F. Delsuc, H. Brinkmann, D. Chourrout, and H. Philippe, Tunicates and not cephalochordates are the closest living relatives of vertebrates, Nature, vol.13, issue.7079, pp.965-968, 2006.
DOI : 10.1038/nature04336

URL : https://hal.archives-ouvertes.fr/halsde-00315436

P. Lemaire, Evolutionary crossroads in developmental biology: the tunicates, Development, vol.138, issue.11, pp.2143-2152, 2011.
DOI : 10.1242/dev.048975

URL : https://hal.archives-ouvertes.fr/hal-00649744

L. Chabry, Embryologie normale et tératologique des Ascidies Felix Alcan Editeur, 1887.

E. Conklin, The organization and cell lineage of the ascidian egg, J. Acad. Nat. Sci. Phila, vol.13, pp.1-119, 1905.

W. R. Jeffery and B. J. Swalla, Evolution of alternate modes of development in ascidians, BioEssays, vol.2, issue.4, pp.219-226, 1992.
DOI : 10.1002/bies.950140404

R. Diogo, R. G. Kelly, L. Christiaen, M. Levine, J. M. Ziermann et al., A new heart for a new head in vertebrate cardiopharyngeal evolution, Nature, vol.112, issue.7548, pp.466-473, 2015.
DOI : 10.1038/nature14435

URL : https://hal.archives-ouvertes.fr/hal-01432404

N. Kaplan, F. Razy-krajka, and L. Christiaen, Regulation and evolution of cardiopharyngeal cell identity and behavior: insights from simple chordates, Current Opinion in Genetics & Development, vol.32, pp.119-128, 2015.
DOI : 10.1016/j.gde.2015.02.008

P. Dehal, Y. Satou, R. K. Campbell, J. Chapman, B. Degnan et al., The Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins, Science, vol.298, issue.5601, pp.2157-2167, 2002.
DOI : 10.1126/science.1080049

URL : https://hal.archives-ouvertes.fr/hal-00311352

J. C. Corbo, M. Levine, and R. W. Zeller, Characterization of a notochord-specific enhancer from the Brachyury promoter region of the ascidian, Ciona intestinalis, Dev. Camb. Engl, vol.124, pp.589-602, 1997.

L. Christiaen, E. Wagner, W. Shi, and M. Levine, Microinjection of Morpholino Oligos and RNAs in Sea Squirt (Ciona) Embryos, Cold Spring Harbor Protocols, vol.2009, issue.12, 2009.
DOI : 10.1101/pdb.prot5347

Y. Satou, K. S. Imai, and N. Satoh, Action of morpholinos inCiona embryos, genesis, vol.122, issue.3, pp.103-106, 2000.
DOI : 10.1002/gene.1040

A. Stolfi, S. Gandhi, F. Salek, and L. Christiaen, Tissue-specific genome editing in Ciona embryos by CRISPR/Cas9, Development, vol.141, issue.21, pp.4115-4120, 2014.
DOI : 10.1242/dev.114488

K. Yoshida, N. Treen, A. Hozumi, T. Sakuma, T. Yamamoto et al., with TALE nucleases, genesis, vol.13, issue.5, pp.431-439, 2000.
DOI : 10.1002/dvg.22770

N. Treen, K. Yoshida, T. Sakuma, H. Sasaki, N. Kawai et al., Tissue-specific and ubiquitous gene knockouts by TALEN electroporation provide new approaches to investigating gene function in Ciona, Development, vol.141, issue.2, pp.481-487, 2014.
DOI : 10.1242/dev.099572

N. Sierro, T. Kusakabe, K. Park, R. Yamashita, K. Kinoshita et al., DBTGR: a database of tunicate promoters and their regulatory elements, Nucleic Acids Research, vol.34, issue.90001, pp.552-555, 2006.
DOI : 10.1093/nar/gkj064

W. Wang and L. Christiaen, Transcriptional Enhancers in Ascidian Development, Curr. Top. Dev. Biol, vol.98, pp.147-172, 2012.
DOI : 10.1016/B978-0-12-386499-4.00006-9

Y. Satou, L. Yamada, Y. Mochizuki, N. Takatori, T. Kawashima et al., A cDNA resource from the basal chordateCiona intestinalis, genesis, vol.1, issue.4, pp.153-154, 2000.
DOI : 10.1002/gene.10119

M. J. Gilchrist, D. Sobral, P. Khoueiry, F. Daian, B. Laporte et al., A pipeline for the systematic identification of non-redundant full-ORF cDNAs for polymorphic and evolutionary divergent genomes: Application to the ascidian Ciona intestinalis, Developmental Biology, vol.404, issue.2, pp.149-163, 2015.
DOI : 10.1016/j.ydbio.2015.05.014

A. Kubo, N. Suzuki, X. Yuan, K. Nakai, N. Satoh et al., Genomic cis-regulatory networks in the early Ciona intestinalis embryo, Development, vol.137, issue.10, pp.1613-1623, 2010.
DOI : 10.1242/dev.046789

K. S. Imai, M. Levine, N. Satoh, and Y. Satou, Regulatory Blueprint for a Chordate Embryo, Science, vol.312, issue.5777, pp.312-1183, 2006.
DOI : 10.1126/science.1123404

U. Rothbächer, V. Bertrand, C. Lamy, and P. Lemaire, A combinatorial code of maternal GATA, Ets and beta-catenin-TCF transcription factors specifies and patterns the early ascidian ectoderm, Dev. Camb. Engl, vol.134, pp.4023-4032, 2007.

C. Lamy, U. Rothbächer, D. Caillol, and P. Lemaire, Ci-FoxA-a is the earliest zygotic determinant of the ascidian anterior ectoderm and directly activates Ci-sFRP1/5, Development, vol.133, issue.15, pp.2835-2844, 2006.
DOI : 10.1242/dev.02448

URL : https://hal.archives-ouvertes.fr/hal-00088579

V. Bertrand, C. Hudson, D. Caillol, C. Popovici, and P. Lemaire, Neural Tissue in Ascidian Embryos Is Induced by FGF9/16/20, Acting via a Combination of Maternal GATA and Ets Transcription Factors, Cell, vol.115, issue.5, pp.615-627, 2003.
DOI : 10.1016/S0092-8674(03)00928-0

A. Stolfi, T. B. Gainous, J. J. Young, A. Mori, M. Levine et al., Early Chordate Origins of the Vertebrate Second Heart Field, Science, vol.329, issue.5991, pp.565-568, 2010.
DOI : 10.1126/science.1190181

B. Davidson, W. Shi, J. Beh, L. Christiaen, and M. Levine, FGF signaling delineates the cardiac progenitor field in the simple chordate, Ciona intestinalis, Genes & Development, vol.20, issue.19, pp.2728-2738, 2006.
DOI : 10.1101/gad.1467706

F. Razy-krajka, K. Lam, W. Wang, A. Stolfi, M. Joly et al., Collier/OLF/EBF-Dependent Transcriptional Dynamics Control Pharyngeal Muscle Specification from Primed Cardiopharyngeal Progenitors, Developmental Cell, vol.29, issue.3, pp.263-276, 2014.
DOI : 10.1016/j.devcel.2014.04.001

W. Wang, F. Razy-krajka, E. Siu, A. Ketcham, and L. Christiaen, NK4 Antagonizes Tbx1/10 to Promote Cardiac versus Pharyngeal Muscle Fate in the Ascidian Second Heart Field, PLoS Biology, vol.133, issue.2, 2013.
DOI : 10.1371/journal.pbio.1001725.s010

P. B. Abitua, E. Wagner, I. A. Navarrete, and M. Levine, Identification of a rudimentary neural crest in a non-vertebrate chordate, Nature, vol.138, issue.7427, pp.104-107, 2012.
DOI : 10.1038/nature11589

L. Christiaen, B. Davidson, T. Kawashima, W. Powell, H. Nolla et al., The Transcription/Migration Interface in Heart Precursors of Ciona intestinalis, Science, vol.320, issue.5881, pp.1349-1352, 2008.
DOI : 10.1126/science.1158170

J. H. Imai and I. A. Meinertzhagen, : I. Central nervous system, The Journal of Comparative Neurology, vol.83, issue.3, pp.316-334, 2007.
DOI : 10.1002/cne.21246

J. H. Imai and I. A. Meinertzhagen, : II. Peripheral nervous system, The Journal of Comparative Neurology, vol.78, issue.3, pp.335-352, 2007.
DOI : 10.1002/cne.21247

Y. Sasakura, K. Mita, Y. Ogura, and T. Horie, Ascidians as excellent chordate models for studying the development of the nervous system during embryogenesis and metamorphosis, Development, Growth & Differentiation, vol.446, issue.3, pp.420-437, 2012.
DOI : 10.1111/j.1440-169X.2012.01343.x

A. Hozumi, T. Horie, and Y. Sasakura, Neuronal map reveals the highly regionalized pattern of the juvenile central nervous system of the ascidian Ciona intestinalis, Dev. Dyn, 2015.

H. Nishida, Cell lineage analysis in ascidian embryos by intracellular injection of a tracer enzyme, Developmental Biology, vol.121, issue.2, pp.526-541, 1987.
DOI : 10.1016/0012-1606(87)90188-6

C. Hudson and H. Yasuo, Similarity and diversity in mechanisms of muscle fate induction between ascidian species, Biology of the Cell, vol.37, issue.5, pp.265-277, 2008.
DOI : 10.1042/BC20070144

J. R. True and E. S. Haag, Developmental system drift and flexibility in evolutionary trajectories, Evolution and Development, vol.122, issue.2, pp.109-119, 2001.
DOI : 10.1101/gad.189500

V. J. Lynch, Use with caution: Developmental systems divergence and potential pitfalls of animal models, Yale J. Biol. Med, vol.82, pp.53-66, 2009.

M. Hamada, S. Goricki, M. S. Byerly, N. Satoh, and W. R. Jeffery, Evolution of the chordate regeneration blastema: Differential gene expression and conserved role of notch signaling during siphon regeneration in the ascidian Ciona, Developmental Biology, vol.405, issue.2, pp.304-315, 2015.
DOI : 10.1016/j.ydbio.2015.07.017

A. Voskoboynik and I. L. Weissman, , an emerging model for the study of aging, stem cells, and mechanisms of regeneration, Invertebrate Reproduction & Development, vol.37, issue.sup1, pp.33-38, 2015.
DOI : 10.1016/j.devcel.2013.01.001

A. Voskoboynik, N. F. Neff, D. Sahoo, A. M. Newman, D. Pushkarev et al., The genome sequence of the colonial chordate, p.569, 2013.

A. Voskoboynik, A. M. Newman, D. M. Corey, D. Sahoo, D. Pushkarev et al., Identification of a Colonial Chordate Histocompatibility Gene, Science, vol.341, issue.6144, pp.384-387, 2013.
DOI : 10.1126/science.1238036

D. Tomaso, A. W. Nyholm, S. V. Palmeri, K. J. Ishizuka, K. J. Ludington et al., Isolation and characterization of a protochordate histocompatibility locus, Nature, vol.220, issue.7067, pp.454-459, 2005.
DOI : 10.1038/nature04150

M. J. Virata and R. W. Zeller, Ascidians: an invertebrate chordate model to study Alzheimer's disease pathogenesis, Disease Models & Mechanisms, vol.3, issue.5-6, pp.377-385, 2010.
DOI : 10.1242/dmm.003434

O. Tassy, D. Dauga, F. Daian, D. Sobral, F. Robin et al., The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program, Genome Research, vol.20, issue.10, pp.1459-1468, 2010.
DOI : 10.1101/gr.108175.110

URL : https://hal.archives-ouvertes.fr/hal-00555212

L. Wolpert, The Unnatural Nature of Science, The Lancet, vol.341, issue.8840, 1994.
DOI : 10.1016/0140-6736(93)92665-G

A. M. Klein, L. Mazutis, I. Akartuna, N. Tallapragada, A. Veres et al., Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells, Cell, vol.161, issue.5, pp.1187-1201, 2015.
DOI : 10.1016/j.cell.2015.04.044

E. Z. Macosko, A. Basu, R. Satija, J. Nemesh, K. Shekhar et al., Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets, Cell, vol.161, issue.5, pp.1202-1214, 2015.
DOI : 10.1016/j.cell.2015.05.002

T. Hashimshony, F. Wagner, N. Sher, and I. Yanai, CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification, Cell Reports, vol.2, issue.3, pp.666-673, 2012.
DOI : 10.1016/j.celrep.2012.08.003

M. Lovett, The applications of single-cell genomics, Human Molecular Genetics, vol.22, issue.R1, pp.22-26, 2013.
DOI : 10.1093/hmg/ddt377

C. J. Mungall and D. B. Emmert, A Chado case study: an ontology-based modular schema for representing genome-associated biological information, Bioinformatics, vol.23, issue.13, pp.337-346, 2007.
DOI : 10.1093/bioinformatics/btm189

M. E. Skinner, A. V. Uzilov, L. D. Stein, C. J. Mungall, and I. H. Holmes, JBrowse: A next-generation genome browser, Genome Research, vol.19, issue.9, 2009.
DOI : 10.1101/gr.094607.109

D. Blankenberg, N. Coraor, V. Kuster, G. Taylor, J. Nekrutenko et al., Integrating diverse databases into an unified analysis framework: a Galaxy approach, Database, vol.2011, issue.0, p.11, 2011.
DOI : 10.1093/database/bar011

C. J. Mungall, C. Batchelor, and K. Eilbeck, Evolution of the Sequence Ontology terms and relationships, Journal of Biomedical Informatics, vol.44, issue.1, pp.87-93, 2011.
DOI : 10.1016/j.jbi.2010.03.002

K. Degtyarenko, J. Hastings, P. De-matos, and M. Ennis, ChEBI: An Open Bioinformatics and Cheminformatics Resource, Curr. Protoc. Bioinforma., Chapter, vol.12, 2009.
DOI : 10.1002/0471250953.bi1409s26

M. C. Chibucos, C. J. Mungall, R. Balakrishnan, K. R. Christie, R. P. Huntley et al., Standardized description of scientific evidence using the Evidence Ontology (ECO), Database, vol.2014, issue.0, p.75, 2014.
DOI : 10.1093/database/bau075

Y. Satou, K. Mineta, M. Ogasawara, Y. Sasakura, E. Shoguchi et al., Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations, Genome Biology, vol.9, issue.10, p.152, 2008.
DOI : 10.1186/gb-2008-9-10-r152

URL : https://hal.archives-ouvertes.fr/hal-00566607

G. Tsagkogeorga, V. Cahais, and N. Galtier, The Population Genomics of a Fast Evolver: High Levels of Diversity, Functional Constraint, and Molecular Adaptation in the Tunicate Ciona intestinalis, Genome Biology and Evolution, vol.4, issue.8, pp.740-749, 2012.
DOI : 10.1093/gbe/evs054

M. L. Nydam and R. G. Harrison, Polymorphism and divergence within the ascidian genus Ciona, Molecular Phylogenetics and Evolution, vol.56, issue.2, pp.718-726, 2010.
DOI : 10.1016/j.ympev.2010.03.042

R. Pennati, G. F. Ficetola, R. Brunetti, F. Caicci, F. Gasparini et al., Morphological Differences between Larvae of the Ciona intestinalis Species Complex: Hints for a Valid Taxonomic Definition of Distinct Species, PLOS ONE, vol.15, issue.5, p.122879, 2015.
DOI : 10.1371/journal.pone.0122879.s005

C. Roux, G. Tsagkogeorga, N. Bierne, and N. Galtier, Crossing the Species Barrier: Genomic Hotspots of Introgression between Two Highly Divergent Ciona intestinalis Species, Molecular Biology and Evolution, vol.30, issue.7, pp.1574-1587, 2013.
DOI : 10.1093/molbev/mst066

P. Jones, D. Binns, H. Chang, M. Fraser, W. Li et al., InterProScan 5: genome-scale protein function classification, Bioinformatics, vol.30, issue.9, pp.1236-1240, 2014.
DOI : 10.1093/bioinformatics/btu031

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998142

L. Li, C. J. Stoeckert, and D. S. Roos, OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes, Genome Research, vol.13, issue.9, pp.2178-2189, 2003.
DOI : 10.1101/gr.1224503

G. Ostlund, T. Schmitt, K. Forslund, T. Ostler, D. N. Messina et al., InParanoid 7: new algorithms and tools for eukaryotic orthology analysis, Nucleic Acids Research, vol.38, issue.Database, pp.196-203, 2010.
DOI : 10.1093/nar/gkp931

A. Mitchell, H. Chang, L. Daugherty, M. Fraser, S. Hunter et al., The InterPro protein families database: the classification resource after 15 years, Nucleic Acids Research, vol.43, issue.D1, pp.213-221, 2015.
DOI : 10.1093/nar/gku1243

URL : https://hal.archives-ouvertes.fr/hal-01222896

A. Stolfi, Y. Sasakura, D. Chalopin, Y. Satou, L. Christiaen et al., Guidelines for the nomenclature of genetic elements in tunicate genomes, genesis, vol.35, issue.2, pp.1-14, 2000.
DOI : 10.1002/dvg.22822

URL : https://hal.archives-ouvertes.fr/hal-01432425

K. Hotta, K. Mitsuhara, H. Takahashi, K. Inaba, K. Oka et al., A web-based interactive developmental table for the ascidian Ciona intestinalis, including 3D real-image embryo reconstructions: I. From fertilized egg to hatching larva, Dev. Dyn. Off. Publ. Am. Assoc. Anat, vol.236, pp.1790-1805, 2007.

C. E. Van-slyke, Y. M. Bradford, M. Westerfield, and M. A. Haendel, The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio, Journal of Biomedical Semantics, vol.5, issue.1, p.12, 2014.
DOI : 10.1093/bioinformatics/btm112

P. L. Whetzel, N. F. Noy, N. H. Shah, P. R. Alexander, C. Nyulas et al., BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications, Nucleic Acids Research, vol.39, issue.suppl, pp.541-545, 2011.
DOI : 10.1093/nar/gkr469

O. Tassy, F. Daian, C. Hudson, V. Bertrand, and P. Lemaire, A Quantitative Approach to the Study of Cell Shapes and Interactions during Early Chordate Embryogenesis, Current Biology, vol.16, issue.4, pp.345-358, 2006.
DOI : 10.1016/j.cub.2005.12.044

URL : https://hal.archives-ouvertes.fr/hal-00088466

K. S. Small, M. Brudno, M. M. Hill, and A. Sidow, A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome, Genome Biology, vol.8, issue.3, p.41, 2007.
DOI : 10.1186/gb-2007-8-3-r41

E. W. Deutsch, C. A. Ball, J. J. Berman, G. S. Bova, A. Brazma et al., Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE), Nature Biotechnology, vol.10, issue.3, pp.305-312, 2008.
DOI : 10.1038/nbt1391

J. D. Buenrostro, P. G. Giresi, L. C. Zaba, H. Y. Chang, and W. J. Greenleaf, Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position, Nature Methods, vol.10, issue.12, pp.1213-1218, 2013.
DOI : 10.1073/pnas.95.25.14863

B. Lenhard, A. Sandelin, L. Mendoza, P. Engströmengstr¨engström, N. Jareborg et al., Identification of conserved regulatory elements by comparative genome analysis, Journal of Biology, vol.2, issue.2, p.13, 2003.
DOI : 10.1186/1475-4924-2-13

K. Sherrard, F. Robin, P. Lemaire, and E. Munro, Sequential Activation of Apical and Basolateral Contractility Drives Ascidian Endoderm Invagination, Current Biology, vol.20, issue.17, pp.1499-1510, 2010.
DOI : 10.1016/j.cub.2010.06.075

URL : https://hal.archives-ouvertes.fr/hal-00566790

M. J. Nakamura, J. Terai, R. Okubo, K. Hotta, and K. Oka, Three-dimensional anatomy of the Ciona intestinalis tailbud embryo at single-cell resolution, Developmental Biology, vol.372, issue.2, pp.274-284, 2012.
DOI : 10.1016/j.ydbio.2012.09.007

M. T. Veeman and W. C. Smith, Whole-organ cell shape analysis reveals the developmental basis of ascidian notochord taper, Developmental Biology, vol.373, issue.2, pp.281-289, 2013.
DOI : 10.1016/j.ydbio.2012.11.009