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 901–1,000 of 1,000
Identification of the mammalian Not gene via a phylogenomic approach
Plouhinec, J.-L., Granier, C., Mentec, C. L., Lawson, K. A., Sabéran‐Djoneidi, D., Aghion, J., Shi, D., Collignon, J., & Mazan, S. (2004) · Gene Expression Patterns · doi:10.1016/j.modgep.2004.06.010 · Cited by 19
A comprehensive survey of cadherin superfamily gene expression patterns in Ciona intestinalis
Noda, T., & Satoh, N. (2008) · Gene Expression Patterns · doi:10.1016/j.gep.2008.01.004 · Cited by 19
Self-citationRegulation of NF-κB/Rel by IκB is essential for ascidian notochord formation
Kawai, N., Takahashi, H., Nishida, H., & Yokosawa, H. (2004) · Developmental Biology · doi:10.1016/j.ydbio.2004.09.007 · Cited by 20
“All of the genomic sequences in this species have been determined (Dehal et al., 2002).”
BackgroundInfluentialEukaryotic Methyl-CpG-Binding Domain Proteins and Chromatin Modification
Hung, M., & Shen, C. ‐. J. (2003) · Eukaryotic Cell · doi:10.1128/ec.2.5.841-846.2003 · Cited by 20
“The draft genome of the sea squirt, Ciona intestinalis, has been released recently ( 6 ).”
BackgroundTakimoto, N., Kusakabe, T. G., Horie, T., Miyamoto, Y., & Tsuda, M. (2006) · Photochemistry and Photobiology · doi:10.1111/j.1751-1097.2006.tb09801.x · Cited by 21
Genomic analyses of the evolution of LGR genes.
Luo, C., & Hsueh, A. J. W. (2006) · PubMed · Cited by 20
No Evidence for AID/MBD4-Coupled DNA Demethylation in Zebrafish Embryos
Shimoda, N., Hirose, K., Kaneto, R., Izawa, T., Yokoi, H., Hashimoto, N., & Kikuchi, Y. (2014) · PLoS ONE · doi:10.1371/journal.pone.0114816 · Cited by 19
Finding cell-specific expression patterns in the early Ciona embryo with single-cell RNA-seq
Ilsley, G. R., Suyama, R., Noda, T., Satoh, N., & Luscombe, N. M. (2020) · Scientific Reports · doi:10.1038/s41598-020-61591-1 · Cited by 22
Self-citationSymbiotic Associations in Ascidians: Relevance for Functional Innovation and Bioactive Potential
Matos, A., & Antunes, A. (2021) · Marine Drugs · doi:10.3390/md19070370 · Cited by 20
Sakamoto, A., Hozumi, A., Shiraishi, A., Satake, H., Horie, T., & Sasakura, Y. (2022) · Development Growth & Differentiation · doi:10.1111/dgd.12801 · Cited by 19
“Ascidians are marine invertebrate chordates that are the closest living relatives of vertebrates (Dehal et al., 2002; Delsuc et al., 2006).”
BackgroundSelf-citationNew Modularity of DAP-Kinases: Alternative Splicing of the DRP-1 Gene Produces a ZIPk-Like Isoform
Shoval, Y., Berissi, H., Kimchi, A., & Pietrokovski, S. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017344 · Cited by 19
“Ciona species belong to a basal urochordate sub phyla that diverged before the emergence of vertebrates [27].”
BackgroundGyoja, F., Kawashima, T., & Satoh, N. (2012) · Development Genes and Evolution · doi:10.1007/s00427-012-0388-6 · Cited by 19
“We next used the genome sequences of B. floridae (Putnam et al. 2008), C. intestinalis (Dehal et al. 2002), Trichoplax adhaerence (Srivastava et al. 2008), and A. queenslandica (Srivastava et al. 2010), to perform bidirectional best hit analyses by BLASTP and TBLASTN using coral orphan bHLH…”
Self-citationRibas, L., Roher, N., Martínez, M., Balasch, J. C., Doñate, C., Goetz, F. W., Iliev, D. B., Planas, J. V., Tort, L., & MacKenzie, S. A. (2007) · Fish & Shellfish Immunology · doi:10.1016/j.fsi.2007.07.009 · Cited by 19
Yoshida, R., & Sasakura, Y. (2012) · ZOOLOGICAL SCIENCE · doi:10.2108/zsj.29.11 · Cited by 19
“Ascidians are urochordates, which form a true sister group of vertebrates (Dehal et al., 2002; Delsuc et al., 2006).”
BackgroundSelf-citationA microRNA-mRNA expression network during oral siphon regeneration in Ciona
Spina, E. J., Guzman, E., Zhou, H., Kosik, K. S., & Smith, W. C. (2017) · Development · doi:10.1242/dev.144097 · Cited by 19
“These traits, in combination with a sequenced and wellannotated genome, make C. robusta a powerful model for identifying the components and interactions that comprise gene regulatory networks that govern biological processes, including regeneration (Dehal et al., 2002; Satou et al., 2008).”
BackgroundKeduka, E., Kaiho, A., Hamada, M., Watanabe‐Takano, H., Takano, K., Ogasawara, M., Satou, Y., Satoh, N., & Endo, T. (2008) · Gene · doi:10.1016/j.gene.2008.10.001 · Cited by 19
Self-citationMaury, B., Martinand‐Mari, C., Chambon, J., Soule, J. D., Degols, G., Sahuquet, A., Weill, M., Berthomieu, A., Fort, P., Mangeat, P. H., et al. (2005) · Developmental Biology · doi:10.1016/j.ydbio.2005.10.021 · Cited by 19
“The fact that dexamethasone exerts such an effect in Ciona could, at first sight, be very surprising since Ciona genome is devoid of an orthologue of the vertebrate glucocorticoid receptor (Dehal et al., 2002).”
BackgroundStuder, R. A., & Robinson‐Rechavi, M. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq149 · Cited by 19
“…(Kasahara et al. 2007), Tetraodon nigroviridis (Jaillon et al. 2004), and Takifugu rubripes (Aparicio et al. 2002); the two Ciona: C. intestinalis (Dehal et al. 2002) and C. savignyi (Hill et al. 2008); and four species of insects: Aedes aegypti (Nene et al. 2007), Anopheles gambiae (Holt et al.…”
BackgroundEvolution of the Groucho/Tle gene family: gene organization and duplication events
Bajoghli, B. (2007) · Development Genes and Evolution · doi:10.1007/s00427-007-0167-y · Cited by 19
“Such Ascidian-specific duplication events are known from the sequence of several developmental signaling molecules and transcription factors such as the Fgf, Smad and Tbx6 genes (Dehal et al. 2002; Satou et al. 2002; Takatori et al. 2004).”
BackgroundComparative analysis of thyroxine distribution in ascidian larvae
D’Agati, P., & Cammarata, M. (2005) · Cell and Tissue Research · doi:10.1007/s00441-005-0015-1 · Cited by 18
“In addition, the genome of Ciona contains orthologous genes of peroxidase enzyme (Ogasawara et al. 1999) and iodine transporters (Dehal et al. 2002) used for thyroid hormone synthesis by the thyroid.”
BackgroundShen, G., Wu, J., Lin, Y., Hua, X., Xia, Q., & Zhao, P. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22094343 · Cited by 18
Li, K.-L., Nakashima, K., Hisata, K., & Satoh, N. (2023) · EvoDevo · doi:10.1186/s13227-023-00215-x · Cited by 18
Self-citationTunicates: exploring the sea shores and roaming the open ocean. A tribute to Thomas Huxley
Lemaire, P., & Piette, J. (2015) · Open Biology · doi:10.1098/rsob.150053 · Cited by 20
Self-citationGene regulatory networks in the early ascidian embryo
Satou, Y., Satoh, N., & Imai, K. S. (2008) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2008.03.005 · Cited by 18
Self-citationStudying the genetic basis of speciation in high gene flow marine invertebrates
Pogson, G. H. (2016) · Current Zoology · doi:10.1093/cz/zow093 · Cited by 18
“…521.9 41.2 28,627 Putnam et al. (2008) Tunicata Oikopleura dioica 70.5 39.8 17,212 Seo et al. (2001) Tunicata Ciona intestinalis 115.2 33.1 15,254 Dehal et al. (2002) Brachiopoda Lingula anatina 425.5 36.9 34,000 Luo et al. (2015) Anthozoa Nematostella vectensis 356.6 40.6 27,173 Putnam et al.…”
BackgroundInfluentialSOXE neofunctionalization and elaboration of the neural crest during chordate evolution
Tai, A. C. P., Cheung, M. C. H., Huang, Y., Jauch, R., Bronner-Fraser, M. E., & Cheah, K. S. E. (2016) · Scientific Reports · doi:10.1038/srep34964 · Cited by 18
Bozzolan, F., Durand, N., Demondion, E., Bourgeois, T. P., Gassias, E., & Debernard, S. (2017) · Insect Molecular Biology · doi:10.1111/imb.12303 · Cited by 18
Sekigami, Y., Kobayashi, T., Omi, A., Nishitsuji, K., Ikuta, T., Fujiyama, A., Satoh, N., & Saiga, H. (2017) · Zoological Letters · doi:10.1186/s40851-017-0078-3 · Cited by 18
“In the ascidian, Ciona intestinalis (Ci), nine Hox genes were identified during draft genome analysis [10].”
Self-citationDeuterostome Genomics: Lineage-Specific Protein Expansions That Enabled Chordate Muscle Evolution
Inoue, J. G., & Satoh, N. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy002 · Cited by 18
“date, Ciona intestinalis (Dehal et al. 2002), a cephalochor-”
BackgroundSelf-citationFerrández‐Roldán, A., Martí‐Solans, J., Cañestro, C., & Albalat, R. (2019) · Results and problems in cell differentiation · doi:10.1007/978-3-030-23459-1_4 · Cited by 18
Liberti, A., Bertocci, I., Pollet, A., Musco, L., Locascio, A., Ristoratore, F., Spagnuolo, A., & Sordino, P. (2020) · Marine Environmental Research · doi:10.1016/j.marenvres.2020.104950 · Cited by 18
Self-citationInsulin and IGF-I Receptor Structure and Binding Mechanism
MEYTS, P. D., Sajid, W., Palsgaard, J., Theede, A., Gauguin, L., Aladdin, H., & Whittaker, J. (2007) · Springer eBooks · doi:10.1007/978-0-387-72204-7_1 · Cited by 18
Topological Control of Life and Death in Non-Proliferative Epithelia
Martinand‐Mari, C., Maury, B., Rousset, F., Sahuquet, A., Mennessier, G., Rochal, S. B., Lorman, V., Mangeat, P. H., & Baghdiguian, S. (2009) · PLoS ONE · doi:10.1371/journal.pone.0004202 · Cited by 18
“Further interest has recently been raised with the sequencing and annotation of Ciona intestinalis and Ciona savignyi genomes [2,3].”
BackgroundDynamic changes in developmental gene expression in the basal chordate Ciona intestinalis
Kawashima, T., Satou, Y., Murakami, S. D., & Satoh, N. (2005) · Development Growth & Differentiation · doi:10.1111/j.1440-169x.2005.00794.x · Cited by 18
“This number of cDNA clusters (17 221) is larger than the number of protein-coding genes (∼16 000) estimated from the draft genome sequence (Dehal et al. 2002).”
BackgroundMethodInfluentialSelf-citationTranscriptional regulation of ZicL in the Ciona intestinalis embryo
Anno, C., Satou, A., & Fujiwara, S. (2006) · Development Genes and Evolution · doi:10.1007/s00427-006-0080-9 · Cited by 18
Inaba, K., Nomura, M., Nakajima, A., & Hozumi, A. (2007) · Developmental Dynamics · doi:10.1002/dvdy.21121 · Cited by 18
“By combining the testis EST information (Inaba et al., 2002) with the genome draft sequence (Dehal et al., 2002), we constructed a local database for the protein primary structure and for the mass of tryptic fragments (MSCITS), along with a Perl-based program, called PerMS, for protein…”
BackgroundMethodSelf-citationMcDougall, A., Lee, K. W.-M., & Dumollard, R. (2014) · Methods in molecular biology · doi:10.1007/978-1-62703-974-1_11 · Cited by 18
Ascidian follicle cells: Multifunctional adjuncts to maturation and development
Lambert, C. C. (2009) · Development Growth & Differentiation · doi:10.1111/j.1440-169x.2009.01127.x · Cited by 18
“genome size (16 000 protein coding genes) and known structure (Dehal et al. 2002), ascidians are highly stud-”
BackgroundPan-vertebrate conserved non-coding sequences associated with developmental regulation
Elgar, G. (2009) · Briefings in Functional Genomics and Proteomics · doi:10.1093/bfgp/elp033 · Cited by 18
Permanyer, J., Gonzàlez‐Duarte, R., & Albalat, R. (2003) · Genome biology · doi:10.1186/gb-2003-4-11-r73 · Cited by 18
“Background The ascidian Ciona intestinalis has joined the select group of fully sequenced genomes [1].”
BackgroundA genomewide survey of developmentally relevant genes in Ciona intestinalis
Kawashima, T., Tokuoka, M., Awazu, S., Satoh, N., & Satou, Y. (2003) · Development Genes and Evolution · doi:10.1007/s00427-003-0323-y · Cited by 18
“The draft genome of the basal chordate Ciona intestinalis has been determined (Dehal et al. 2002).”
BackgroundSelf-citationDanchin, É., & Pontarotti, P. (2004) · Journal of Molecular Evolution · doi:10.1007/s00239-004-2648-1 · Cited by 19
“2002) and Gallus gallus as well as for the Urochordate Ciona intestinalis (Dehal et al. 2002).”
BackgroundKugler, J. E., Wu, Y., Katikala, L., Passamaneck, Y. J., Addy, J., Caballero, N., Oda‐Ishii, I., Maguire, J. E., Li, R., & Gregorio, A. D. (2019) · Developmental Biology · doi:10.1016/j.ydbio.2019.01.002 · Cited by 17
Kuhl, H., Tine, M., Beck, A., Timmermann, B., Kodira, C. D., & Reinhardt, R. (2011) · Genomics · doi:10.1016/j.ygeno.2011.06.004 · Cited by 17
The Evolutionary Dynamics of Operon Distributions in Eukaryote Genomes
Cutter, A. D., & Agrawal, A. F. (2010) · Genetics · doi:10.1534/genetics.110.115766 · Cited by 17
“Species of Ciona, however, have exceptionally large Ne (Dehal et al. 2002; Vinson et al. 2005; Small et al. 2007).”
BackgroundThe Degenerate Tale of Ascidian Tails
Fodor, A., Powers, M. M., Andrykovich, K. R., Liu, J., Lowe, E. K., Brown, C. T., Gregorio, A. D., Stolfi, A., & Swalla, B. J. (2021) · Integrative and Comparative Biology · doi:10.1093/icb/icab022 · Cited by 17
Harada, Y., & Sawada, H. (2007) · Molecular Reproduction and Development · doi:10.1002/mrd.20616 · Cited by 17
“Ciona intestinalis is a close relative of H. roretzi, although in a different order, whose draft genome sequence was recently released (Dehal et al., 2002).”
BackgroundMolecular biology of ion motive proteins in comparative models
Wheatly, M. G., & Gao, Y. (2004) · Journal of Experimental Biology · doi:10.1242/jeb.01132 · Cited by 17
Neural complex-specific expression of xylosyl N-glycan in Ciona intestinalis
Yagi, H., Nakagawa, M., Takahashi, N., Kondo, S., Matsubara, M., & Kato, K. (2007) · Glycobiology · doi:10.1093/glycob/cwm128 · Cited by 17
“html) (Dehal et al. 2002; Satou et al. 2005), which shows that the Ciona genome contains approximately 16 000 protein-coding genes including those encoding putative enzymes catalyzing biosynthesis and processing of N-glycans.”
BackgroundGenomics Reveal Ancient Forms of Stanniocalcin in Amphioxus and Tunicate
Roch, G. J., & Sherwood, N. M. (2010) · Integrative and Comparative Biology · doi:10.1093/icb/icq010 · Cited by 17
Cell-Cycle Control in Oocytes and During Early Embryonic Cleavage Cycles in Ascidians
McDougall, A., Chenevert, J. M., & Dumollard, R. (2012) · International review of cytology · doi:10.1016/b978-0-12-394308-8.00006-6 · Cited by 17
Ohtsuka, Y., & Inagaki, H. (2020) · Scientific Reports · doi:10.1038/s41598-020-69485-y · Cited by 17
Wada, S., Hamada, M., Kobayashi, K., & Satoh, N. (2008) · Development Growth & Differentiation · doi:10.1111/j.1440-169x.2008.01012.x · Cited by 17
“The draft genome sequence of Ciona intestinalis has been determined (Dehal et al. 2002).”
BackgroundSelf-citationThe vitamin D3 transcriptomic response in skin cells derived from the Atlantic bottlenose dolphin
Ellis, B. C., Gattoni‐Celli, S., Mancia, A., & Kindy, M. S. (2009) · Developmental & Comparative Immunology · doi:10.1016/j.dci.2009.02.008 · Cited by 17
“The notion that the vitamin D pathway is functionally important beyond calcium metabolism and transport is supported by expression of VDR within several different organs and tissues [12–14] and within aquatic organisms lacking calcified skeletons, such as the sea lamprey [15] and sea squirts [16].”
BackgroundOrigine des vertébrés : la tunique fait-elle le moine ?
Delsuc, F., Baurain, D., & Philippe, H. (2006) · médecine/sciences · doi:10.1051/medsci/20062289688 · Cited by 17
“Parmi les Tuniciers, la Cione intestinale (Ciona intestinalis) est en passe de devenir l’un des animaux modèles les mieux caractérisés sur les plans génomique et développemental [1] après notamment le séquençage de son génome achevé en 2002 [2].”
BackgroundNilsson, I. B. M., Svensson, S., & Monstein, H. (2003) · Gene · doi:10.1016/j.gene.2003.09.002 · Cited by 17
Gyoja, F., Satou, Y., Shin‐I, T., Kohara, Y., Swalla, B. J., & Satoh, N. (2007) · Developmental Biology · doi:10.1016/j.ydbio.2007.03.035 · Cited by 17
Self-citationInoue, Y., Ogasawara, M., Moroi, T., Satake, M., Azumi, K., Moritomo, T., & Nakanishi, T. (2005) · Immunogenetics · doi:10.1007/s00251-005-0010-4 · Cited by 17
Self-citationYamaguchi, N., Amakawa, Y., Yamada, H., Ueki, T., & Michibata, H. (2006) · ZOOLOGICAL SCIENCE · doi:10.2108/zsj.23.909 · Cited by 17
Expression profiles of urbilaterian genes uniquely shared between honey bee and vertebrates
Matsui, T., Yamamoto, T., Wyder, S., Zdobnov, E. M., & Kadowaki, T. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-17 · Cited by 17
Evolutionary genomics of the recently duplicated amphioxus Hairy genes
Jiménez‐Delgado, S., Crespo, M., Permanyer, J., García‐Fernàndez, J., & Manzanares, M. (2006) · International Journal of Biological Sciences · doi:10.7150/ijbs.2.66 · Cited by 17
“Furthermore, we were unable to find any similarity in the available genomic sequences from amphioxus, nor in the urochordate Ciona intestinalis [37], the closest relative to amphioxus whose genome has been sequenced.”
Circadian clock in Ciona intestinalis revealed by microarray analysis and oxygen consumption
Minamoto, T., Hanai, S., Kadota, K., Oishi, K., Matsumae, H., Fujie, M., Azumi, K., Satoh, N., Satake, M., & Ishida, N. (2009) · The Journal of Biochemistry · doi:10.1093/jb/mvp160 · Cited by 17
Self-citationKhalturin, K., Kürn, U., Pinnow, N., & BOSCH, T. (2005) · Developmental & Comparative Immunology · doi:10.1016/j.dci.2005.01.006 · Cited by 17
“2%, which is nearly 15-fold more than that observed in humans and 3-fold more than that found in puffer fish [15].”
BackgroundZP genes in avian species illustrate the dynamic evolution of the vertebrate egg envelope
Hughes, D. C. (2007) · Cytogenetic and Genome Research · doi:10.1159/000103168 · Cited by 17
“Fax +41 61 306 12 34 E-Mail karger@karger.ch www.karger.com published data) also contain proteins with a ZP domain suggests that this motif was adopted by a common chordate ancestor approximately 550 million years ago (Dehal et al., 2002), and has been maintained by a diverse set of vertebrates.”
BackgroundMaglich, J. M., Sluder, A. E., Willson, T. M., & Moore, J. T. (2003) · American Journal of PharmacoGenomics · doi:10.2165/00129785-200303050-00005 · Cited by 17
“[16] Despite this, the provided one of the important clues linking this receptor to CYP3A sea squirt NR family had at least one representative of all of the gene regulation.”
BackgroundEvolutionary and Functional Diversification of the Vitamin D Receptor-Lithocholic Acid Partnership
Kollitz, E. M., Zhang, G., Hawkins, M. B., Whitfield, G. K., Reif, D. M., & Kullman, S. W. (2016) · PLoS ONE · doi:10.1371/journal.pone.0168278 · Cited by 16
Yamagishi, M., Huang, T., Hozumi, A., Onuma, T. A., Sasakura, Y., & Ogasawara, M. (2022) · Cell and Tissue Research · doi:10.1007/s00441-022-03679-w · Cited by 16
Self-citationEvaluation of drug toxicity profiles based on the phenotypes of ascidian Ciona intestinalis
Mizotani, Y., Itoh, S., Hotta, K., Tashiro, E., Oka, K., & Imoto, M. (2015) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2015.05.119 · Cited by 16
Self-citationProcurement and Culture of Ascidian Embryos
Swalla, B. J. (2004) · Methods in cell biology · doi:10.1016/s0091-679x(04)74006-6 · Cited by 16
The adaptive phenotype of cortical thymic epithelial cells
Boehm, T. L. J. (2009) · European Journal of Immunology · doi:10.1002/eji.200939315 · Cited by 16
Identification of chondroitin/dermatan sulfotransferases in the protochordate, Ciona intestinalis
Tetsukawa, A., Nakamura, J., & Fujiwara, S. (2010) · Comparative Biochemistry and Physiology Part B Biochemistry and Molecular Biology · doi:10.1016/j.cbpb.2010.06.009 · Cited by 16
“Next, a C. intestinalis genome database (Dehal et al., 2002; Satou et al., 2008; http://hoya.zool.kyoto-u.ac.jp/cgi-bin/gbrowse/kh/) was searched in a similar way.”
Ueki, T., Koike, K., Fukuba, I., & Yamaguchi, N. (2018) · ZOOLOGICAL SCIENCE · doi:10.2108/zs180051 · Cited by 16
Morphogenesis: a focus on marine invertebrates
Lv, Z., Lu, Q., & Dong, B. (2019) · Marine Life Science & Technology · doi:10.1007/s42995-019-00016-z · Cited by 16
Osugi, T., Miyasaka, N., Shiraishi, A., Matsubara, S., & Satake, H. (2021) · Scientific Reports · doi:10.1038/s41598-021-90295-3 · Cited by 16
Ueki, T., Shintaku, K., Yonekawa, Y., Takatsu, N., Yamada, H., Hamada, T., Hirota, H., & Michibata, H. (2007) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2007.02.003 · Cited by 16
The chordate ancestor possessed a single copy of the Brachyury gene for notochord acquisition
Inoue, J. G., Yasuoka, Y., Takahashi, H., & Satoh, N. (2017) · Zoological Letters · doi:10.1186/s40851-017-0064-9 · Cited by 14
“In contrast, urochordates have only a single copy [20].”
Self-citationPatel, B., Banerjee, R., Samanta, M., & Das, S. (2018) · Molecular Biotechnology · doi:10.1007/s12033-018-0081-8 · Cited by 16
Three multi-allelic gene pairs are responsible for self-sterility in the ascidian Ciona intestinalis
Sawada, H., Yamamoto, K., Yamaguchi, A., Yamada, L., Higuchi, A., Nukaya, H., Fukuoka, M., Sakuma, T., Yamamoto, T., Sasakura, Y., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-59147-4 · Cited by 16
Self-citationHammond, J. A., Nakao, M., & SMITH, V. (2004) · Molecular Immunology · doi:10.1016/j.molimm.2004.09.017 · Cited by 16
Okamura, Y., Izumi‐Nakaseko, H., Nakajo, K., Ohtsuka, Y., & Ebihara, T. (2003) · Neurosignals · doi:10.1159/000072161 · Cited by 16
Takada, N., Yamaguchi, H., Shida, K., Terajima, D., Satou, Y., Kasuya, A., Satoh, N., Satake, M., & Wang, H. (2005) · APOPTOSIS · doi:10.1007/s10495-005-1391-4 · Cited by 16
Self-citationYamada, S., Hotta, K., Yamamoto, T. S., Ueno, N., Satoh, N., & Takahashi, H. (2009) · Developmental Biology · doi:10.1016/j.ydbio.2008.12.037 · Cited by 16
Self-citationAspects of cell production in mantle tissue of Ciona intestinalis L. (Tunicata, Ascidiacea)
Bella, M. A. D., Carbone, M. C., & Leo, G. D. (2005) · Micron · doi:10.1016/j.micron.2005.01.007 · Cited by 16
Marino, R., Melillo, D., Filippo, M. D., Yamada, A., Pinto, M. R., Santis, R. D., Brown, E. R., & Matassi, G. (2007) · The Journal of Comparative Neurology · doi:10.1002/cne.21370 · Cited by 16
“Two AMT genes are present in the completely sequenced genome of C. intestinalis (Dehal et al., 2002), which we have named Ci-AMT1a and Ci-AMT1b (gene models ci0100150376 and ci0100147628, respectively; Joint Genome Institute, C. intestinalis v1.”
BackgroundSelf-citationEgertová, M., & Elphick, M. R. (2007) · The Journal of Comparative Neurology · doi:10.1002/cne.21331 · Cited by 16
“With the availability of the Ciona intestinalis genome sequence (Dehal et al., 2002), it should in due course be possible to identify all of the genes encoding enzymes and precursor proteins involved in generation of neuroactive molecules such as amines and neuropeptides.”
BackgroundPhylogeny, taxonomy, and evolution of the endothelin receptor gene family
Hyndman, K. A., Miyamoto, M. M., & Evans, D. H. (2009) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2009.04.015 · Cited by 16
Fluorescentin situHybridization to Ascidian Chromosomes
Shoguchi, E., Ikuta, T., Yoshizaki, F., Satou, Y., Satoh, N., Asano, K., Saiga, H., & Nishikata, T. (2004) · ZOOLOGICAL SCIENCE · doi:10.2108/zsj.21.153 · Cited by 16
“The C. intestinalis draft genome consists of ~3,500 scaffolds, although nearly 60 Mbp sequences are covered with 119 scaffolds longer than 190 kb (Dehal et al ., 2002).”
BackgroundInfluentialSelf-citationMarine systems: moving into the genomics era
Wilson, K., Thorndyke, M. C., Nilsen, F., Rogers, A. D., & Martı́nez, P. (2005) · Marine Ecology · doi:10.1111/j.1439-0485.2005.00041.x · Cited by 16
“Whilst examples of single-gene changes directly responsible for the acquisition of new adaptive traits are rare (but see de Bono & Bargmann 1998; Rogers et al. 2003), we believe that the characterization of QTLs is an avenue that should be explored further in marine animals, because they can provide more accurate mult…”
BackgroundCleto, C. (2003) · Molecular Biology and Evolution · doi:10.1093/molbev/msg227 · Cited by 16
“Moreover, the available Ciona genome sequence data, which are thought to be near-complete, suggest that Ci-TnI is the only TnI gene in Ciona (Dehal et al. 2002); there is no evidence for an additional gene, either closely or distantly related, that might encode a C-terminally truncated isoform…”
InfluentialAncestral glycoprotein hormone-receptor pathway controls growth in C. elegans
Kenis, S., Istiban, M. N., Damme, S. V., Vandewyer, E., Watteyne, J., Schoofs, L., & Beets, I. (2023) · Frontiers in Endocrinology · doi:10.3389/fendo.2023.1200407 · Cited by 15
Nagy, A., Bányai, L., & Patthy, L. (2011) · Genes · doi:10.3390/genes2030516 · Cited by 15
Transcriptional Enhancers in Ascidian Development
Wang, W., & Christiaen, L. (2012) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/b978-0-12-386499-4.00006-9 · Cited by 16
Embryo Microinjection and Electroporation in the Chordate Ciona intestinalis
Kari, W., Zeng, F., Zitzelsberger, L., Will, J., & Rothbächer, U. (2016) · Journal of Visualized Experiments · doi:10.3791/54313 · Cited by 15
Tigano, A., Sackton, T. B., & Friesen, V. L. (2017) · Molecular Ecology Resources · doi:10.1111/1755-0998.12712 · Cited by 15
“, 2016), our analyses show that high genomic heterozygosity can negatively affect the quality of genome assembly, as has been shown in other taxa (Dehal et al., 2002; Kajitani et al., 2014; Vinson et al., 2005; Zhang et al., 2012).”
BackgroundImprovement of molecular phylogenetic inference and the phylogeny of Bilateria
Lartillot, N., & Philippe, H. (2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.003.0012 · Cited by 15
Simple model systems: a challenge for Alzheimer's disease
Carlo, M. D. (2012) · Immunity & Ageing · doi:10.1186/1742-4933-9-3 · Cited by 17
“Ciona intestinalis has attracted the interest of biologists for developmental studies and its mitochondrial and nuclear genomes have been sequenced [50].”
BackgroundGee, H. (2008) · Nature · doi:10.1038/453999a · Cited by 15
The carboxylesterase/cholinesterase gene family in invertebrate deuterostomes
Johnson, G., & Moore, S. W. (2011) · Comparative Biochemistry and Physiology Part D Genomics and Proteomics · doi:10.1016/j.cbd.2011.11.003 · Cited by 15
Selection of Surrogate Animal Species for Comparative Toxicogenomics
Denslow, N. D., Colbourne, J. K., Dix, D. J., Freedman, J. H., Helbing, C. C., Kennedy, S. W., & Williams, P. L. (2006) · CRC Press eBooks · doi:10.1201/9781420043648.ch2 · Cited by 15
Accuracy Assessment of Diploid Consensus Sequences
Kim, J., Waterman, M., & Li, L. (2007) · IEEE/ACM Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2007.1007 · Cited by 11
“Based on this likelihood calculation, we define a confidence score for estimated haplotypes.”
BackgroundMethod
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
