References
Azumi K,
Sabau SV,
Fujie M et al.
(2007)
Gene expression profile during the life cycle of the urochordate Ciona intestinalis.
Developmental Biology
308:
572–582.
Christiaen L,
Davidson B,
Kawashima T et al.
(2008)
The transcription/migration interface in heart precursors of Ciona intestinalis.
Science
320:
1349–1352.
Cloney L
(1978)
Ascidian metamophosis; review and analysis.
In: Chia F‐S and
Rice ME (eds)
Settlement and Metamorphosis of Marine Invertebrate Larvae,
pp. 255–282.
Amsterdam: Elsevier.
Conklin EG
(1905)
The organization and cell lineage of the ascidian egg.
Journal of the Academy of Natural Sciences of Philadelphia
13:
1–119.
Corbo JC,
Levine M and
Zeller RW
(1997)
Characterization of a notochord‐specific enhancer from the Brachyury promoter region of the ascidian, Ciona intestinalis.
Development
124:
589–602.
Davidson B
(2007)
Ciona intestinalis as a model for cardiac development.
Seminars in Cell and Developmental Biology
18:
16–26.
Davidson B,
Shi W,
Beb J,
Christiaen L and
Levine M
(2006)
FGF signaling delineates the cardiac progenitor field in the simple chordate, Ciona intestinalis.
Genes and Development
20:
2728–2738.
Davidson EH
(2006)
The Regulatory Genome. Gene Regulatory Networks in Development and Evolution.
San Diego, CA: Academic Press.
Dehal P,
Satou Y,
Campbell RK et al.
(2002)
The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins.
Science
298:
2157–2167.
Di Gregorio A and
Levine M
(2002)
Analyzing gene regulation in ascidian embryos: new tools for new perspectives.
Differentiation
70:
132–139.
Gilbert S
(2010)
Developmental Biology,
9th edn.
Sunderland, MA: Sinauer Associates, Inc.
Hamada M,
Shimozono N,
Ohta N et al.
(2011)
Expression of neuropeptide‐ and hormone‐encoding genes in the Ciona intestinalis larval brain.
Developmental Biology
352:
202–214.
Hirano T and
Nishida H
(1997)
Developmental fates of larval tissues after metamorphosis in ascidian Halocynthia roretzi. I. Origin of mesodermal tissues of the juvenile.
Developmental Biology
192:
199–210.
Horie T,
Shinki R,
Ogura Y et al.
(2011)
Ependymal cells of chordate larvae are stem‐like cells that form the adult nervous system.
Nature
469:
525–528.
Hotta K,
Takahashi H,
Satoh N and
Gojobori T
(2008)
Brachyury‐downstream gene sets in a chordate, Ciona intestinalis: integrating notochord specification, morphogenesis and chordate evolution.
Evolution and Development
10:
37–51.
Ikuta T,
Satoh N and
Saiga H
(2010)
Limited functions of Hox genes in the larval development of the ascidian Ciona intestinalis.
Development
137:
1505–1513.
Ikuta T,
Yoshida N,
Satoh N and
Saiga H
(2004)
Ciona intestinalis Hox gene cluster: its dispersed structure and residual colinear expression in development.
Proceedings of the National Academy of Sciences of the USA
101:
15118–15123.
Imai KS,
Hino K,
Yagi K,
Satoh N and
Satou Y
(2004)
Gene expression profiles of transcription factors and signaling molecules in the ascidian embryo: towards a comprehensive understanding of gene networks.
Development
131:
4047–4058.
Imai KS,
Levine M,
Satoh N and
Satou Y
(2006)
Regulatory blueprint for a chordate embryo.
Science
312:
1183–1187.
Imai KS,
Stolfi A,
Levine M and
Satou Y
(2009)
Gene regulatory networks underlying the compartmentalization of the Ciona central nervous system.
Development
136:
285–293.
Johnson DS,
Davidson B,
Brown CD et al.
(2004)
Noncoding regulatory sequences of Ciona exhibit strong correspondence between evolutionary constraint and functional importance.
Genome Research
14:
2448–2456.
Joly JS,
Kano S,
Matsuoka T et al.
(2007)
Culture of Ciona intestinalis in closed systems.
Developmental Dynamics
236:
1832–1840.
Keys DN,
Lee BI,
Di Gregorio A et al.
(2005)
A saturation screen for cis‐acting regulatory DNA in the Hox genes of Ciona intestinalis.
Proceedings of the National Academy of Sciences of the USA
102:
679–683.
Khoueiry P,
Rothbacher U,
Ohtsuka Y et al.
(2010)
A cis‐regulatory signature in ascidians and flies, independent of transcription factor binding sites.
Current Biology
20:
792–802.
Kumano G and
Nishida H
(2007)
Ascidian embryonic development: an emerging model system for the study of cell fate specification in chordates.
Developmental Dynamics
236:
1732–1746.
Kusakabe T,
Yoshida R,
Ikeda Y and
Tsuda M
(2004)
Computational discovery of DNA motifs associated with cell if type‐specfic gene expression in Ciona.
Developmental Biology
276:
563–580.
Lemaire P
(2009)
Unfolding a chordate developmental program, one cell at a time: invariant cell lineages, short‐range inductions and evolutionary plasticity in ascidians.
Developmental Biology
332:
48–60.
Nakatani Y and
Nishida H
(1994)
Induction of notochord during ascidian embryogenesis.
Developmental Biology
166:
289–299.
Nakatani Y,
Moody R and
Smith WC
(1999)
Mutations affecting tail and notochord development in the ascidian Ciona savignyi.
Development
126:
3293–3301.
Nishida H
(1987)
Cell lineage analysis in ascidian embryos by intracellular injection of a tracer enzyme III. Up to the tissue restricted stage.
Developmental Biology
121:
526–541.
Nishida H
(2005)
Specification of embryonic axis and mosaic development in ascidians.
Developmental Dynamics
233:
1177–1193.
Nishiyama A and
Fujiwara S
(2008)
RNA interference by expressing short hairpin RNA in the Ciona intestinalis embryo.
Development, Growth and Differentiation
50:
521–529.
Reverberi G
(1971)
Ascidians.
In: Reverberi G (ed.)
Experimental Embryology of Marine and Fresh‐water Invertebrates,
pp. 507–550.
Amsterdam: North Holland.
Rosner A,
Rabinowitz C,
Moiseeva E et al.
(2007)
BS‐Cadherin in the colonial urochordate Botryllus schlosseri: one protein, many functions.
Developmental Biology
304:
687–700.
Sasakura Y
(2007)
Germline transgenesis and insertional mutagenesis in the ascidian Ciona intestinalis.
Developmental Dynamics
236:
1758–1767.
Sasakura Y,
Awazu S,
Chiba S and
Satoh N
(2003)
Germ‐line transgenesis of the Tc1/mariner superfamily transposon Minos in Ciona intestinalis.
Proceedings of the National Academy of Sciences of the USA
100:
7726–7730.
Sasakura Y,
Kanda M,
Ikeda T et al.
(2012)
Retinoic acid‐driven Hox1 is required in the epidermis for forming the otic/atrial placodes during ascidian metamorphosis.
Development
139:
2156–2160.
Sasakura Y,
Nakashima K,
Awazu S et al.
(2005)
Trnsposon‐mediated insertional mutagenesis revealed the functions of animal cellulose synthase in the ascidian Ciona intestinalis.
Proceedings of the National Academy of Sciences of the USA
102:
15134–15139.
Satoh N
(1994)
Developmental Biology of Ascidians.
Cambridge: Cambridge University Press.
Satoh N,
Satou Y,
Davidson B and
Levine M
(2003)
Ciona intestinalis: an emerging model for whole‐genome analyses.
Trends in Genetics
19:
376–381.
Satou Y and
Satoh N
(1996)
Two cis‐regulatory elements are essential for the muscle‐specific expression of an actin gene in the ascidian embryo.
Development Growth & Differentiation
38:
565–573.
Satou Y and
Satoh N
(2003)
Genomewide surveys of developmentally relevant genes in Ciona intestinalis.
Development Genes and Evolution
213:
211–212.
Satou Y,
Mineta K,
Ogasawara M et al.
(2008)
Improved genome assembly and evidence‐based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations.
Genome Biology
9:
R152.
Shi W,
Levine M and
Davidson B
(2005)
Unraveling genomic regulatory networks in the simple chordate, Ciona intestinalis.
Genome Research
15:
1668–1674.
Shoguchi E,
Hamaguchi M and
Satoh N
(2008)
Genome‐wide network of regulatory genes for construction of a chordate embryo.
Developmental Biology
316:
498–509.
Shoguchi E,
Kawashima T,
Satou Y et al.
(2006)
Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis.
Genome Research
16:
297–303.
Small KS,
Brudno M,
Hill MM and
Sidow A
(2007)
A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome.
Genome Biology
8:
R41.
Tassy O,
Dauga D,
Daian F et al.
(2010)
The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program.
Genome Research
20:
1459–1468.
Tsagkogeorga G,
Cahais V and
Galtier N
(2012)
The population genomics of a faster evolver: high level of diversity, functional constrain and molecular adaptation in the tunic Ciona intestinalis.
Genome Biology and Evolution
4:
852–861. doi:10.1093/gbe/evs054.
Yamada L,
Kobayashi K,
Satou Y and
Satoh N
(2005)
Microarray analysis of localization of maternal transcripts in eggs and early embryos of the ascidian, Ciona intestinalis.
Developmental Biology
284:
536–550.
Yamada L,
Shoguchi E,
Wada S et al.
(2003)
Morpholino‐based gene knockdown screen of novel genes with developmental function in Ciona intestinalis.
Development
130:
6485–6495.
Yang J‐H,
Shao P,
Zhou H,
Chen Y‐Q and
Qu L‐H
(2010)
deepBase: a database for deeply annotating and mining deep sequencing data.
Nucleic Acids Research
38:
D123–D130.
Further Reading
Butts T,
Holland PW and
Ferrier DE
(2008)
The urbilaterian Super‐Hox cluster.
Trends in Genetics
24:
259–262.
Jeffery WR and
Swalla BJ
(1997)
Tunicates.
In: Gilbert SF and
Raunio AM (eds)
Embryology,
pp. 331–364.
Sunderland, MA: Sinauer.
Meinertzhagen IA,
Lemaire P and
Okamura Y
(2004)
The neurobiology of the ascidian tadpole larva: recent development in an ancient chordate.
Annual Review of Neurosciences
27:
453–458.
Satoh N
(2001)
Ascidian embryos as a model system to analyze expression and function of developmental genes.
Differentiation
68:
1–12.
Satoh N
(2008)
An aboral‐dorsalization hypothesis for chordate origin.
Genesis
46:
614–622.
Satou Y,
Satoh N and
Imai KS
(2009)
Gene regulatory networks in the early ascidian embryo.
Biochimica et Biophysica Acta
1789:
268–273.