian larvae
Inada, K., Horie, T., Kusakabe, T. G., & Tsuda, M. (2003) · Neuroscience Letters · doi:10.1016/s0304-3940(03)00689-x · Cited by 40
The galaxy of the non-Linnaean nomenclature
Minelli, A. (2019) · History & Philosophy of the Life Sciences · doi:10.1007/s40656-019-0271-0 · Cited by 39
Comparative genomics of microsporidia
Keeling, P. J., Fast, N. M., Law, J. S., Williams, B., & Slamovits, C. H. (2005) · Folia Parasitologica · doi:10.14411/fp.2005.002 · Cited by 39
Ciona as a Simple Chordate Model for Heart Development and Regeneration
Evans‐Anderson, H. J., & Christiaen, L. (2016) · Journal of Cardiovascular Development and Disease · doi:10.3390/jcdd3030025 · Cited by 38
“Second, since the Ciona genome has been sequenced and annotated [16], Ciona are amenable to many sophisticated molecular tools, including transgenic lines with specifically-expressed molecular markers [123] that have been used to track regenerative responses [111].”
BackgroundA mechanism for graded motor control encoded in the channel properties of the muscle ACh receptor
Nishino, A., Baba, S. A., & Okamura, Y. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1013547108 · Cited by 39
“Recent research on the Ciona genome provides an opportunity to examine the molecular mechanisms underlying the physiology of this animal (12, 13).”
BackgroundRNA interference by expressing short hairpin RNA in the Ciona intestinalis embryo
Nishiyama, A., & Fujiwara, S. (2008) · Development Growth & Differentiation · doi:10.1111/j.1440-169x.2008.01039.x · Cited by 40
“intestinalis genome is 153–159 Mb, which is as compact as that of Drosophila melanogaster (Dehal et al. 2002).”
BackgroundSkjoedt, M., Palarasah, Y., Rasmussen, K. J., Vitved, L., Salomonsen, J., Kliem, A., Hansen, S., Koch, C., & Skjødt, K. (2009) · Developmental & Comparative Immunology · doi:10.1016/j.dci.2009.08.004 · Cited by 39
Ishibashi, T., Usami, T., Fujie, M., Azumi, K., Satoh, N., & Fujiwara, S. (2005) · Developmental Dynamics · doi:10.1002/dvdy.20486 · Cited by 39
“This microarray covers approximately 85% of the transcripts (estimated to be around 16,000) of protein-coding genes in this species (Dehal et al., 2002).”
BackgroundSelf-citationCloning and functional expression of invertebrate connexins from Halocynthia pyriformis
White, T. W., Wang, H., Mui, R., Litteral, J., & Brink, P. R. (2004) · FEBS Letters · doi:10.1016/j.febslet.2004.09.071 · Cited by 39
Self-citationTerajima, D., Shida, K., Takada, N., Kasuya, A., Rokhsar, D. S., Satoh, N., Satake, M., & Wang, H.-G. (2003) · Cell Death and Differentiation · doi:10.1038/sj.cdd.4401223 · Cited by 39
Self-citationPop, M. (2004) · Advances in computers · doi:10.1016/s0065-2458(03)60006-9 · Cited by 38
Nitric Oxide Acts as a Positive Regulator to Induce Metamorphosis of the Ascidian Herdmania momus
Ueda, N., & Degnan, S. M. (2013) · PLoS ONE · doi:10.1371/journal.pone.0072797 · Cited by 38
Neural Map of the Larval Central Nervous System in the AscidianCiona intestinalis
Takamura, K., Minamida, N., & Okabe, S. (2010) · ZOOLOGICAL SCIENCE · doi:10.2108/zsj.27.191 · Cited by 38
“Since EST and the draft genome information is now available for Ciona intestinalis (Satou Y et al., 2003; Dehal et al., 2002), several neuronal marker genes have recently been searched by using these databases (http// ghost.zool.kyoto-u.ac.jp/indexr1.html; http//www.jgi.doe.gov/ ciona).”
MethodGenomic basis of environmental adaptation in the leathery sea squirt (Styela clava)
Wei, J., Zhang, J., Lu, Q., Ren, P., Guo, X. H., Wang, J., Li, X., Chang, Y., Duan, S., Wang, S., et al. (2020) · Molecular Ecology Resources · doi:10.1111/1755-0998.13209 · Cited by 38
Ballarin, L., Karahan, A., Salvetti, A., Rossi, L., Manni, L., Rinkevich, B., Rosner, A., Voskoboynik, A., Rosental, B., Canesi, L., et al. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.688106 · Cited by 38
Parrinello, N., Arizza, V., Cammarata, M., Giaramita, F. T., Pergolizzi, M., Vazzana, M., Vizzini, A., & Parrinello, D. (2007) · Cell and Tissue Research · doi:10.1007/s00441-007-0415-5 · Cited by 38
“intestinalis have provided a comprehensive picture of immune-related genes (Dehal et al. 2002; Shida et al. 2003; Azumi et al. 2003; Terajima et al. 2003) and shown that IL1 genes are not contained in the genome, whereas the recorded C-type lectin and galectin genes can be expressed by hemocytes from untreated ascidia…”
BackgroundInfluentialZeller, R. W., Virata, M. J., & Cone, A. C. (2006) · Developmental Dynamics · doi:10.1002/dvdy.20815 · Cited by 38
A saturation screen for cis-acting regulatory DNA in the Hox genes of Ciona intestinalis
Keys, D. N., Lee, B.-I., Gregorio, A. D., Harafuji, N., Detter, J. C., Wang, M., Kahsai, O. J., Ahn, S., Zhang, C., Doyle, S. A., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0408952102 · Cited by 38
Self-citationStudying non-mammalian models? Not a fool's ERRand!
Bardet, P., Laudet, V., & Vanacker, J.-M. (2006) · Trends in Endocrinology and Metabolism · doi:10.1016/j.tem.2006.03.005 · Cited by 38
Yoshizaki, F., Ikawa, S., Satake, M., Satoh, N., & Nonaka, M. (2005) · Immunogenetics · doi:10.1007/s00251-004-0752-4 · Cited by 38
Self-citationKugler, J. E., Kerner, P., Bouquet, J., Jiang, D., & Gregorio, A. D. (2011) · BMC Evolutionary Biology · doi:10.1186/1471-2148-11-21 · Cited by 37
“The retention of duplicate genes might also explain why, despite its smaller size and the lack of several genes that are found in Ciona, the Oikopleura genome is estimated to contain approximately 18,020 genes ([22,37], a number comparable to that assessed for Ciona [66].”
The mouth, the anus, and the blastopore—open questions about questionable openings
Hejnol, A., & Martindale, M. Q. (2009) · Animal Evolution · doi:10.1093/acprof:oso/9780199549429.003.0004 · Cited by 37
Mitotic Membrane Turnover Coordinates Differential Induction of the Heart Progenitor Lineage
Cota, C. D., & Davidson, B. (2015) · Developmental Cell · doi:10.1016/j.devcel.2015.07.001 · Cited by 37
Self-citationBacterial diversity associated with the tunic of the model chordate Ciona intestinalis
Blasiak, L. C., Zinder, S. H., Buckley, D. H., & Hill, R. T. (2013) · The ISME Journal · doi:10.1038/ismej.2013.156 · Cited by 43
“Several factors have contributed to the resurgence of Ciona as a model organism, not least the availability of both the C. intestinalis and the related C. saviygni genome sequences (Dehal et al., 2002; Small et al., 2007).”
BackgroundHox10-regulated endodermal cell migration is essential for development of the ascidian intestine
Kawai, N., Ogura, Y., Ikuta, T., Saiga, H., Hamada, M., Sakuma, T., Yamamoto, T., Satoh, N., & Sasakura, Y. (2015) · Developmental Biology · doi:10.1016/j.ydbio.2015.03.018 · Cited by 37
Self-citationAn Advanced Filter-Feeder Hypothesis for Urochordate Evolution
Satoh, N. (2009) · ZOOLOGICAL SCIENCE · doi:10.2108/zsj.26.97 · Cited by 37
“1B), an emerging model organism whose genome has been decoded (Dehal et al., 2002; Satoh et al., 2003; Satoh and Levine, 2005; Shi et al., 2005; Nishida, 2005; Passamaneck and Di Gregorio, 2005).”
BackgroundSelf-citationPeterson, K. J., & Eernisse, D. J. (2016) · Organisms Diversity & Evolution · doi:10.1007/s13127-016-0270-x · Cited by 37
Ontogeny, Anatomy, Metabolism and Physiology of the Thyroid
Maenhaut, C., Christophe, D., Vassart, G., Dumont, J. E., Roger, P. P., & Opitz, R. (2015) · Europe PMC (PubMed Central) · Cited by 38
An Introduction to the Invertebrates
Moore, J. (2006) · Cambridge University Press eBooks · doi:10.1017/cbo9780511754760 · Cited by 40
Similarity and diversity in mechanisms of muscle fate induction between ascidian species
Hudson, C., & Yasuo, H. (2008) · Biology of the Cell · doi:10.1042/bc20070144 · Cited by 37
“intestinalis is available, as well as extensive EST (expressed sequence tag) collections, virtual three-dimensional embryos and a draft whole embryo gene-regulatory network (Dehal et al., 2002; Satou et al., 2005; Imai et al., 2006; Tassy et al., 2006).”
BackgroundInfluentialWada, S., Hamada, M., & Satoh, N. (2006) · Cell Stress and Chaperones · doi:10.1379/csc-137r.1 · Cited by 37
Self-citationMayorova, T. D., Tian, S., Cai, W., Semmens, D. C., Odekunle, E., Zandawala, M., Badi, Y. E., Rowe, M. L., Egertová, M., & Elphick, M. R. (2016) · Frontiers in Neuroscience · doi:10.3389/fnins.2016.00553 · Cited by 37
“Turning to deuterostomian marine invertebrates, sequencing of the genome of the urochordate Ciona intestinalis (Dehal et al., 2002) has enabled a comprehensive analysis of larval neuropeptide expression in this species.”
BackgroundMolecular Conservation and Novelties in Vertebrate Ear Development
Fritzsch, B., & Beisel, K. W. (2003) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/s0070-2153(03)57001-6 · Cited by 39
“These data could simply indicate that gene multiplication has already in urbilaterians generated various bHLH genes (Dehal et al., 2002).”
BackgroundInfluentialCharacterization of novel ascidian � integrins as primitive complement receptor subunits
Miyazawa, S., & Nonaka, M. (2004) · Immunogenetics · doi:10.1007/s00251-004-0651-8 · Cited by 37
Self-citationLangeland, J. A., Holland, L. Z., Chastain, R. A., & Holland, N. D. (2006) · International Journal of Biological Sciences · doi:10.7150/ijbs.2.110 · Cited by 36
“LIM-homeobox genes in tunicates, hemichordates and sea urchins In the ascidian tunicate, Ciona intestinalis, five LIM-homeobox genes have been found in the genome, one in each subfamily except for Lhx6/7 [8].”
BackgroundProteome-wide classification and identification of mammalian-type GPCRs by binary topology pattern
Inoue, Y., Ikeda, M., & Shimizu, T. (2004) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2003.11.003 · Cited by 37
Leveugle, M., Prat, K., Popovici, C., Birnbaum, D., & Coulier, F. (2004) · Journal of Molecular Evolution · doi:10.1007/s00239-003-2538-y · Cited by 37
Wagner, G. P., Takahashi, K., Lynch, V. J., Prohaska, S. J., Fried, C., Stadler, P. F., & Amemiya, C. T. (2005) · Journal of Molecular Evolution · doi:10.1007/s00239-004-0252-z · Cited by 39
Editorial: the evolutionary origin of neural crest and placodes
Baker, C. V. H., & Schlosser, G. (2005) · Journal of Experimental Zoology Part B Molecular and Developmental Evolution · doi:10.1002/jez.b.21060 · Cited by 37
Unraveling genomic regulatory networks in the simple chordate, Ciona intestinalisPreprint
Shi, W., Levine, M., & Davidson, B. (2005) · Genome Research · doi:10.1101/gr.3768905 · Cited by 37
Self-citationDifferential expression pattern of the novel serine/threonine kinase, STK33, in mice and men
Mujica, A. O., Brauksiepe, B., Saaler‐Reinhardt, S., Reuss, S., & Schmidt, E. R. (2005) · FEBS Journal · doi:10.1111/j.1742-4658.2005.04900.x · Cited by 36
The caspase family in urochordates: distinct evolutionary fates in ascidians and larvaceans
Weill, M., Philips, A., Chourrout, D. M., & Fort, P. (2005) · Biology of the Cell · doi:10.1042/bc20050018 · Cited by 36
“In this study, we undertook a search for caspase genes in three recently sequenced tunicate genomes [the ascidians C. intestinalis (Dehal et al., 2002) and C. savignyi, and the appendicularian Oikopleura dioica].”
BackgroundAllorecognition in a Basal Chordate Consists of Independent Activating and Inhibitory Pathways
McKitrick, T. R., Muscat, C., Pierce, J. D., Bhattacharya, D., & Tomaso, A. W. D. (2011) · Immunity · doi:10.1016/j.immuni.2011.01.019 · Cited by 36
Hozumi, A., Padma, P., Toda, T., Ide, H., & Inaba, K. (2008) · Cell Motility and the Cytoskeleton · doi:10.1002/cm.20258 · Cited by 36
“Recent progress in genome project in Ciona has made it possible to extensively study the molecular mechanism of sperm activation [Nomura et al., 2000; Dehal et al., 2002; Inaba et al., 2002; Satou et al., 2002; Padma et al., 2003].”
BackgroundMethodSelf-citationEvolution of the Max and Mlx Networks in Animals
McFerrin, L. G., & Atchley, W. R. (2011) · Genome Biology and Evolution · doi:10.1093/gbe/evr082 · Cited by 38
How Fast Is the Sessile Ciona?
Berná, L., Álvarez-Valín, F., & D’Onofrio, G. (2009) · Comparative and Functional Genomics · doi:10.1155/2009/875901 · Cited by 36
“savignyi are available since 2002 and 2005, respectively, [7, 9], it is now possible to make more accurate assessment of sequences divergence (with low impact of stochastic effects due to the fact that we use large gene samples).”
BackgroundSequencing, Assembling, and Correcting Draft Genomes Using Recombinant Populations
Hahn, M. W., Zhang, S. V., & Moyle, L. C. (2014) · G3 Genes Genomes Genetics · doi:10.1534/g3.114.010264 · Cited by 36
“One approach to dealing with the problem of allelic variation is to allow greater numbers of mismatches between the sequences combined together into a single locus during the assembly process ( e.g. , Dehal et al. 2002).”
BackgroundBorges, R., Johnson, W. E., O’Brien, S. J., Vasconcelos, V. M., & Antunes, A. (2012) · PLoS ONE · doi:10.1371/journal.pone.0052413 · Cited by 37
“generally assumed to be common, and it was already reported for the well-studied Hox genes [42,43] so we hypothesize that melanopsin may have been lost during a genomic rearrangement process.”
Trivedi, S., Ueki, T., Yamaguchi, N., & Michibata, H. (2003) · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression · doi:10.1016/j.bbaexp.2003.09.007 · Cited by 36
“intestinalis genome sequence [17], we found that these five groups of cDNAs were encoded by five independent genes and there were no other vanabin-like genes or pseudogenes in the genome.”
BackgroundTowards the reconstruction of the bilaterian ancestral pre-MHC region
Danchin, É., & Pontarotti, P. (2004) · Trends in Genetics · doi:10.1016/j.tig.2004.09.009 · Cited by 37
Development and Evolution of the Ascidian Cardiogenic Mesoderm
Tolkin, T. R., & Christiaen, L. (2012) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/b978-0-12-387786-4.00011-7 · Cited by 36
“intestinalis and its sibling species Ciona savignyi were published in the early 2000s (Dehal et al., 2002; Hill et al., 2008; Small et al., 2007; Vinson et al., 2005); comprehensive annotations were compiled using large amounts of express sequence tags (ESTs) and state-of-the-art databases created to provide user-frie…”
BackgroundPeptidomics in Drosophila melanogaster
Schoofs, L. (2003) · Briefings in Functional Genomics and Proteomics · doi:10.1093/bfgp/2.2.114 · Cited by 36
Kowalevsky, comparative evolutionary embryology, and the intellectual lineage of evo‐devo
Raff, R. A., & Love, A. C. (2004) · Journal of Experimental Zoology Part B Molecular and Developmental Evolution · doi:10.1002/jez.b.20004 · Cited by 35
Hill, M. M., Broman, K. W., Stupka, E., Smith, W. C., Jiang, D., & Sidow, A. (2008) · Genome Research · doi:10.1101/gr.078576.108 · Cited by 36
“The ∼ 170-Mb genomes of C. savignyi and C. intestinalis had both been sequenced to draft-level coverage (12.7 (cid:1) and 8 (cid:1) , respectively) (Dehal et al. 2002; Vinson et al. 2005).”
InfluentialSato, A., Shimeld, S. M., & Bishop, J. (2014) · ZOOLOGICAL SCIENCE · doi:10.2108/zs130249 · Cited by 35
Rebscher, N., Deichmann, C., Sudhop, S., Fritzenwanker, J. H., Green, S., & Hassel, M. (2009) · Development Genes and Evolution · doi:10.1007/s00427-009-0309-5 · Cited by 37
“It remains to be shown how in nondeuterostome taxa the few FGFRs cope with the multiple FGFs like Tribolium (one FGFR, four FGFs, Beermann and Schroder 2008 )o r Drosophila (Heartless FGFR, two FGFs, see Kadam et al. 2009 and Klingseisen et al. 2009).”
BackgroundCharacterizing the Embryonic Transcriptome of the Snail Ilyanassa
Lambert, J. D., Chan, X. Y., Spiecker, B. J., & Sweet, H. C. (2010) · Integrative and Comparative Biology · doi:10.1093/icb/icq121 · Cited by 35
Hapsembler: An Assembler for Highly Polymorphic Genomes
Donmez, N., & Brudno, M. (2011) · Lecture notes in computer science · doi:10.1007/978-3-642-20036-6_5 · Cited by 35
“Previous efforts to assemble these highly polymorphic genomes have used one of two approaches: either they allow for promiscuous overlaps, to connect the reads from different haplotypes[20], or they enforce strict overlapping requirements, thus separating the haploid genomes (haplomes) [10].”
BackgroundExpression of neuropeptide- and hormone-encoding genes in the Ciona intestinalis larval brain
Hamada, M., Shimozono, N., Ohta, N., Satou, Y., Horie, T., Kawada, T., Satake, H., Sasakura, Y., & Satoh, N. (2011) · Developmental Biology · doi:10.1016/j.ydbio.2011.01.006 · Cited by 36
Self-citationA Basal Chordate Model for Studies of Gut Microbial Immune Interactions
Dishaw, L. J., Flores-Torres, J., Mueller, M. G., Karrer, C. R., Skapura, D. P., Melillo, D., Zucchetti, I., Santis, R. D., Pinto, M. R., & Litman, G. W. (2012) · Frontiers in Immunology · doi:10.3389/fimmu.2012.00096 · Cited by 35
Kugler, J. E., Gazdoiu, S., Oda‐Ishii, I., Passamaneck, Y. J., Erives, A. J., & Gregorio, A. D. (2010) · Journal of Cell Science · doi:10.1242/jcs.066910 · Cited by 35
“the Ci-Tbx6b locus as shown in the JGI Ciona intestinalis genome browser (Dehal et al., 2002) (http://genome.”
BackgroundMethodYajima, I., Endo, K., Sato, S., Toyoda, R., Wada, H., Shibahara, S., Numakunai, T., Ikeo, K., Gojobori, T., Goding, C. R., et al. (2003) · Mechanisms of Development · doi:10.1016/j.mod.2003.08.009 · Cited by 35
Realistic artificial DNA sequences as negative controls for computational genomics
Caballero, J., Smit, A. F. A., Hood, L., & Glusman, G. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku356 · Cited by 35
“uk/Projects/D rerio/); Ciona intestinalis: ci2 (39); purple sea urchin: strPur2 (40); Anopheles gambiae: anoGam1 (41); bee: apiMel2 (42); Drosophila melanogaster: dm3 (6); Caenorhabditis elegans: ce3 (43).”
Andachi, Y. (2004) · Genes to Cells · doi:10.1111/j.1356-9597.2004.00725.x · Cited by 35
Takeuchi, K., Satou, Y., Yamamoto, H., & Satoh, N. (2005) · ZOOLOGICAL SCIENCE · doi:10.2108/zsj.22.723 · Cited by 35
“The draft genome sequence (Dehal et al ., 2002) and a cDNA/EST database (Satou et al ., 2002) of Ciona intestinalis were TBlastN searched for homologous ascidian protein sequences using human and Drosophila proteins.”
BackgroundMethodSelf-citationConstruction of a cDNA Microarray Derived from the Ascidian Ciona intestinalis
Azumi, K., Takahashi, H., Miki, Y., Fujie, M., Usami, T., Ishikawa, H., Kitayama, A., Satou, Y., Ueno, N., & Satoh, N. (2003) · ZOOLOGICAL SCIENCE · doi:10.2108/zsj.20.1223 · Cited by 35
Self-citationBioadhesion in ascidians: a developmental and functional genomics perspective
Pennati, R., & Rothbächer, U. (2014) · Interface Focus · doi:10.1098/rsfs.2014.0061 · Cited by 35
Molecular Cytogenetic Characterization of Ciona intestinalis Chromosomes
Shoguchi, E., Kawashima, T., Nishida‐Umehara, C., Matsuda, Y., & Satoh, N. (2005) · ZOOLOGICAL SCIENCE · doi:10.2108/zsj.22.511 · Cited by 35
“The draft sequence of the Ciona intestinalis genome indicates that 18S/28S rDNA repeats are those of the highest copy number (Dehal et al ., 2002).”
BackgroundMethodInfluentialSelf-citationA Celebration of the New Head and an Evaluation of the New Mouth
Manzanares, M., & Nieto, M. A. (2003) · Neuron · doi:10.1016/s0896-6273(03)00161-2 · Cited by 35
“…shown how fine tinkering of neural sequence of the genome from the ascidia Ciona intesticrest populations may be behind some of the classical nalis (Dehal et al., 2002) and the promise of an amphiexamples of evolutionary theory, such as the morpho- oxus genome project (http://tbx.wustl.edu/…”
BackgroundChurcher, A. M., & Taylor, J. S. (2010) · Genome Biology and Evolution · doi:10.1093/gbe/evq079 · Cited by 35
Veeman, M. T., Chiba, S., & Smith, W. C. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-210-6_15 · Cited by 35
McKenzie, P., Chadalavada, S. C., Bohrer, J. C., & Adams, J. C. (2006) · BMC Evolutionary Biology · doi:10.1186/1471-2148-6-33 · Cited by 34
“The Ciona intestinalis (an invertebrate chordate) genome encodes a smaller number of TSPs; yet, because both A and B forms of TSPs are present, it is clear that the existence of A and B forms predates the whole genome duplications that occurred in the early stages of vertebrate evolution ([5,64]; our unpublished data).”
Eukaryotic domain evolution inferred from genome comparisons
Copley, R. R., Goodstadt, L., & Ponting, C. P. (2003) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2003.10.004 · Cited by 34
Yamaguchi, N., Kamino, K., Ueki, T., & Michibata, H. (2003) · Marine Biotechnology · doi:10.1007/s10126-003-0024-6 · Cited by 35
De novo discovery of a tissue-specific gene regulatory module in a chordatePreprint
Johnson, D. S., Zhou, Q., Yagi, K., Satoh, N., Wong, W. H., & Sidow, A. (2005) · Genome Research · doi:10.1101/gr.4062605 · Cited by 35
“A small genome (180 Mb) with a number of expressed genes (15,000) similar to that of Drosophila (Dehal et al. 2002) ensures that the search space for noncoding functional elements is smaller than in vertebrates.”
BackgroundSelf-citationTransposon mediated transgenesis in a marine invertebrate chordate: Ciona intestinalis
Sasakura, Y., Oogai, Y., Matsuoka, T., Satoh, N., & Awazu, S. (2007) · Genome biology · doi:10.1186/gb-2007-8-s1-s3 · Cited by 35
“The genome project reported that 1.2% of nucleotide differences were observed between alleles of the single individual [ 35 ].”
InfluentialSelf-citationMolecular evolution of nitric oxide synthases in metazoans
González-Domenech, C. M., & Muñoz‐Chápuli, R. (2010) · Comparative Biochemistry and Physiology Part D Genomics and Proteomics · doi:10.1016/j.cbd.2010.08.004 · Cited by 34
Genes Encoding Vitamin-K Epoxide Reductase Are Present in Drosophila and Trypanosomatid Protists
Robertson, H. M. (2004) · Genetics · doi:10.1534/genetics.104.029744 · Cited by 34
“Sinauer Associates, Sunderland, MA.have been deposited in the TPA database at NCBI (accession nos.”
BackgroundInfluential
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
