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ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates.

Lancelets ("amphioxus") are the modern survivors of an ancient chordate lineage, the cephalochordates, with a fossil record dating back to the Cambrian. We describe the structure and gene content of the highly polymorphic genome of the Florida lancelet, in the context of the known genomes from the other chordate lineages, including the tunicate Ciona, human, and other vertebrates. This whole-genome comparison illuminates the murky relationship between the three principal chordate subphyla (tunicates, cephalochordates, and vertebrates), and provides a new perspective on the nature of the chordate common ancestor and key events in the emergence of vertebrates. The amphioxus sequence allows reconstruction of not only the gene complement of the ancestral chordate, but also a partial reconstruction of its genomic organization and a description of subsequent duplications and reorganizations in the vertebrate lineage.

Lancelets ('amphioxus') are the modern survivors of an ancient chordate lineage, with a fossil record dating back to the Cambrian period. Here we describe the structure and gene content of [...]

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2007.03.035 Byline: Fuki Gyoja (a), Yutaka Satou (a), Tadasu Shin-i (b), Yuji Kohara (b), Billie J. Swalla (c), Nori Satoh (a)(d) Keywords: Anural ascidian; EST analysis; Evolution of ascidians; Genes that show no similarity with known proteins of other organisms; Putative metamorphosis-related genes; Embryonic/larval muscle development; Notochord development Abstract: Anural ascidians show embryogenesis during which tail formation does not take place. This mode of development is a derived character acquired several times independently in ascidian evolution. We identified approximately 20,000 each ESTs (i. e. 10,000 clones each were sequenced from both 5' and 3' ends) of adult gonads, cleaving-embryos, gastrulae/neurulae, embryos before hatching, and hatched larvae of the anural ascidian Molgula tectiformis, in order to comprehensively investigate the molecular mechanism of tailless evolution. Analyses of these ESTs showed that in this species, (1) the expression of embryonic/larval muscle structural genes which are expressed abundantly during embryogenesis of the urodele ascidian Ciona intestinalis, is suppressed; (2) genes that encode proteins with no similarity to known proteins of other organisms are abundantly expressed; (3) genes that show similarity with those up-regulated at metamorphosis in urodele ascidians are up-regulated within several hours after hatching; and (4) 15 of 35 putative orthologues of the downstream components of Brachyury, a key transcription factor for ascidian notochord formation, were found in the ESTs, even though differentiation of notochord is suppressed in this species. We discuss these remarkable results that allow insight into the molecular mechanism(s) responsible for the anural mode of ascidian development. Author Affiliation: (a) Department of Zoology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan (b) Center for Genetic Resource Informations, National Institute of Genetics, Mishima 411-8540, Japan (c) Department of Biology, University of Washington, Seattle, Washington 98195, USA (d) International Coastal Research Center, Ocean Research Institute of University of Tokyo, Otsuchi, Iwate 028-1102, Japan Article History: Received 21 October 2006; Revised 19 March 2007; Accepted 23 March 2007

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2006.01.024 Byline: Kyoko Miwata, Takuto Chiba, Reiko Horii, Lixy Yamada, Atsushi Kubo, Daisuke Miyamura, Nori Satoh, Yutaka Satou Keywords: Ciona intestinalis; Ascidian; Zinc finger; Expression profile Abstract: The recent decoding of a number of animal genomes has provided unprecedented information regarding evolution and gene structures, but this information must be supplemented with precise gene annotations and the temporal and spatial expression patterns of individual genes. In the present study, we systematically identified and characterized 566 zinc finger genes in the genome of Ciona intestinalis, an emerging model system for genome-wide studies of development and evolution. Of these genes, 356 genes encoded a potential transcription factor based on putative nucleic acid binding activity or domains of unknown function. We further examined the expression patterns of 225 genes during embryogenesis, and, when considered with a previous study [Imai, K.S., Hino, K., Yagi, K., Satoh, N., 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], we have characterized the developmental expression patterns of nearly 85% of the potential zinc finger-containing transcription factors. Overall, zinc finger genes are preferentially maternally expressed with little larval expression during development. The present study provides a valuable reference for genome-wide studies in this species and for future studies wishing to examine zinc finger gene expression patterns in other animals. Author Affiliation: Department of Zoology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan Article History: Received 30 September 2005; Revised 20 January 2006; Accepted 21 January 2006

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2005.09.018 Byline: Miki Tokuoka (a), Nori Satoh (a)(b), Yutaka Satou (a) Keywords: Cell lineages; Mesenchyme cells; Ciona savignyi; Twist-like1; Juvenile; Mesoderm development Abstract: Ascidian larval mesenchyme cells, comprising about 900 cells, are derived from the A7.6, B8.5 and B7.7 blastomere pairs in the 110-cell embryo. Previous studies showed that the properties of mesenchyme cells are not uniform among the three lines in embryos of Ciona savignyi and Ciona intestinalis. After metamorphosis, the larval mesenchyme cells form the mesodermal tissues or organs of the adult body. In the present study, the developmental fates of A7.6-, B8.5- and B7.7-line mesenchyme cells were traced using DiI to determine the origins of juvenile mesodermal tissues of C. savignyi. It was demonstrated that each of the A7.6-, B8.5- and B7.7-line mesenchyme cells is distributed in different positions of the larval trunk, and then give rise to the different mesodermal tissues of juveniles. Twist-like1 is a transcription factor gene essential for the specification of larval mesenchyme cells. Knockdown of this gene with specific morpholino antisense oligonucleotides affected not only the specification of larval mesenchyme cells, but also the formation of most of the mesodermal tissues of juveniles. The juvenile mesodermal tissues in the Twist-like1-knockdown specimen were never compensated by the surrounding tissues. The present results therefore indicate that Twist-like1 is required for the differentiation of most mesodermal precursors of adults. Author Affiliation: (a) Department of Zoology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan (b) CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 330-0012, Japan Article History: Received 4 April 2005; Revised 9 September 2005; Accepted 10 September 2005

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2005.05.027 Byline: Lixy Yamada (a), Kenji Kobayashi (a), Yutaka Satou (a), Nori Satoh (a)(b) Keywords: Ciona intestinalis; Maternal transcripts; Localization; Microarray Abstract: The establishment of body axes and specification of early embryonic cells depend on maternally supplied transcripts and/or proteins, several of which are localized at specific regions of fertilized eggs and early embryos. The ascidian is known to exhibit a mosaic mode of development, and this mode is largely dependent on localized maternal factors. Using blastomere isolation, microarray and whole-mount in situ hybridization, the present study of Ciona intestinalis demonstrates that maternal transcripts of a total of 17 genes are localized at the posterior-most region of fertilized eggs and early embryos. Ten of them are newly identified in the present study, while the remaining seven genes have already been characterized in previous studies. In addition, maternal transcripts of two genes, in addition to 14 genes encoded by the mitochondrial genome, showed a mitochondria-like distribution. Despite the present comprehensive approach, we could not identify maternal transcripts that are clearly localized to the animal-pole side, the vegetal-pole side, the anterior-side or other specific regions of the early embryo. Therefore, we concluded that the posterior-most localization and mitochondria-like distribution appear to be major specialized patterns of maternal transcripts in early Ciona embryos. Author Affiliation: (a) Department of Zoology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan (b) CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 330-0012, Japan Article History: Received 1 April 2005; Revised 11 May 2005; Accepted 18 May 2005

Maternally deposited mRNA encoding the Zic family zinc-finger protein Ci-macho1 is a determinant responsible for muscle cell differentiation in Ciona intestinalis embryos. In a previous study, we identified possible Ci-macho1 downstream genes, which include seven transcription factor genes and seven signaling molecule genes (Yagi, K., Satoh, N., Satou, Y., 2004. Identification of downstream genes of the ascidian muscle determinant gene Ci-macho1. Dev. Biol. 274, 478-489), suggesting complex Ci-macho1 downstream cascades. Here, we show that of the Ci-macho1 downstream genes, only Ci-Tbx6b and Ci-Tbx6c promote ectopic differentiation of muscle cells when misexpressed in non-muscle blastomeres. Overexpression of Ci-Tbx6b or Ci-Tbx6c in Ci-macho1 knockdown embryos is able to compensate for the functional loss of Ci-macho1 and promote differentiation of muscle cells. In addition, we show that knockdown of each of Ci-Tbx6b or Ci-Tbx6c suppresses the initiation of muscle protein gene expression, and both gene products appear to recognize a similar binding sequence. However, later expression of muscle protein genes at the tailbud stage is only reduced in Ci-Tbx6b knockdown embryos and undisturbed in Ci-Tbx6c knockdown embryos. Although ectopic expression or knockdown of Ci-ZicL alone does not affect muscle cell differentiation, simultaneous knockdown of Ci-Tbx6b, Ci-Tbx6c, and Ci-ZicL completely abolishes muscle cell differentiation, as in the case of knockdown of Ci-macho1 and Ci-ZicL. These results strongly suggest that muscle cell differentiation in Ciona embryos is controlled by four key factors: maternal macho1 and zygotic Tbx6b, Tbx6c, and ZicL. The two T-box genes are primary mediators of macho1 function, and cooperation between the zygotically expressed transcription factors is indispensable for muscle cell differentiation in Ciona embryos. Keywords: Ciona intestinalis; Autonomous muscle differentiation; Determinant gene macho1; Mediators Tbx6b and Tbx6c; A cooperator ZicL