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.

A genomewide survey of developmentally relevant genes in Ciona intestinalis. V. Genes for receptor tyrosine kinase pathway and Notch signaling pathway

In the present survey, we identified most of the genes involved in the receptor tyrosine kinase (RTK), mitogen activated protein kinase (MAPK) and Notch signaling pathways in the draft genome sequence of Ciona intestinalis, a basal chordate. Compared to vertebrates, most of the genes found in the Ciona genome had fewer paralogues, although several genes including ephrin, Eph and fringe appeared to have multiplied or duplicated independently in the ascidian genome. In contrast, some genes including kit/flt, PDGF and Trk receptor tyrosine kinases were not found in the present survey, suggesting that these genes are innovations in the vertebrate lineage or lost in the ascidian lineage. The gene set identified in the present analysis provides an insight into genes for the RTK, MAPK and Notch signaling pathways in the ancient chordate genome and thereby how chordates evolved these signaling pathway.

A genomewide survey of developmentally relevant genes in Ciona intestinalis. VII. Molecules involved in the regulation of cell polarity and actin dynamics

In the present study, genes involved in the pathways that establish cell polarity and cascades regulating actin dynamics were identified in the completely sequenced genome of Ciona intestinalis, a basal chordate. It was revealed that the Ciona genome contains orthologous genes of each component of aPKC-Par and PCP pathways and WASP/WAVE/SCAR and ADF/cofilin cascades, with less redundancy than the vertebrate genomes, suggesting that the conserved pathways/cascades function in Ciona development. In addition, the present study found that the orthologous proteins of five gene groups (Tc10, WRCH, RhoD, PLC-L, and PSKH) are conserved in humans and Ciona but not in Drosophila melanogaster, suggesting a similarity in the gene composition of Ciona to that of vertebrates. Ciona intestinalis, therefore, may provide refined clues for the study of vertebrate development and evolution.

A genomewide survey of developmentally relevant genes in Ciona intestinalis. III. Genes for Fox, ETS, nuclear receptors and NFkappaB

A survey against the draft genome sequence and the cDNA/EST database of Ciona intestinalis identified a number of genes encoding transcription factors regulating a variety of processes including development. In the present study, we describe almost complete sets of genes for Fox, ETS-domain transcription factors, nuclear receptors, and NFkappaB as well as other factors regulating NFkappaB activity, with their phylogenetic nature. Vertebrate Fox transcription factors are currently delineated into 17 subfamilies: FoxA to FoxQ. The present survey yielded 29 genes of this family in the Ciona genome, 24 of which were Ciona orthologues of known Fox genes. In addition, we found 15 ETS genes, 17 nuclear receptor genes, and several NFkappaB signaling pathway genes in the Ciona genome. The number of Ciona genes in each family is much smaller than that of vertebrates, which represents a simplified feature of the ascidian genome. For example, humans have two NFkappaB genes, three Rel genes, and five NFAT genes, while Ciona has one gene for each family. The Ciona genome also contains smaller numbers of genes for the NFkappaB regulatory system, i.e. after the split of ascidians/vertebrates, vertebrates evolved a more complex NFkappaB system. The present results therefore provide molecular information for the investigation of complex developmental processes, and an insight into chordate evolution.

A genomewide survey of developmentally relevant genes in Ciona intestinalis. IX. Genes for muscle structural proteins

Ascidians are simple chordates that are related to, and may resemble, vertebrate ancestors. Comparison of ascidian and vertebrate genomes is expected to provide insight into the molecular genetic basis of chordate/vertebrate evolution. We annotated muscle structural (contractile protein) genes in the completely determined genome sequence of the ascidian Ciona intestinalis, and examined gene expression patterns through extensive EST analysis. Ascidian muscle protein isoform families are generally of similar, or lesser, complexity in comparison with the corresponding vertebrate isoform families, and are based on gene duplication histories and alternative splicing mechanisms that are largely or entirely distinct from those responsible for generating the vertebrate isoforms. Although each of the three ascidian muscle types - larval tail muscle, adult body-wall muscle and heart - expresses a distinct profile of contractile protein isoforms, none of these isoforms are strictly orthologous to the smooth-muscle-specific, fast or slow skeletal muscle-specific, or heart-specific isoforms of vertebrates. Many isoform families showed larval-versus-adult differential expression and in several cases numerous very similar genes were expressed specifically in larval muscle. This may reflect different functional requirements of the locomotor larval muscle as opposed to the non-locomotor muscles of the sessile adult, and/or the biosynthetic demands of extremely rapid larval development.

Microarray analysis of embryonic retinoic acid target genes in the ascidian Ciona intestinalis

Many chordate- and vertebrate-specific characteristics develop depending on retinoic acid (RA). Because the gene encoding the RA receptor exists only in chordates, RA function seems to be involved in chordate evolution. A cDNA microarray analysis of 9287 non-redundant cDNA clones was used to screen for RA target genes in the ascidian Ciona intestinalis. In addition, the spatial expression pattern of 94 candidate RA target genes was examined by in situ hybridization in RA-treated and control embryos. Strong RA-induced upregulation of Hox-1 and Cyp26 was observed, as is the case in vertebrates. In addition, a number of novel candidate target genes was identified. These included transcription factors and signaling molecules, suggesting that various differentiation and/or morphogenetic pathways are modulated by RA. The expression of cell adhesion molecules, cytoskeletal proteins and extracellular matrix components was affected by RA. Changes in the expression pattern of these genes may be a direct cause of abnormal morphogenesis of the anterior neural tissues. RA also affected the expression of genes that seemed to be involved in neuronal functions. Although obvious homeotic transformation has not been observed, the function of various neural cell types seemed to be impaired by RA. The microarray data are reliable and will contribute to comprehensive understanding of RA action in the development and evolution of chordates.

A genomewide survey of developmentally relevant genes in Ciona intestinalis. X. Genes for cell junctions and extracellular matrix

Cell junctions and the extracellular matrix (ECM) are crucial components in intercellular communication. These systems are thought to have become highly diversified during the course of vertebrate evolution. In the present study, we have examined whether the ancestral chordate already had such vertebrate systems for intercellular communication, for which we have searched the genome of the ascidian Ciona intestinalis. From this molecular perspective, the Ciona genome contains genes that encode protein components of tight junctions, hemidesmosomes and connexin-based gap junctions, as well as of adherens junctions and focal adhesions, but it does not have those for desmosomes. The latter omission is curious, and the ascidian type-I cadherins may represent an ancestral form of the vertebrate type-I cadherins and desmosomal cadherins, while Ci-Plakin may represent an ancestral protein of the vertebrate desmoplakins and plectins. If this is the case, then ascidians may have retained ancestral desmosome-like structures, as suggested by previous electron-microscopic observations. In addition, ECM genes that have been regarded as vertebrate-specific were also found in the Ciona genome. These results suggest that the last common ancestor shared by ascidians and vertebrates, the ancestor of the entire chordate clade, had essentially the same systems of cell junctions as those in extant vertebrates. However, the number of such genes for each family in the Ciona genome is far smaller than that in vertebrate genomes. In vertebrates these ancestral cell junctions appear to have evolved into more diverse, and possibly more complex, forms, compared with those in their urochordate siblings.

A genomewide survey of developmentally relevant genes in Ciona intestinalis. VIII. Genes for PI3K signaling and cell cycle

Cell growth and cell divisions are two fundamental biological processes for cells in multi-cellular organisms. The molecules involved in these biological processes are highly conserved within eukaryotes, including plants and unicellular organisms such as yeast. However, some regulatory molecules seem to be innovated during animal evolution. Therefore, to understand how the ubiquitous systems have evolved or have been conserved, we examined genes for the phosphoinositide 3-kinase (PI3K) pathway that is important for cell growth, and genes for cell cycle regulation in the genome of Ciona intestinalis. It was found that the Ciona intestinalis genome contains all the essential constituents of the PI3K pathway. In addition, the class IB PI3K catalytic and regulatory subunits, which had not previously been known in animals other than mammals, were found in the Ciona genome. Similarly, all essential cyclins and CDKs were found in the Ciona genome, while cyclin G and cyclin L were likely to be independently lost in the ascidian lineage, which may be dispensable for the cell cycle. Cyclin F, which was previously known only in vertebrates, was not found in the Ciona genome. Therefore, this gene was probably innovated during the evolution of vertebrates to be involved in vertebrate-specific cell cycle regulation. Since Ciona is regarded as one of the most primitive extant chordates, the present analysis gives us an insight into how these fundamental biological genes are evolved or are conserved during chordate evolution.

A genomewide survey of developmentally relevant genes in Ciona intestinalis. I. Genes for bHLH transcription factors

The basic helix-loop-helix (bHLH) proteins are transcription factors that play important roles in many biological processes, including the development of various animals. We identified 46 genes encoding bHLH proteins in the draft genome sequence of the basal chordate Ciona intestinalis. These 46 genes represent an almost complete set of bHLH genes in this animal. This number is comparable to 39 and 58 bHLH genes in those of Caenorhabditis elegans and Drosophila melanogaster but is much smaller than the 125 in the human genome. Genes that encode NeuroD, Beta3, Oligo, SCL, NSCL, SRC, Clock and Bmal were not found in the Ciona genome. We could also identify groucho and CBP orthologues in the Ciona genome. In addition, the comparison between the numbers of orthologous human and Ciona bHLH factors reveals the simplicity of the Ciona genome, in accordance with its phylogenetic position within chordates. The present analysis provides an insight into the basic set of bHLH genes that the last common ancestor of ascidians and vertebrates had, and will provide important background information for future studies using ascidians as a model system for vertebrate development.

A genomewide survey of developmentally relevant genes in Ciona intestinalis. IV. Genes for HMG transcriptional regulators, bZip and GATA/Gli/Zic/Snail

Many kinds of transcription factors and regulators play key roles in a variety of developmental processes. In the present survey, genes encoding proteins with conserved HMG-box, bZip domains, and some types of zinc finger motifs were surveyed in the completely sequenced genome of Ciona intestinalis. In the present analysis, 21 HMG-box-containing genes and 26 bZip genes were identified as well as four small groups of zinc finger genes in the Ciona genome. The results also showed that a less redundant set of genes is present in the Ciona genome compared with vertebrate genomes. In addition, cDNA clones for almost all genes identified have been cloned and distributed as a " Ciona intestinalis Gene Collection Release I". The present comprehensive analysis therefore provides a means to study the role of these transcription factors in developmental processes of basal chordates.

A genomewide survey of developmentally relevant genes in Ciona intestinalis. II. Genes for homeobox transcription factors

Homeobox-containing genes play crucial roles in various developmental processes, including body-plan specification, pattern formation and cell-type specification. The present study searched the draft genome sequence and cDNA/EST database of the basal chordate Ciona intestinalis to identify 83 homeobox-containing genes in this animal. This number of homeobox genes in the Ciona genome is smaller than that in the Caenorhabditis elegans, Drosophila melanogaster, human and mouse genomes. Of the 83 genes, 76 have possible human orthologues and 7 may be unique to Ciona. The ascidian homeobox genes were classified into 11 classes, including Hox class, NK class, Paired class, POU class, LIM class, TALE class, SIX class, Prox class, Cut class, ZFH class and HNF1 class, according to the classification scheme devised for known homeobox genes. As to the Hox cluster, the Ciona genome contains single copies of each of the paralogous groups, suggesting that there is a single Hox cluster, if any, but genes orthologous to Hox7, 8, 9 and 11 were not found in the genome. In addition, loss of genes had occurred independently in the Ciona lineage and was noticed in Gbx of the EHGbox subclass, Sax, NK3, Vax and vent of the NK class, Cart, Og9, Anf and Mix of the Paired class, POU-I, III, V and VI of the POU class, Lhx6/7 of the LIM class, TGIF of the TALE class, Cux and SATB of the Cut class, and ZFH1 of the ZFH class, which might have reduced the number of Ciona homeobox genes. Interestingly, one of the newly identified Ciona intestinalis genes and its vertebrate counterparts constitute a novel subclass of HNF1 class homeobox genes. Furthermore, evidence for the gene structures and expression of 54 of the 83 homeobox genes was provided by analysis of ESTs, suggesting that cDNAs for these 54 genes are available. The present data thus reveal the repertoire of homeodomain-containing transcription factors in the Ciona genome, which will be useful for future research on the development and evolution of chordates.

Large scale EST analyses in Ciona intestinalis: its application as Northern blot analyses

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.

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.

The ascidian tadpole larva: comparative molecular development and genomics

Evolution is of interest not only to developmental biology but also to genetics and genomics. We are witnessing a new era in which evolution, development, genetics and genomics are merging to form a new discipline, a good example of which is the study of the origin and evolution of the chordates. Recent studies on the formation of the notochord and the dorsal neural tube in the increasingly famous Ciona intestinalis tadpole larva, and the availability of its draft genome, show how the combination of comparative molecular development and evolutionary genomics might help us to better understand our chordate ancestor.

Retinoic acid affects gene expression and morphogenesis without upregulating the retinoic acid receptor in the ascidian Ciona intestinalis

Many chordate-specific morphological features develop depending on retinoic acid (RA). We isolated cDNA clones encoding a retinoic acid receptor (CiRAR) and a retinoid X receptor (CiRXR) in the ascidian Ciona intestinalis. CiRAR mRNA was detected in the anterior ectoderm and endoderm during gastrulation. The expression persists in the head endoderm and two discrete regions of the nerve cord in the tailbud embryo. CiRXR mRNA was ubiquitously expressed. RA affected closure of the neural tube and formation of the adhesive papillae. However, no obvious upregulation in CiRAR expression was observed. Expression of some, but not all, of the neural and papilla-specific genes was reduced in the RA-treated embryo. These results suggest limited roles of CiRAR in ascidian embryos.

Comparative expression analysis of Adh3 during arthropod, urochordate, cephalochordate, and vertebrate development challenges its predicted housekeeping role

Gene and genome duplications in the vertebrate lineage explain the complexity of extant gene families. Among these, the medium-chain alcohol dehydrogenase (ADH), which expanded by tandem duplications after the cephalochordate-vertebrate split, is a good model with which to analyze the evolution of gene function. Although the ancestral member of this family, ADH3, has been strictly conserved throughout animal evolution, its physiological role is still controversial. Previous evidence indicates that it contributes to formaldehyde cytoprotection, retinoic acid metabolism, and nitric oxide homeostasis. We performed in situ hybridization during Drosophila, ascidian (Ciona intestinalis), and zebrafish (Danio rerio) development. We showed that Adh3 expression was restricted to the fat body in Drosophila embryos at stage 17 and to the anterior endoderm in C. intestinalis tail bud, whereas in the zebrafish 2.5-day larvae the signal appeared widespread. A more comprehensive expression analysis including amphioxus and mice revealed that ancestral Adh3 was tissue specific, whereas a widespread expression was later attained in vertebrates. These variations occurred concomitantly with the expansion of the ADH family and the acquisition of new functions but were unlinked to the genomic changes that led to the transition from fractional to global methylation in vertebrates. Our data challenge the housekeeping role of ADH3 and question its involvement in the prevertebrate retinoic acid pathway.

A conserved role for the MEK signalling pathway in neural tissue specification and posteriorisation in the invertebrate chordate, the ascidian Ciona intestinalis

Ascidians are invertebrate chordates with a larval body plan similar to that of vertebrates. The ascidian larval CNS is divided along the anteroposterior axis into sensory vesicle, neck, visceral ganglion and tail nerve cord. The anterior part of the sensory vesicle comes from the a-line animal blastomeres, whereas the remaining CNS is largely derived from the A-line vegetal blastomeres. We have analysed the role of the Ras/MEK/ERK signalling pathway in the formation of the larval CNS in the ascidian, Ciona intestinalis. We show evidence that this pathway is required, during the cleavage stages, for the acquisition of: (1) neural fates in otherwise epidermal cells (in a-line cells); and (2) the posterior identity of tail nerve cord precursors that otherwise adopt a more anterior neural character (in A-line cells). Altogether, the MEK signalling pathway appears to play evolutionary conserved roles in these processes in ascidians and vertebrates, suggesting that this may represent an ancestral chordate strategy.

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.

Tail regression in Ciona intestinalis (Prochordate) involves a Caspase-dependent apoptosis event associated with ERK activation

Two apoptotic events take place during embryonic development of Ciona intestinalis. The first concerns extra-embryonic cells and precedes hatching. The second controls tail regression at metamorphosis, occurs through a polarized wave originating from tail extremity, and is caspase dependent. This was shown by: (1) in vivo incorporation of a fluorescent marker of caspase activation in different cell types of the tail; (2) detection of an activated form of caspase 3-like protein by western blotting; and (3) failure of 30% of larvae to undergo metamorphosis after treatment of fertilized eggs with a pan-caspase inhibitor. In addition, Ciona embryos express a single ERK protein, specifically phosphorylated at metamorphosis. ERK activation was shown to be located in cells of the tail. Addition of MEK inhibitor in the culture medium prevented ERK activation and metamorphosis. In silico analysis of Ciona genome pointed to 15 caspases with high homology with humans, and a single ERK gene with high homology to both mammalian ERK1 and ERK2. It is concluded that the sequence of events leading to metamorphosis includes ERK phosphorylation followed by caspase-dependent apoptosis and tail regression.

Movies available on-line

Control of intercalation is cell-autonomous in the notochord of Ciona intestinalis

Dishevelled signaling plays a critical role in the control of cell intercalation during convergent extension in vertebrates. This study presents evidence that Dishevelled serves a similar function in the Ciona notochord. Embryos transgenic for mutant Dishevelled fail to elongate their tails, and notochord cells fail to intercalate, though notochord cell fates are unaffected. Analysis of mosaic transgenics revealed that the effects of mutant Dishevelled on notochord intercalation are cell-autonomous in Ciona, though such defects have nonautonomous effects in Xenopus. Furthermore, our data indicate that notochord cell intercalation in Ciona does not require the progressive signals which coordinate cell intercalation in the Xenopus notochord, highlighting an important difference in how mediolateral cell intercalation is controlled in the two animals. Finally, this study establishes the Ciona embryo as an effective in vivo system for the study of the molecular control of morphogenetic cell movements in chordates.

Gene expression profiles in young adult Ciona intestinalis

Comparison of 12,230 expressed sequence tags (ESTs) of 3' ends of cDNA clones derived from young adults of Ciona intestinalis allowed us to categorize them into 976 independent clusters. When the 5'-end sequences of 10,400 ESTs of the 976 clusters were compared with the sequences in databases, 406 of the clusters showed significant matches ( P < E-15) with reported proteins with defined functions, while 117 showed matches with putative proteins for which there is not enough information to categorize their function, and 453 had no significant sequence similarities to known proteins. The 406 clusters with sequence similarity to proteins with defined functions consisted of 304 clusters related to proteins with functions common to many kinds of cells, 73 related to proteins associated with cell-cell communication and 29 related to transcription factors. Spatial expression of all of the 976 clusters was examined by a newly improved whole-mount in situ hybridization method. A total of 430 clusters did not show distinct in situ hybridization signals, while 122 clusters showed ubiquitous distribution of signals, and 253 clusters showed signals in multiple tissues. The remaining 171 clusters showed signals specific to a certain organ or tissue: 16 showed epidermis-specific expression, 3 were specific to the neural complex, 1 to heart, 6 to body-wall muscle, 94 to pharyngeal gill, 3 to esophagus, 26 to stomach, 1 to intestine and 21 to endostyle. Many of these organ-specific genes encode proteins with no sequence similarity to known proteins. The present analysis thus highlights characteristic gene expression profiles of Ciona young adults and provides not only molecular markers for organs and tissues but also transcriptomic information useful for further genomic analyses of this model organism.

Tail morphogenesis in the ascidian, Ciona intestinalis, requires cooperation between notochord and muscle

We present evidence that notochord and muscle differentiation are crucial for morphogenesis of the ascidian tail. We developed a novel approach for embryological manipulation of the developing larval tissues using a simple method to introduce DNA into Ciona intestinalis and the several available tissue-specific promoters. With such promoters, we misexpressed the Xenopus homeobox gene bix in notochord or muscle of Ciona embryos as a means of interfering with development of these tissues. Ciona embryos expressing bix in the notochord from the 64-cell stage develop into larvae with very short tails, in which the notochord precursors fail to intercalate and differentiate. Larvae with mosaic expression of bix have intermediate phenotypes, in which a partial notochord is formed by the precursor cells that did not receive the transgene while the precursors that express the transgene cluster together and fail to undergo any of the cell-shape changes associated with notochord differentiation. Muscle cells adjacent to differentiated notochord cells are properly patterned, while those next to the notochord precursor cells transformed by bix exhibit various patterning defects. In these embryos, the neural tube extends in the tail to form a nerve cord, while the endodermal strand fails to enter the tail region. Similarly, expression of bix in muscle progenitors impairs differentiation of muscle cells, and as a result, notochord cells fail to undergo normal extension movements. Hence, these larvae have a shorter tail, due to a block in the elongation of the notochord. Taken together, these observations suggest that tail formation in ascidian larvae requires not only signaling from notochord to muscle cells, but also a "retrograde" signal from muscle cells to notochord.

Pitx genes in Tunicates provide new molecular insight into the evolutionary origin of pituitary

We have initiated a project aimed at documenting molecular and cellular changes underlying the emergence of the hypothalamo-hypophyseal axis in Chordates. Considering the phylogenetic position of Tunicates and the 'pan-hypophyseal' expression pattern of Pitx genes in Vertebrate pituitary, we searched for a Pitx-related homeobox gene in the ascidian Ciona intestinalis, and identified Ci-Pitx (ona intestinalis uitary homeobo gene). We also isolated Cs-Pitx and Bs-Pitx, the Ci-Pitx respective counterparts of Ciona savignyi and Botryllus schlosseri, two other Tunicate species. Ci-Pitx mRNA encodes a putative protein exhibiting the diagnostic K50-Paired-class homeodomain and a conserved C-terminal Aristaless domain. Embryonic expression pattern of Ci-Pitx revealed a conserved expression domain in the anterior neural ridge and subsequently in the pharyngeal primordium, defined in Vertebrates as the stomodeal ectomere, which encompasses the presumptive pituitary territory. This shows that expression at early steps of pituitary development is a feature of Pitx-related genes that was already present in the last common ancestor of Chordates.

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.