Ciona Genetics

Methods in Molecular Biology

Volumn 770, Issue , 2011, Pages 401-422

  Veeman, Michael T ^a   Chiba, Shota ^a   Smith, William C ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

ascidian; Ciona; genetics; invertebrate chordate

Indexed keywords

ASCIDIACEA; CHORDATA; CIONA; CONTROLLED STUDY; EMBRYO; GAMETE; GENETIC ANALYSIS; HUMAN CELL; NONHUMAN; SPAWNING; ANIMAL; ARTICLE; CHROMOSOME MAP; CRYOPRESERVATION; CYTOLOGY; FEMALE; FERTILIZATION IN VITRO; GENETIC PROCEDURES; GENETICS; HYBRIDIZATION; INSTRUMENTATION; ISOLATION AND PURIFICATION; LARVA; MALE; MICROINJECTION; MOLECULAR CLONING; MUTATION; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; POLYMERASE CHAIN REACTION; SINGLE NUCLEOTIDE POLYMORPHISM; UROCHORDATA;

ASCIDIA; ASCIDIACEA; CHORDATA; CIONA; INVERTEBRATA; VERTEBRATA;

DNA;

ANIMALS; CHROMOSOME MAPPING; CLONING, MOLECULAR; CRYOPRESERVATION; DNA; DNA MUTATIONAL ANALYSIS; FEMALE; FERTILIZATION IN VITRO; GENETIC TECHNIQUES; HYBRIDIZATION, GENETIC; LARVA; MALE; MICROINJECTIONS; MUTATION; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; UROCHORDATA;

EID: 80052956441     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-210-6_15     Document Type: Chapter

References (37)

1. Delsuc, F., Brinkmann, H., Chourrout, D., and Philippe, H. (2006) Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 439, 965–968.
2. Imai, K.S., Levine, M., Satoh, N., and Satou, Y. (2006) Regulatory blueprint for a chordate embryo. Science 312, 1183–1187.
3. Passamaneck, Y.J. and Di Gregorio, A. (2005) Ciona intestinalis: chordate development made simple. Dev. Dyn. 233, 1–19.
4. Lemaire, P., Smith, W.C., and Nishida, H. (2008) Ascidians and the plasticity of the chordate developmental program. Curr. Biol. 18, R620–631.
5. Dehal, P., Satou, Y., Campbell, R.K., Chapman, J., Degnan, B., De Tomaso, A., Davidson, B., Di Gregorio, A., Gelpke, M., Goodstein, D.M., et al. (2002) The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 298, 2157–2167.
6. Satou, Y., Mineta, K., Ogasawara, M., Sasakura, Y., Shoguchi, E., Ueno, K., Yamada, L., Matsumoto, J., Wasserscheid, J., Dewar, K., 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 Biol. 9, R152.
7. Small, K.S., Brudno, M., Hill, M.M., and Sidow, A. (2007) A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome. Genome Biol. 8, R41.
8. Vinson, J.P., Jaffe, D.B., O‘Neill, K., Karlsson, E.K., Stange-Thomann, N., Anderson, S., Mesirov, J.P., Satoh, N., Satou, Y., Nus-baum, C., et al. (2005) Assembly of polymorphic genomes: algorithms and application to Ciona savignyi. Genome Res. 15, 1127–1135.
9. Hino, K., Satou, Y., Yagi, K., and Satoh, N. (2003) A genomewide survey of developmentally relevant genes in Ciona intestinalis. VI. Genes for Wnt, TGFbeta, Hedgehog and JAK/STAT signaling pathways. Dev. Genes Evol. 213, 264–272.
10. Sasakura, Y., Shoguchi, E., Takatori, N., Wada, S., Meinertzhagen, I.A., Satou, Y., and Satoh, N. (2003) A genomewide survey of developmentally relevant genes in Ciona intestinalis. X. Genes for cell junctions and extracellular matrix. Dev. Genes Evol. 213, 303–313.
11. Satou, Y., Sasakura, Y., Yamada, L., Imai, K.S., Satoh, N., and Degnan, B. (2003) A genomewide survey of developmentally relevant genes in Ciona intestinalis. V. Genes for receptor tyrosine kinase pathway and Notch signaling pathway. Dev. Genes Evol. 213, 254–263.
12. Wada, S., Tokuoka, M., Shoguchi, E., Kobayashi, K., Di Gregorio, A., Spagnuolo, A., Branno, M., Kohara, Y., Rokhsar, D., Levine, M., et al. (2003) A genomewide survey of developmentally relevant genes in Ciona intestinalis. II. Genes for homeobox transcription factors. Dev. Genes Evol. 213, 222–234.
13. Dehal, P. and Boore, J.L. (2005) Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol 3, e314.
14. Hughes, A.L. and Friedman, R. (2005) Loss of ancestral genes in the genomic evolution of Ciona intestinalis. Evol. Dev. 7, 196–200.
15. Chiba, S., Jiang, D., Satoh, N., and Smith, W.C. (2009) Brachyury null mutant-induced defects in juvenile ascidian endodermal organs. Development 136, 35–39.
16. Jiang, D., Munro, E.M., and Smith, W.C. (2005) Ascidian prickle regulates both medi- olateral and anterior-posterior cell polarity of notochord cells. Curr. Biol. 15, 79–85.
17. Veeman, M.T., Nakatani, Y., Hendrickson, C., Ericson, V., Lin, C., and Smith, W.C. (2008) Chongmague reveals an essential role for laminin-mediated boundary formation in chordate convergence and extension movements. Development 135, 33–41.
18. Jiang, D. and Smith, W.C. (2005) Self-and cross-fertilization in the solitary ascidian Ciona savignyi. Biol. Bull. 209, 107–112.
19. Harada, Y., Takagaki, Y., Sunagawa, M., Saito, T., Yamada, L., Taniguchi, H., Shoguchi, E., and Sawada, H. (2008) Mechanism of self-sterility in a hermaphroditic chordate. Science 320, 548–550.
20. Hendrickson, C., Christiaen, L., Deschet, K., Jiang, D., Joly, J.S., Legendre, L., Nakatani, Y., Tresser, J., and Smith, W.C. (2004) Culture of adult ascidians and ascidian genetics. Meth. Cell Biol. 74, 143–170.
21. Small, K.S., Brudno, M., Hill, M.M., and Sidow, A. (2007) Extreme genomic variation in a natural population. Proc. Natl. Acad. Sci. USA 104, 5698–5703.
22. Kim, J.H., Waterman, M.S., and Li, L.M. (2007) Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi. Genome Res. 17, 1101–1110.
23. Shoguchi, E., Kawashima, T., Satou, Y., Hamaguchi, M., Sin, I.T., Kohara, Y., Putnam, N., Rokhsar, D.S., and Satoh, N. (2006) Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis. Genome Res. 16, 297–303.
24. Hill, M.M., Broman, K.W., Stupka, E., Smith, W.C., Jiang, D., and Sidow, A. (2008) The C. savignyi genetic map and its integration with the reference sequence facilitates insights into chordate genome evolution. Genome Res. 18, 1369–1379.
25. Satou, Y., Takatori, N., Fujiwara, S., Nishikata, T., Saiga, H., Kusakabe, T., Shin-i, T., Kohara, Y., and Satoh, N. (2002) Ciona intestinalis cDNA projects: expressed sequence tag analyses and gene expression profiles during embryogenesis. Gene 287, 83–96.
26. Satou, Y., Yamada, L., Mochizuki, Y., Takatori, N., Kawashima, T., Sasaki, A., Hamaguchi, M., Awazu, S., Yagi, K., Sasakura, Y., et al. (2002) A cDNA resource from the basal chordate Ciona intestinalis. Genesis 33, 153–154.
27. Imai, K.S., 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.
28. Kusakabe, T., Yoshida, R., Kawakami, I., Kusakabe, R., Mochizuki, Y., Yamada, L., Shin-i, T., Kohara, Y., Satoh, N., Tsuda, M., et al. (2002) Gene expression profiles in tadpole larvae of Ciona intestinalis. Dev. Biol. 242, 188–203.
29. Sasakura, Y. (2007) Germline transgenesis and insertional mutagenesis in the ascidian Ciona intestinalis. Dev. Dyn. 236, 1758–1767.
30. Deschet, K., Nakatani, Y., and Smith, W.C. (2003) Generation of Ci-Brachyury-GFP stable transgenic lines in the ascidian Ciona savignyi. Genesis 35, 248–259.
31. Zeller, R.W., Virata, M.J., and Cone, A.C. (2006) Predictable mosaic transgene expression in ascidian embryos produced with a simple electroporation device. Dev. Dyn. 235, 1921–1932.
32. Nydam, M.L. and Harrison, R.G. (2007) Genealogical relationships within and among shallow-water Ciona species (Ascidiacea). Mar. Biol. 151, 1839–1847.
33. Hoshino, Z. and Nishikawa, T. (1985) Taxonomic studies of Ciona intestinalis (L.) and its allies. Publ. Seto Mar. Biol. Lab 30, 61–79.
34. Silva, N. and Smith, W.C. (2008) Inverse correlation of population similarity and introduction date for invasive ascidians. PLoS One 3, e2552.
35. Dybern, B.I. (1965) The life cycle of Ciona intestinalis (L.) f. typica in relation to the environmental temperature. Oikos 16, 109–131.
36. Joly, J.S., Kano, S., Matsuoka, T., Auger, H., Hirayama, K., Satoh, N., Awazu, S., Legendre, L., and Sasakura, Y. (2007) Culture of Ciona intestinalis in closed systems. Dev. Dyn. 236, 1832–1840.
37. Suzuki, M.M., Nishikawa, T., and Bird, A. (2005) Genomic approaches reveal unexpected genetic divergence within Ciona intestinalis. J. Mol. Evol. 61, 627–635.