Abstract
We have conducted large-scale EST analyses of transcripts expressed in the basal chordate Ciona intestinalis. The cDNA libraries examined were from fertilized eggs, cleaving embryos, gastrulae/neurulae, tailbud embryos, larvae and whole young adults, and the gonad (ovary and testis), endostyle, neural complex, heart, and blood cells of the adult. Because the libraries were not normalized or amplified, the occurrence of cDNA clones or EST counts in each library may reflect the quantity of transcripts of the corresponding genes. Thus, comparison of the EST counts of a certain gene at the six developmental stages may reflect the temporal expression pattern of the gene, while the comparison of EST counts in different tissues of the adult may reflect the spatial expression pattern of the gene. Here we present evidence that this is the case, and that the EST count can therefore be used like "Northern blot analysis" of Ciona genes.
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References
Chiba S, Satou Y, Nishikata T, Satoh N (1998) Isolation and characterization of cDNA clones for epidermis-specific and muscle-specific genes in Ciona savignyi embryos. Zool Sci 15:239–246
Chiba S, Awazu S, Itoh M, Chin-Bow ST, Satoh N, Satou Y, Hastings KEM (2003) A genomewide survey of developmentally relevant genes in Ciona intestinalis. IX. Genes for muscle structural proteins. Dev Genes Evol DOI 10.1007/s00427-003-0324-x
Corbo JC, Levine M, Zeller RW (1997) Characterization of a notochord-specific enhancer from the Brachyury promoter region of the ascidian, Ciona intestinalis. Development 124:589–602
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
Etani K, Nishikata T (2002) Novel G-protein-coupled receptor gene expressed specifically in the entire neural tube of the ascidian Ciona intestinalis. Dev Genes Evol 212:447–451
Fujimura M, Takamura K (2000) Characterization of an ascidian DEAD-box gene, Ci-DEAD1: specific expression in the germ cells and its mRNA localization in the posterior-most blastomeres in early embryos. Dev Genes Evol 210:64–72
Fujiwara S, Corbo JC, Levine M (1998) The Snail repressor establishes a muscle/notochord boundary in the Ciona embryo. Development 125:2511–2520
Fujiwara S, Maeda Y, Shin-i T, Kohara Y, Takatori N, Satou Y, Satoh N (2002) Gene expression profiles in Ciona intestinalis cleavage-stage embryos. Mech Dev 112:115–127
Hotta K, Takahashi H, Asakura T, Saitoh B, Takatori N, Satou Y, Satoh N (2000) Characterization of Brachyury-downstream notochord genes in the Ciona intestinalis embryo. Dev Biol 224:69–80
Hudson C, Lemaire P (2001) Induction of anterior neural fates in the ascidian Ciona intestinalis. Mech Dev 2:189–203
Imai K, Takada N, Satoh N, Satou Y (2000) β-catenin mediates the specification of endoderm cells in ascidian embryos. Development 14:3009–3020
Imai KS, Satoh N, Satou Y (2002a) Early embryonic expression of FGF4/6/9 gene and its role in the induction of mesenchyme and notochord in Ciona savignyi embryos. Development 129:1729–1738
Imai KS, Satoh N, Satou Y (2002b) Region specific gene expressions in the central nervous system of the ascidian embryo. Gene Exp Patt 3–4:319–321
Inaba K, Padma P, Satouh Y, Shin-i T, Kohara Y, Satoh N, Satou Y (2002) EST analysis of gene expression in testis of the ascidian Ciona intestinalis. Mol Reprod Dev 62:431–445
Kusakabe T, Yoshida R, Kawakami I, Kusakabe R, Mochizuki Y, Yamada L, Shin-i T, Kohara Y, Satoh N, Tsuda M, Satou Y (2002) Gene expression profiles in tadpole larvae of Ciona intestinalis. Dev Biol 242:188–203
Meedel TH, Farmer SC, Lee JJ (1997) The single MyoD family gene of Ciona intestinalis encodes two differentially expressed proteins: implications for the evolution of the evolution of chordate muscle gene regulation. Development 9:1711–1721
Nakayama A, Satou Y, Satoh N (2002) Further characterization of genes expressed during Ciona intestinalis metamorphosis. Differentiation 70:429–437
Nishida H, Sawada K (2001) macho-1 encodes a localized mRNA in ascidian eggs that specifies muscle fate during embryogenesis. Nature 409:724–729
Nishikata T, Yamada L, Mochizuki Y, Satou Y, Shin-i T, Kohara Y, Satoh N (2001) Profiles of maternally expressed genes in fertilized eggs of Ciona intestinalis. Dev Biol 238:315–331
Ogasawara M, Sasaki A, Metoki H, Shin-i T, Kohara Y, Satoh N, Satou Y (2002) Gene expression profiles in young adult Ciona intestinalis. Dev Genes Evol 212:173–185
Satou Y, Takatori N, Yamada L, Mochizuki Y, Hamaguchi M, Ishikawa H, Chiba S, Imai K, Kano S, Murakami SD, Nakayama A, Nishino A, Sasakura Y, Satoh G, Shimotori T, Shin-i T, Shoguchi E, Suzuki MM, Takada N, Utsumi N, Yoshida N, Saiga H, Kohara Y, Satoh N (2001) Gene expression profiles in Ciona intestinalis tailbud embryos. Development 128:2893–2904
Satou Y, Yamada L, Mochizuki Y, Takatori N, Kawashima T, Sasaki A, Hamaguchi M, Awazu S, Yagi K, Sasakura Y, Nakayama A, Ishikawa H, Inaba K, Satoh N (2002a) A cDNA resource from the basal chordate Ciona intestinalis. Genesis 33:153–154
Satou Y, Takatori N, Fujiwara S, Nishikata T, Saiga H, Kusakabe T, Shin-i T, Kohara Y, Satoh N (2002b) Ciona intestinalis cDNA projects: expressed sequence tag analyses and gene expression profiles during embryogenesis. Gene 287:83–96
Satou Y, Yagi K, Imai KS, Yamada L, Nishida H, Satoh N (2002c) macho-1-related genes in Ciona embryos. Dev Genes Evol 212:87–92
Satou Y, Imai KS, Levine M, Kohara Y, Rokhsar D, Satoh N (2003) A genomewide survey of developmentally relevant genes in Ciona intestinalis. I. Genes for bHLH transcription factors. Dev Genes Evol DOI 10.1007/s00427-003-0319-7
Wada S, Tokuoka M, Shoguchi E, Kobayashi K, Di Gregorio A, Spagnuolo A, Branno M, Kohara Y, Rokhsar D, Levine M, Saiga H, Satoh N, Satou Y (2003) A genomewide survey of developmentally relevant genes in Ciona intestinalis. II. Genes for homeobox transcription factors. Dev Genes Evol DOI 10.1007/s00427-003-0321-0
Yagi K, Satou Y, Mazet F, Shimeld SM, Degnan B, Rokhsar D, Levine M, Kohara Y, Satoh N (2003) A genomewide survey of developmentally relevant genes in Ciona intestinalis. III. Genes for Fox, ETS, nuclear receptors and NFκB. Dev Genes Evol DOI 10.1007/s00427-003-0322-z
Yamada L, Kobayashi K, Degnan B, Satoh N, Satou Y(2003) A genomewide survey of developmentally relevant genes in Ciona intestinalis. IV. Genes for HMG transcriptional regulators, bZip and GATA/Gli/Zic/Snail. Dev Genes Evol DOI 10.1007/s00427-003-0316-x
Yoshida S, Marikawa Y, Satoh N (1996) posterior end mark, a novel maternal gene encoding a localized factor in the ascidian embryo. Development 122:2005–2012
Acknowledgements
We wish to thank our laboratory members for their help in EST analyses. This work was supported by Grants-in-Aid from the MEXT of Japan to Y.S. (14704070), Y.K. (12201001) and N.S. (12202001). T.K. was a postdoctoral fellow of JSPS with a research grant (13060049).
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Satou, Y., Kawashima, T., Kohara, Y. et al. Large scale EST analyses in Ciona intestinalis . Dev Genes Evol 213, 314–318 (2003). https://doi.org/10.1007/s00427-003-0327-7
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DOI: https://doi.org/10.1007/s00427-003-0327-7