Developmental gene activities in ascidian embryos

Sexual and asexual development: two distinct programs producing the same tunicate

Colonial tunicates are the only chordate that possess two distinct developmental pathways to produce an adult body: either sexually through embryogenesis or asexually through a stem cell-mediated renewal termed blastogenesis. Using the colonial tunicate Botryllus schlosseri, we combine transcriptomics and microscopy to build an atlas of the molecular and morphological signatures at each developmental stage for both pathways. The general molecular profiles of these processes are largely distinct. However, the relative timing of organogenesis and ordering of tissue-specific gene expression are conserved. By comparing the developmental pathways of B. schlosseri with other chordates, we identify hundreds of putative transcription factors with conserved temporal expression. Our findings demonstrate that convergent morphology need not imply convergent molecular mechanisms but that it showcases the importance that tissue-specific stem cells and transcription factors play in producing the same mature body through different pathways.

Ontology for the asexual development and anatomy of the colonial chordate Botryllus schlosseri

Ontologies provide an important resource to integrate information. For developmental biology and comparative anatomy studies, ontologies of a species are used to formalize and annotate data that are related to anatomical structures, their lineage and timing of development. Here, we have constructed the first ontology for anatomy and asexual development (blastogenesis) of a bilaterian, the colonial tunicate Botryllus schlosseri. Tunicates, like Botryllus schlosseri, are non-vertebrates and the only chordate taxon species that reproduce both sexually and asexually. Their tadpole larval stage possesses structures characteristic of all chordates, i.e. a notochord, a dorsal neural tube, and gill slits. Larvae settle and metamorphose into individuals that are either solitary or colonial. The latter reproduce both sexually and asexually and these two reproductive modes lead to essentially the same adult body plan. The Botryllus schlosseri Ontology of Development and Anatomy (BODA) will facilitate the comparison between both types of development. BODA uses the rules defined by the Open Biomedical Ontologies Foundry. It is based on studies that investigate the anatomy, blastogenesis and regeneration of this organism. BODA features allow the users to easily search and identify anatomical structures in the colony, to define the developmental stage, and to follow the morphogenetic events of a tissue and/or organ of interest throughout asexual development. We invite the scientific community to use this resource as a reference for the anatomy and developmental ontology of B. schlosseri and encourage recommendations for updates and improvements.

Transcriptional regulation of ZicL in the Ciona intestinalis embryo

We identified 5' upstream enhancers of two Ci-ZicL genes and characterized one of them in detail. Although the genes are tandemly repeated in the genome, the transcription of each seemed to be individually regulated. The 259-bp 5' flanking sequence contained essential elements for driving a correct spatiotemporal expression. This enhancer can be divided into two distinct modules. The A module was located between nucleotide positions -259 and -205 upstream of the putative transcription start site, and was necessary for activation in A6.2 and A6.4 blastomeres at the 32-cell stage. The BM module lay between nucleotide positions -205 and -89 and was responsible for activation in B6.2 and B6.4 blastomeres at the 32-cell stage and in A-line presumptive notochord, nerve cord, and muscle lineage cells at later stages. Two putative Fox-binding sites, one located within and the other downstream of the BM module, were necessary for the latter activity. Mutation at a potential Ets-binding site, located downstream of the BM module, caused ectopic activation of the reporter gene in a-line presumptive ectoderm cells. This suggests that repression in the a-line blastomeres is necessary for correct transcriptional control of the Ci-ZicL gene.

Systematic analysis of embryonic expression profiles of zinc finger genes in Ciona intestinalis

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.

Both the functional specificity and autoregulative activity of two ascidian T-box genes HrBra and HrTbx6 are likely to be mediated by the DNA-binding domain

T-box genes encode a family of transcription factors having conserved DNA-binding domains and diverged transcription regulatory domains, and each family member shows a specific expression pattern and plays a specific and crucial role in animal development. Two fundamental questions to be answered are whether the T-box gene functional specificity is located in the DNA-binding domain or in the transcription regulatory domain and how the specific expression of T-box genes is controlled. In the ascidian Halocynthia roretzi, Brachyury (HrBra) is expressed only in notochord cells while Tbx6 (HrTbx6) is expressed in muscle cells. In the present study, we made chimeric constructs of the two genes to determine the above mentioned questions. Our results suggest that the functional specificity of these two ascidian T-box genes is associated with the DNA-binding domain but not with the transcription regulatory domain. The 5' flanking region of both HrBra and HrTbx6 contains T-protein binding motifs near their minimal promoters that are associated with the autoregulative activation of these genes. Using the chimeric constructs, we also determined whether the autoregulative activity is mediated by the DNA-binding domain or by the transcription activation domain of the gene products. Our results suggest that the autoregulative activity of these two ascidian T-box genes is also mediated by the DNA-binding domain, not by the transcription activation domain of the encoded proteins.

Decoding cis-regulatory systems in ascidians

Ascidians, or sea squirts, are lower chordates, and share basic gene repertoires and many characteristics, both developmental and physiological, with vertebrates. Therefore, decoding cis-regulatory systems in ascidians will contribute toward elucidating the genetic regulatory systems underlying the developmental and physiological processes of vertebrates. cis-Regulatory DNAs can also be used for tissue-specific genetic manipulation, a powerful tool for studying ascidian development and physiology. Because the ascidian genome is compact compared with vertebrate genomes, both intergenic regions and introns are relatively small in ascidians. Short upstream intergenic regions contain a complete set of cis-regulatory elements for spatially regulated expression of a majority of ascidian genes. These features of the ascidian genome are a great advantage in identifying cis-regulatory sequences and in analyzing their functions. Function of cis-regulatory DNAs has been analyzed for a number of tissue-specific and developmentally regulated genes of ascidians by introducing promoter-reporter fusion constructs into ascidian embryos. The availability of the whole genome sequences of the two Ciona species, Ciona intestinalis and Ciona savignyi, facilitates comparative genomics approaches to identify cis-regulatory DNAs. Recent studies demonstrate that computational methods can help identify cis-regulatory elements in the ascidian genome. This review presents a comprehensive list of ascidian genes whose cis-regulatory regions have been subjected to functional analysis, and highlights the recent advances in bioinformatics and comparative genomics approaches to cis-regulatory systems in ascidians.

Using ascidian embryos to study the evolution of developmental gene regulatory networks

Ascidians are ideally positioned taxonomically at the base of the chordate tree to provide a point of comparison for developmental regulatory mechanisms that operate among protostomes, non-chordate deuterostomes, invertebrate chordates, and vertebrates. In this review, we propose a model for the gene regulatory network that gives rise to the ascidian notochord. The purpose of this model is not to clarify all of the interactions between molecules of this network, but to provide a working schematic of the regulatory architecture that leads to the specification of endoderm and the patterning of mesoderm in ascidian embryos. We describe a series of approaches, both computational and biological, that are currently being used, or are in development, for the study of ascidian embryo gene regulatory networks. It is our belief that the tools now available to ascidian biologists, in combination with a streamlined mode of development and small genome size, will allow for more rapid dissection of developmental gene regulatory networks than in more complex organisms such as vertebrates. It is our hope that the analysis of gene regulatory networks in ascidians can provide a basic template which will allow developmental biologists to superimpose the modifications and novelties that have arisen during deuterostome evolution.

Gene expression profiles of transcription factors and signaling molecules in the ascidian embryo: towards a comprehensive understanding of gene networks

Achieving a real understanding of animal development obviously requires a comprehensive rather than partial identification of the genes working in each developmental process. Recent decoding of genome sequences will enable us to perform such studies. An ascidian, Ciona intestinalis, one of the animals whose genome has been sequenced, is a chordate sharing a basic body plan with vertebrates, although its genome contains less paralogs than are usually seen in vertebrates. In the present study, we discuss the genomewide approach to networks of developmental genes in Ciona embryos. We focus on transcription factor genes and some major groups of signal transduction genes. These genes are comprehensively listed and examined with regard to their embryonic expression by in situ hybridization (http://ghost.zool.kyoto-u.ac.jp/tfst.html). The results revealed that 74% of the transcription factor genes are expressed maternally and that 56% of the genes are zygotically expressed during embryogenesis. Of these, 34% of the transcription factor genes are expressed both maternally and zygotically. The number of zygotically expressed transcription factor genes increases gradually during embryogenesis. As an example, and taking advantage of this comprehensive description of gene expression profiles, we identified transcription factor genes and signal transduction genes that are expressed at the early gastrula stage and that work downstream of beta-catenin, FoxD and/or Fgf9/16/20. Because these three genes are essential for ascidian endomesoderm specification, transcription factor genes and signal transduction genes involved in each of the downstream processes can be deduced comprehensively using the present approach.

The ascidian Mesp gene specifies heart precursor cells

Understanding the molecular basis of heart development is an important research area, because malformation of the cardiovascular system is among the most frequent inborn defects. Although recent research has identified molecules responsible for heart morphogenesis in vertebrates, the initial specification of heart progenitors has not been well characterized. Ascidians provide an appropriate experimental system for exploring this specification mechanism, because the lineage for the juvenile heart is well characterized, with B7.5 cells at the 110-cell stage giving rise to embryonic trunk ventral cells (TVCs) or the juvenile heart progenitors. Here, we show that Cs-Mesp, the sole ortholog of vertebrate Mesp genes in the ascidian Ciona savignyi, is specifically and transiently expressed in the embryonic heart progenitor cells (B7.5 cells). Cs-Mesp is essential for the specification of heart precursor cells, in which Nkx, HAND and HAND-like (NoTrlc) genes are expressed. As a result, knockdown of Cs-Mesp with specific morpholino antisense oligonucleotides causes failure of the development of the juvenile heart. Together with previous evidence obtained in mice, the present results suggest that a mechanism for heart specification beginning with Mesp through Nkx and HAND is conserved among chordates.

A Twist-like bHLH gene is a downstream factor of an endogenous FGF and determines mesenchymal fate in the ascidian embryos

Ascidian larvae develop mesenchyme cells in their trunk. A fibroblast growth factor (FGF9/16/20) is essential and sufficient for induction of the mesenchyme in Ciona savignyi. We have identified two basic helix-loop-helix (bHLH) genes named Twist-like1 and Twist-like2 as downstream factors of this FGF. These two genes are phylogenetically closely related to each other, and were expressed specifically in the mesenchymal cells after the 110-cell stage. Gene-knockdown experiments using a specific morpholino oligonucleotide demonstrated that Twist-like1 plays an essential role in determination of the mesenchyme and that Twist-like2 is a downstream factor of Twist-like1. In addition, both overexpression and misexpression of Twist-like1 converts non-mesenchymal cells to mesenchymal cells. We also demonstrate that the upstream regulatory mechanisms of Twist-like1 are different between B-line mesenchymal cells and the A-line mesenchymal cells called 'trunk lateral cells'. FGF9/16/20 is required for the expression of Twist-like1 in B-line mesenchymal precursor cells, whereas FGF, FoxD and another novel bHLH factor called NoTrlc are required for Twist-like1 to be expressed in the A-line mesenchymal precursor cells. Therefore, two different but partially overlapping mechanisms are required for the expression of Twist-like1 in the mesenchymal precursors, which triggers the differentiation of the mesenchyme in Ciona embryos.

Isolation and characterization of beta-catenin downstream genes in early embryos of the ascidian Ciona savignyi

Nuclear localization of beta-catenin is most likely the first step of embryonic axis formation or embryonic cell specification in a wide variety of animal groups. Therefore, the elucidation of beta-catenin target genes is a key research subject in understanding the molecular mechanisms of the early embryogenesis of animals. In Ciona savignyi embryos, nuclear accumulation of beta-catenin is the first step of endodermal cell specification. Previous subtractive hybridization screens of mRNAs between beta-catenin-overexpressed embryos and nuclear beta-catenin-depleted embryos have resulted in the identification of beta-catenin downstream genes in Ciona embryos. In the present study, I characterize seven additional beta-catenin downstream genes, Cs-cadherinII, Cs-protocadherin, Cs-Eph, Cs-betaCD1, Cs-netrin, Cs-frizzled3/6, and Cs-lefty/antivin. All of these genes were expressed in vegetal blastomeres between the 16-cell and 110-cell stages, although their spatial and temporal expression patterns were different from one another. In situ hybridizations and real-time PCR revealed that the expression of all of these genes was up-regulated in beta-catenin-overexpressed embryos, and down-regulated in beta-catenin-suppressed embryos. Therefore, the accumulation of beta-catenin in the nuclei of vegetal blastomeres activates various vegetally expressed genes with potentially important functions in the specification of these cells.

Expression of Raldh2, Cyp26 and Hox-1 in normal and retinoic acid-treated Ciona intestinalis embryos

Spatially regulated synthesis and degradation of retinoic acid (RA) organize embryonic pattern formation in vertebrate embryos. Here, we show expression pattern of genes encoding Ciona intestinalis homologs of the retinaldehyde dehydrogenase, RALDH2, and the cytochrome P450 RA-degrading enzyme, CYP26, in normal and RA-treated embryos. The Ciona homolog of Raldh2, Ci-Raldh2, was expressed in a few muscle-lineage blastomeres in the middle gastrula. Strong expression was then restricted to the anterior-most three muscle cells on each side of the tailbud embryo. The Ciona homolog of Cyp26, Ci-Cyp26, was expressed in the presumptive brain cells in the middle gastrula. The expression was then upregulated in the neck region. The posterior end of the tail was also weakly stained. Non-overlapping expression domains of Ci-Raldh2 and Ci-Cyp26 look similar to those in vertebrates, although the expression of both genes was restricted to a small number of cells in Ciona embryos. RA upregulated Ci-Cyp26 expression and slightly downregulated Ci-Raldh2 expression in the tailbud embryo. We also show expression pattern of a Hox-1 ortholog (CiHox-1) in the Ciona embryo. CiHox-1 was expressed in two separated regions of the nerve cord and neck epidermis at the neurula stage. Expression pattern of these three genes are essentially similar to that in vertebrates.

Application of Minos, one of the Tc1/mariner superfamily transposable elements, to ascidian embryos as a tool for insertional mutagenesis

As it has a simple genome structure, Ciona intestinalis is a good chordate species for studying the function of genes. To this end, it is a key requirement to introduce insertional mutagenesis using a transposable element to the ascidian system. The present study focuses on Minos, one of the Tc1/mariner superfamily transposons that is already used in a human cell line. By extrachromosomal excision and transposition assays, we found that Minos activity is very high in C. intestinalis. We also demonstrated the nuclear localization activity of Minos transposase in Ciona embryos. From these tests, we concluded that Minos transposase has complete activity when it is expressed in C. intestinalis, suggesting that Minos has the potential to be used for genome-wide insertional mutagenesis of C. intestinalis.

EST analysis of gene expression in testis of the ascidian Ciona intestinalis

To explore the gene expression underlying spermatogenesis, a large-scale analysis has been done on the cDNAs from testis of the ascidian, Ciona intestinalis. A set of 5,461 expressed sequence tags was analyzed and grouped into 2,806 independent clusters. Approximately 30% of the clusters showed significant sequence matches to the proteins reported in DDBJ/GenBank/EMBL database including a set of proteins closely related to the gene regulation during spermatogenesis, functional and morphological changes of spermatogenic cells during spermiogenesis, and physiological functions of sperm, as well as those with housekeeping functions commonly expressed in other cells. Some clones show similarities to the proteins present in vertebrate lymphocytes, suggesting a primitive immune system in ascidians. We have also found some genes that are known to participate in hormonal regulation of spermatogenesis in vertebrates. The large majority of the genes expressed in Ciona testis show no significant matches to known proteins and the further analysis of these genes may shed new light on the molecular mechanism of spermatogenesis and sperm functions.

Expression of hedgehog genes in Ciona intestinalis embryos

The configuration of the ascidian tadpole larva represents the most simplified and primitive chordate body plan. The present study revealed that Ciona intestinalis contains two hedgehog genes (Ci-hh1 and Ci-hh2), which are likely to be independent duplicate genes in this animal and ancestral to the three types of hedgehog gene of vertebrates. Ci-hh1 was expressed maternally and its maternal transcript was distributed evenly in fertilized eggs and early embryos. Ci-hh2 was expressed zygotically in the tailbud embryo and its transcript was evident only in cells of the ventral nerve cord. The notochord cells did not express the hedgehog genes in Ciona embryos.

Multiple functions of a Zic-like gene in the differentiation of notochord, central nervous system and muscle inCiona savignyiembryos

Multiple functions of a Zic-like zinc finger transcription factor gene (Cs-ZicL) were identified in Ciona savignyi embryos. cDNA clones for Cs-ZicL, a β-catenin downstream genes, were isolated and the gene was transiently expressed in the A-line notochord/nerve cord lineage and in B-line muscle lineage from the 32-cell stage and later in a-line CNS lineage from the 110-cell stage. Suppression of Cs-ZicL function with specific morpholino oligonucleotide indicated that Cs-ZicL is essential for the formation of A-line notochord cells but not of B-line notochord cells, essential for the CNS formation and essential for the maintenance of muscle differentiation. The expression of Cs-ZicL in the A-line cells is downstream of β-catenin and a β-catenin-target gene, Cs-FoxD, which is expressed in the endoderm cells from the 16-cell stage and is essential for the differentiation of notochord. In spite of its pivotal role in muscle specification, the expression of Cs-ZicL in the muscle precursors is independent of Cs-macho1, which is another Zic-like gene encoding a Ciona maternal muscle determinant, suggesting another genetic cascade for muscle specification independent of Cs-macho1. Cs-ZicL may provide a future experimental system to explore how the gene expression in multiple embryonic regions is controlled and how the single gene can perform different functions in multiple types of embryonic cells.

Analyzing gene regulation in ascidian embryos: new tools for new perspectives

Ascidians are marine protochordates at the evolutionary boundary between invertebrates and vertebrates. Ascidian larvae provide a simple system for unraveling gene regulation networks underlying the formation of the basic chordate body plan. After being used for over a century as a model for embryological studies, ascidians have become, in the past decade, an increasingly popular organism for studying gene regulation. Part of the renewed appeal of this system is the use of electroporation to introduce transgenic DNAs into developing embryos. This method is considerably more efficient than conventional microinjection assays and permits the simultaneous transformation of hundreds of embryos. Electroporation has allowed the identification and characterization of cis-regulatory DNAs that mediate gene expression in a variety of tissues, including the notochord, tail muscles, CNS, and endoderm. Electroporation has also provided a simple method for misexpressing patterning genes and producing dominant mutant phenotypes. Recent studies have used electroporation to create "knock-out" phenotypes by overexpressing dominant negative forms of particular proteins. Here we review the past and present uses of electroporation in ascidian development, and speculate on potential future uses.

Ciona intestinalis cDNA projects: expressed sequence tag analyses and gene expression profiles during embryogenesis

Ascidians are primitive chordates. Their fertilized egg develops quickly into a tadpole-type larva, which consists of a small number but distinct types of cells, including those of epidermis, central nervous system with two sensory organs, endoderm and mesenchyme in the trunk, and notochord and muscle in the tail. This configuration of the ascidian tadpole is thought to represent the most simplified and primitive chordate body plan. In addition, the free-swimming and non-feeding larvae metamorphose into sessile and filter-feeding adults. The genome size of Ciona intestinalis is estimated to be about 160 Mb, and the number of genes approximately 15,500. The present Ciona cDNA projects focused on gene expression profiles of fertilized eggs, 32-110-cell stage embryos, tailbud embryos, larvae, and young adults. Expressed sequence tags (ESTs) of the 5'-most end and 3'-most end of more than 3000 clones were determined at each developmental stage, and the clones were categorized into independent clusters using the 3'-end sequences. Nearly 1000 clusters of them were then analyzed in detail of their sequences against a BLASTX search. This analysis demonstrates that, on average, half of the clusters showed proteins with sequence similarities to known proteins and the other half did not show sequence similarities to known proteins. Genes with sequence similarities were further categorized into three major subclasses, depending on their functions. Furthermore, the expression profiles of all of the clusters were analyzed by whole-mount in situ hybridization. This analysis highlights gene expression patterns characteristic to each developmental stage. As a result, the present study provides many new molecular markers for each of the tissues and/or organs that constitutes the Ciona tailbud embryo. This sequence information will be used for further comparative genome studies to explore molecular mechanisms involved in the formation of one of the most primitive chordate body plans. All of the data fully characterized may be viewed at the web site http://ghost.zool.kyoto-u.ac.jp.

Gene expression profiles in Ciona intestinalis cleavage-stage embryos

A total of 1612 expression sequence tags derived from Ciona intestinalis cleavage-stage embryos were examined to explore detailed gene expression profiles. The 3' sequences indicate that the 1612 clones can be categorized into 1066 independent clusters. DDBJ database search suggested that 496 of them showed significant matches to reported proteins with distinct functions. Among them 69 are associated with cell-cell communications and 41 with transcription factors. In situ hybridization of all 1066 clusters showed that 84 clusters exhibited blastomere-specific pattern of expression, and many of these genes seem to encode for novel proteins. One of the interesting findings is that most of them were expressed in the precursor cells of multiple tissues. Among them 28 genes were expressed in the marginal zone of the 32-cell embryo. The blastomeres in this region are thought to receive an inductive signal from the vegetal blastomeres. Many of the blastomere-specific genes did not show similarity to known proteins. The present analysis therefore provides new information for further analyses on the cell fate specification in the Ciona embryo.

Regulation of the muscle-specific expression and function of an ascidian T-box gene, As-T2

The Tbx6 T-box genes are expressed in somite precursor cells of vertebrate embryos and are essential for the differentiation of paraxial mesoderm. However, it is unclear how spatial regulation of the gene expression is controlled and how the genes function to promote muscle differentiation. The Tbx6-related gene As-T2 of the ascidian Halocynthia roretzi is first expressed very transiently in endodermal cells around the 32-∼44-cell stage, is then expressed distinctly and continuously in muscle precursor cells, and later in epidermal cells situated in the distal tip region of the elongating tail. We now show that inhibition of As-T2-mediated transcriptional activation by microinjection of As-T2/EnR into one-cell embryos resulted in suppression of the expression of the muscle-specific actin gene (HrMA4) and myosin heavy chain gene (HrMHC), but the injection did not affect the differentiation of endodermal cells or tail tip cells, suggesting that the primary function of As-T2 is associated with muscle cell differentiation. The 5′ flanking region of As-T2 contains two promoter modules that regulate its specific expression: a distal module that responsible for its specific expression in the tail, and a proximal module required for its muscle-specific expression. Around the proximal module, there are two putative T protein-binding motifs (TTCACACTT). Co-injection of an As-T2/lacZ construct with or without the T-binding motifs together with As-T2 mRNA revealed that these motifs are essential for autoregulatory activation of the gene itself. In addition, we found that the minimal promoter regions of HrMA4 and HrMHC contain T-binding motifs. Co-injection of HrMA4/lacZ or HrMHC/lacZ containing the T-binding motifs along with As-T2 mRNA revealed that As-T2 protein binds to these motifs to upregulate the gene activity. Taking into account the recent finding of maternal molecules for muscle differentiation, we propose a model for a genetic cascade that includes As-T2 as a regulator of muscle cell differentiation in the ascidian embryo.

Gene expression profiles in Ciona intestinalis tailbud embryos

A set of 3423 expressed sequence tags derived from the Ciona intestinalis tailbud embryos was categorized into 1213 independent clusters. When compared with DNA Data Bank of Japan database, 502 clusters of them showed significant matches to reported proteins with distinct function, whereas 184 lacked sufficient information to be categorized (including reported proteins with undefined function) and 527 had no significant similarities to known proteins. Sequence similarity analyses of the 502 clusters in relation to the biosynthetic function, as well as the structure of the message population at this stage, demonstrated that 390 of them were associated with functions that many kinds of cells use, 85 with cell-cell communication and 27 with transcription factors and other gene regulatory proteins. All of the 1213 clusters were subjected to whole-mount in situ hybridization to analyze the gene expression profiles at this stage. A total of 387 clusters showed expression specific to a certain tissue or organ; 149 showed epidermis-specific expression; 34 were specific to the nervous system; 29 to endoderm; 112 to mesenchyme; 32 to notochord; and 31 to muscle. Many genes were also specifically expressed in multiple tissues. The study also highlighted characteristic gene expression profiles dependent on the tissues. In addition, several genes showed intriguing expression patterns that have not been reported previously; for example, four genes were expressed specifically in the nerve cord cells and one gene was expressed only in the posterior part of muscle cells.

This study provides molecular markers for each of the tissues and/or organs that constitutes the Ciona tailbud embryo. The sequence information will also be used for further genome scientific approach to explore molecular mechanisms involved in the formation of one of the most primitive chordate body plans.

Ascidian embryos as a model system to analyze expression and function of developmental genes

Ascidians have served as an appropriate experimental system in developmental biology for more than a century. The fertilized egg develops quickly into a tadpole larva, which consists of a small number of organs including epidermis, central nervous system with two sensory organs, endoderm and mesenchyme in the trunk, and notochord and muscle in the tail. This configuration of the ascidian tadpole is thought to represent the most simplified and primitive chordate body plan. Their embryogenesis is simple, and lineage of embryonic cells is well documented. The ascidian genome contains a basic set of genes with less redundancy compared to the vertebrate genome. Cloning and characterization of developmental genes indicate that each gene is expressed under discrete spatio-temporal pattern within their lineage. In addition, the use of various molecular techniques in the ascidian embryo system highlights its advantages as a future experimental system to explore the molecular mechanisms underlying the expression and function of developmental genes as well as genetic circuitry responsible for the establishment of the basic chordate body plan. This review is aimed to highlight the recent advances in ascidian embryology.