Retaux S, Casane D. Evolution of eye development in the darkness of caves: adaptation, drift, or both? Evodevo. 2013;4(1):26.
Article
PubMed
PubMed Central
Google Scholar
Kowalko JE, Rohner N, Rompani SB, Peterson BK, Linden TA, Yoshizawa M, Kay EH, Weber J, Hoekstra HE, Jeffery WR, et al. Loss of schooling behavior in cavefish through sight-dependent and sight-independent mechanisms. Curr Biol. 2013;23(19):1874–83.
Article
CAS
PubMed
PubMed Central
Google Scholar
McGaugh SE, Gross JB, Aken B, Blin M, Borowsky R, Chalopin D, Hinaux H, Jeffery WR, Keene A, Ma L, et al. The cavefish genome reveals candidate genes for eye loss. Nat Commun. 2014;5:5307.
Article
CAS
PubMed
PubMed Central
Google Scholar
Protas ME, Hersey C, Kochanek D, Zhou Y, Wilkens H, Jeffery WR, Zon LI, Borowsky R, Tabin CJ. Genetic analysis of cavefish reveals molecular convergence in the evolution of albinism. Nat Genet. 2006;38(1):107–11.
Article
CAS
PubMed
Google Scholar
Protas ME, Trontelj P, Patel NH. Genetic basis of eye and pigment loss in the cave crustacean, Asellus aquaticus. Proc Natl Acad Sci USA. 2011;108(14):5702–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jeffery AK, Swalla BJ. Tunicates. In: Gilbert SF, Raunio AM, editors. Embryology, constructing the organism. London: Elsevier; 1997.
Google Scholar
Satoh N. Developmental biology of ascidians. Cambridge: Cambridge University Press; 1994.
Google Scholar
Ryan K, Lu Z, Meinertzhagen IA. The CNS connectome of a tadpole larva of Ciona intestinalis (L) highlights sidedness in the brain of a chordate sibling. Elife. 2016;5:1.
Article
Google Scholar
Dilly PN. Studies on the receptors in the cerebral vesicle of the ascidian tadpole. I. The otolith. Q J Microsc Sci. 1962;103:393–8.
Google Scholar
Tsuda M, Sakurai D, Goda M. Direct evidence for the role of pigment cells in the brain of ascidian larvae by laser ablation. J Exp Biol. 2003;206(8):1409–17.
Article
PubMed
Google Scholar
Nishida H. Cell lineage analysis in ascidian embryos by intracellular injection of a tracer enzyme. III. Up to the tissue restricted stage. Dev Biol. 1987;121(2):526–41.
Article
CAS
PubMed
Google Scholar
Stolfi A, Ryan K, Meinertzhagen IA, Christiaen L. Migratory neuronal progenitors arise from the neural plate borders in tunicates. Nature. 2015;527(7578):371–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yu JK, Meulemans D, McKeown SJ, Bronner-Fraser M. Insights from the amphioxus genome on the origin of vertebrate neural crest. Genome Res. 2008;18(7):1127–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Abitua PB, Wagner E, Navarrete IA, Levine M. Identification of a rudimentary neural crest in a non-vertebrate chordate. Nature. 2012;492(7427):104–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wada H, Holland PW, Sato S, Yamamoto H, Satoh N. Neural tube is partially dorsalized by overexpression of HrPax-37: the ascidian homologue of Pax-3 and Pax-7. Dev Biol. 1997;187(2):240–52.
Article
CAS
PubMed
Google Scholar
Esposito R, D’Aniello S, Squarzoni P, Pezzotti MR, Ristoratore F, Spagnuolo A. New insights into the evolution of metazoan tyrosinase gene family. PLOS ONE. 2012;7(4):e35731.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jiang D, Tresser JW, Horie T, Tsuda M, Smith WC. Pigmentation in the sensory organs of the ascidian larva is essential for normal behavior. J Exp Biol. 2005;208(3):433–8.
Article
PubMed
Google Scholar
Tief K, Hahne M, Schmidt A, Beermann F. Tyrosinase, the key enzyme in melanin synthesis, is expressed in murine brain. Eur J Biochem. 1996;241(1):12–6.
Article
CAS
PubMed
Google Scholar
Berrill NJ. Studies in tunicate development. Part II. Abbreviation of development in the Molgulidae. Philos Trans R Soc B Biol Sci. 1931;219:281–346.
Article
Google Scholar
Lacaze-Duthiers H. Histoire des ascidies simples des cotes de France: 2: Etudes des especes; 1874.
Jeffery WR, Swalla BJ. The myoplasm of ascidian eggs: a localized cytoskeletal domain with multiple roles in embryonic development. Semin Cell Biol. 1990;1(5):373–81.
CAS
PubMed
Google Scholar
Huber JL, da Silva KB, Bates WR, Swalla BJ. The evolution of anural larvae in molgulid ascidians. Semin Cell Dev Biol. 2000;11(6):419–26.
Article
CAS
PubMed
Google Scholar
Bates WR. Direct development in the Ascidian Molgula-retortiformis (Verrill, 1871). Biol Bull. 1995;188(1):16–22.
Article
Google Scholar
Bates WR, Mallett JE. Ultrastructural and histochemical-study of anural development in the ascidian Molgula-pacifica (Huntsman). Roux Arch Dev Biol. 1991;200(4):193–201.
Article
PubMed
Google Scholar
Swalla BJ, Jeffery WR. Modification of the myoplasm in eggs of anural ascidians. Am Zool. 1990;30(4):A42.
Google Scholar
Swalla BJ, Jeffery WR. Vestigial brain melanocyte development during embryogenesis of an anural ascidian. Dev Growth Differ. 1992;34(1):17–25.
Article
Google Scholar
Tagawa K, Jeffery WR, Satoh N. The recently-described ascidian species Molgula tectiformis is a direct developer. Zool Sci. 1997;14(2):297–303.
Article
CAS
PubMed
Google Scholar
Whittaker JR. Development of vestigial tail muscle acetylcholinesterase in embryos of an anural ascidian species. Biol Bull. 1979;156(3):393–407.
Article
CAS
PubMed
Google Scholar
Jeffery WR, Swalla BJ, Ewing N, Kusakabe T. Evolution of the ascidian anural larva: evidence from embryos and molecules. Mol Biol Evol. 1999;16(5):646–54.
Article
CAS
PubMed
Google Scholar
Kusakabe T, Swalla BJ, Satoh N, Jeffery WR. Mechanism of an evolutionary change in muscle cell differentiation in ascidians with different modes of development. Dev Biol. 1996;174(2):379–92.
Article
CAS
PubMed
Google Scholar
Gyoja F, Satou Y, Shin-i T, Kohara Y, Swalla BJ, Satoh N. Analysis of large scale expression sequenced tags (ESTs) from the anural ascidian, Molgula tectiformis. Dev Biol. 2007;307(2):460–82.
Article
CAS
PubMed
Google Scholar
Takada N, Satoh N, Swalla BJ. Expression of Tbx6, a muscle lineage T-box gene, in the tailless embryo of the ascidian Molgula tectiformis. Dev Genes Evol. 2002;212(7):354–6.
Article
CAS
PubMed
Google Scholar
Swalla BJ, Jeffery WR. Interspecific hybridization between an anural and urodele ascidian: differential expression of urodele features suggests multiple mechanisms control anural development. Dev Biol. 1990;142(2):319–34.
Article
CAS
PubMed
Google Scholar
Grave C. Molgula citrina (Alder and Hancock). Activities and structure of the free-swimming larva. J Morphol. 1926;42:453–71.
Article
Google Scholar
Gertz EM, Yu YK, Agarwala R, Schaffer AA, Altschul SF. Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST. BMC Biol. 2006;4:41.
Article
PubMed
PubMed Central
Google Scholar
Stolfi A, Lowe EK, Racioppi C, Ristoratore F, Brown CT, Swalla BJ, Christiaen L. Divergent mechanisms regulate conserved cardiopharyngeal development and gene expression in distantly related ascidians. eLife. 2014. doi:10.7554/eLife.03728.
PubMed
PubMed Central
Google Scholar
Brunetti R, Gissi C, Pennati R, Caicci F, Gasparini F, Manni L. Morphological evidence that the molecularly determined Ciona intestinalis type A and type B are different species: Ciona robusta and Ciona intestinalis. J Zool Syst Evol Res. 2015;53(3):186–93.
Article
Google Scholar
Sato S, Masuya H, Numakunai T, Satoh N, Ikeo K, Gojobori T, Tamura K, Ide H, Takeuchi T, Yamamoto H. Ascidian tyrosinase gene: its unique structure and expression in the developing brain. Dev Dyn. 1997;208(3):363–74.
Article
CAS
PubMed
Google Scholar
Lowe E, Swalla BJ, Brown CT. Evaluating a lightweight transcriptome assembly pipeline on two closely related ascidian species. PeerJ Prepr. 2014;2:e505v1.
Google Scholar
Racioppi C, Kamal AK, Razy-Krajka F, Gambardella G, Zanetti L, di Bernardo D, Sanges R, Christiaen LA, Ristoratore F. Fibroblast growth factor signalling controls nervous system patterning and pigment cell formation in Ciona intestinalis. Nat Commun. 2014;5:4830.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kobayashi T, Urabe K, Winder A, Jimenez-Cervantes C, Imokawa G, Brewington T, Solano F, Garcia-Borron JC, Hearing VJ. Tyrosinase related protein 1 (TRP1) functions as a DHICA oxidase in melanin biosynthesis. EMBO J. 1994;13(24):5818–25.
CAS
PubMed
PubMed Central
Google Scholar
Loftus SK, Larson DM, Baxter LL, Antonellis A, Chen Y, Wu X, Jiang Y, Bittner M, Hammer JA 3rd, Pavan WJ. Mutation of melanosome protein RAB38 in chocolate mice. Proc Natl Acad Sci USA. 2002;99(7):4471–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Oiso N, Riddle SR, Serikawa T, Kuramoto T, Spritz RA. The rat Ruby (R) locus is Rab38: identical mutations in Fawn-hooded and Tester-Moriyama rats derived from an ancestral Long Evans rat sub-strain. Mamm Genome. 2004;15(4):307–14.
Article
CAS
PubMed
Google Scholar
Squarzoni P, Parveen F, Zanetti L, Ristoratore F, Spagnuolo A. FGF/MAPK/Ets signaling renders pigment cell precursors competent to respond to Wnt signal by directly controlling Ci-Tcf transcription. Development. 2011;138(7):1421–32.
Article
CAS
PubMed
Google Scholar
Jeffery WR. Evolution and development of brain sensory organs in molgulid ascidians. Evol Dev. 2004;6(3):170–9.
Article
PubMed
Google Scholar
Brozovic M, Martin C, Dantec C, Dauga D, Mendez M, Simion P, Percher M, Laporte B, Scornavacca C, Di Gregorio A. ANISEED 2015: a digital framework for the comparative developmental biology of ascidians. Nucleic Acids Res. 2015; 44:D808–18.
Article
PubMed
PubMed Central
Google Scholar
Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein DM. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science. 2002;298(5601):2157.
Article
CAS
PubMed
Google Scholar
Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994;22(22):4673–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30(12):2725–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huson DH, Scornavacca C. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst Biol. 2012;61(6):1061–7.
Article
PubMed
Google Scholar
Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods. 2017;4:417–9.
Article
Google Scholar
Stolfi A, Sasakura Y, Chalopin D, Satou Y, Christiaen L, Dantec C, Endo T, Naville M, Nishida H, Swalla BJ, et al. Guidelines for the nomenclature of genetic elements in tunicate genomes. Genesis. 2015;53(1):1–14.
Article
PubMed
Google Scholar
Beh J, Shi W, Levine M, Davidson B, Christiaen L. FoxF is essential for FGF-induced migration of heart progenitor cells in the ascidian Ciona intestinalis. Development. 2007;134(18):3297–305.
Article
CAS
PubMed
Google Scholar
Christiaen L, Wagner E, Shi W, Levine M. Whole-mount in situ hybridization on sea squirt (Ciona intestinalis) embryos. Cold Spring Harb Protoc. 2009;2009(12):pdb prot5348.
PubMed
Google Scholar
Ikuta T, Saiga H. Dynamic change in the expression of developmental genes in the ascidian central nervous system: revisit to the tripartite model and the origin of the midbrain-hindbrain boundary region. Dev Biol. 2007;312(2):631–43.
Article
CAS
PubMed
Google Scholar
Satou Y, Yamada L, Mochizuki Y, Takatori N, Kawashima T, Sasaki A, Hamaguchi M, Awazu S, Yagi K, Sasakura Y, et al. A cDNA resource from the basal chordate Ciona intestinalis. Genesis. 2002;33(4):153–4.
Article
CAS
PubMed
Google Scholar
Christiaen L, Wagner E, Shi W, Levine L. Electroporation of transgenic DNAs in the sea squirt Ciona. Cold Spring Harb Protoc. 2009;12:pdb.prot5345.
Google Scholar
Letunic I, Doerks T, Bork P. SMART: recent updates, new developments and status in 2015. Nucleic Acids Res. 2014;43(D1):D257–60.
Article
PubMed
PubMed Central
Google Scholar