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Kasumi Yagi - One of the best experts on this subject based on the ideXlab platform.

  • a genomewide survey of developmentally relevant genes in ciona intestinalis iii genes for fox ets nuclear receptors and nfkappab
    Development Genes and Evolution, 2003
    Co-Authors: Kasumi Yagi, Francoise Mazet, Yatuka Satou, Daniel S Rokhsar, Bernhard M Degnan, Sebastian M. Shimeld, Michael S Levine, Yuji Kohara
    Abstract:

    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 vi genes for wnt tgfβ hedgehog and jak stat signaling pathways
    Development Genes and Evolution, 2003
    Co-Authors: Kyosuke Hino, Yutaka Satou, Kasumi Yagi
    Abstract:

    : Cell-cell interactions play important roles in a variety of developmental processes, and therefore molecules involved in the signaling pathways have been studied extensively. Recently, the draft genome sequence of the basal chordate, Ciona intestinalis, was determined. Here we annotated genes for the signaling pathways of Wnt, transforming growth factor beta (TGFbeta), Hedgehog, and JAK/STAT in the genome of Ciona intestinalis. The Ciona genome contains ten wnt genes, six frizzled genes, four sFRP genes, ten TGFbeta family member genes, five TGFbeta-receptor genes, and five Smad genes; most of the genes were found with less redundancy than in vertebrate genomes. The other genes in the signaling pathways are present as a single copy in the Ciona genome. In addition, all of the identified genes for the signaling pathway, except for a few genes, have EST evidence, and their cDNAs are available from the Ciona intestinalis gene collection. Therefore, Ciona intestinalis may provide an experimental system for exploring the basic genetic cascade associated with the signaling pathways in chordates.

  • a genomewide survey of developmentally relevant genes in ciona intestinalis vi genes for wnt tgfbeta hedgehog and jak stat signaling pathways
    Development Genes and Evolution, 2003
    Co-Authors: Kyosuke Hino, Yutaka Satou, Kasumi Yagi
    Abstract:

    Cell-cell interactions play important roles in a variety of developmental processes, and therefore molecules involved in the signaling pathways have been studied extensively. Recently, the draft genome sequence of the basal chordate, Ciona intestinalis, was determined. Here we annotated genes for the signaling pathways of Wnt, transforming growth factor beta (TGFbeta), Hedgehog, and JAK/STAT in the genome of Ciona intestinalis. The Ciona genome contains ten wnt genes, six frizzled genes, four sFRP genes, ten TGFbeta family member genes, five TGFbeta-receptor genes, and five Smad genes; most of the genes were found with less redundancy than in vertebrate genomes. The other genes in the signaling pathways are present as a single copy in the Ciona genome. In addition, all of the identified genes for the signaling pathway, except for a few genes, have EST evidence, and their cDNAs are available from the Ciona intestinalis gene collection. Therefore, Ciona intestinalis may provide an experimental system for exploring the basic genetic cascade associated with the signaling pathways in chordates.

  • a cdna resource from the basal chordate ciona intestinalis
    Genesis, 2002
    Co-Authors: Yutaka Satou, Makoto Hamaguchi, Satoko Awazu, Kasumi Yagi, Yasuaki Mochizuki, Akane Sasaki, Lixy Yamada, Naohito Takatori, Takeshi Kawashima, Yasunori Sasakura
    Abstract:

    Summary: The genome of the basal choradate Ciona intestinalis contains a basic set of genes with less redundancy compared to the vertebrate genome. Extensive EST analyses, cDNA sequencing, and clustering yielded “Ciona intestinalis Gene Collection Release 1,” which contains cDNA clones for 13,464 genes, covering nearly 85% of the Ciona mRNA species. This release is ready for use in cDNA cloning, micro/macroarray analysis, and other comprehensive genome-wide analyses for further molecular studies of basal chordates. genesis 33:153–154, 2002. © 2002 Wiley-Liss, Inc.

López-victoria Mateo - One of the best experts on this subject based on the ideXlab platform.

Alberto Stolfi - One of the best experts on this subject based on the ideXlab platform.

  • single cell transcriptome profiling of the ciona larval brain
    Developmental Biology, 2019
    Co-Authors: Sarthak Sharma, Alberto Stolfi
    Abstract:

    Abstract The tadpole-type larva of Ciona has emerged as an intriguing model system for the study of neurodevelopment. The Ciona intestinalis connectome has been recently mapped, revealing the smallest central nervous system (CNS) known in any chordate, with only 177 neurons. This minimal CNS is highly reminiscent of larger CNS of vertebrates, sharing many conserved developmental processes, anatomical compartments, neuron subtypes, and even specific neural circuits. Thus, the Ciona tadpole offers a unique opportunity to understand the development and wiring of a chordate CNS at single-cell resolution. Here we report the use of single-cell RNAseq to profile the transcriptomes of single cells isolated by fluorescence-activated cell sorting (FACS) from the whole brain of Ciona robusta (formerly intestinalis Type A) larvae. We have also compared these profiles to bulk RNAseq data from specific subsets of brain cells isolated by FACS using cell type-specific reporter plasmid expression. Taken together, these datasets have begun to reveal the compartment- and cell-specific gene expression patterns that define the organization of the Ciona larval brain.

  • Developmental system drift in motor ganglion patterning between distantly related tunicates
    EvoDevo, 2018
    Co-Authors: Elijah K. Lowe, Alberto Stolfi
    Abstract:

    Background The larval nervous system of the solitary tunicate Ciona is a simple model for the study of chordate neurodevelopment. The development and connectivity of the Ciona motor ganglion have been studied in fine detail, but how this important structure develops in other tunicates is not well known. Methods and Results By comparing gene expression patterns in the developing MG of the distantly related tunicate Molgula occidentalis, we found that its patterning is highly conserved compared to the Ciona MG. MG neuronal subtypes in Molgula were specified in the exact same positions as in Ciona, though the timing of subtype-specific gene expression onset was slightly shifted to begin earlier, relative to mitotic exit and differentiation. In transgenic Molgula embryos electroporated with Dmbx reporter plasmids, we were also able to characterize the morphology of the lone pair of descending decussating neurons (ddNs) in Molgula, revealing the same unique contralateral projection seen in Ciona ddNs and their putative vertebrate homologs the Mauthner cells. Although Dmbx expression labels the ddNs in both species, cross-species transgenic assays revealed significant changes to the regulatory logic underlying Dmbx transcription. We found that Dmbx cis -regulatory DNAs from Ciona can drive highly specific reporter gene expression in Molgula ddNs, but Molgula sequences are not active in Ciona ddNs. Conclusions This acute divergence in the molecular mechanisms that underlie otherwise functionally conserved cis -regulatory DNAs supports the recently proposed idea that the extreme genetic plasticity observed in tunicates may be attributed to the extreme rigidity of the spatial organization of their embryonic cell lineages.

  • evaluation and rational design of guide rnas for efficient crispr cas9 mediated mutagenesis in ciona
    Developmental Biology, 2017
    Co-Authors: Shashank Gandhi, Florian Razykrajka, Maximilian Haeussler, Lionel Christiaen, Alberto Stolfi
    Abstract:

    The CRISPR/Cas9 system has emerged as an important tool for various genome engineering applications. A current obstacle to high throughput applications of CRISPR/Cas9 is the imprecise prediction of highly active single guide RNAs (sgRNAs). We previously implemented the CRISPR/Cas9 system to induce tissue-specific mutations in the tunicate Ciona. In the present study, we designed and tested 83 single guide RNA (sgRNA) vectors targeting 23 genes expressed in the cardiopharyngeal progenitors and surrounding tissues of Ciona embryo. Using high-throughput sequencing of mutagenized alleles, we identified guide sequences that correlate with sgRNA mutagenesis activity and used this information for the rational design of all possible sgRNAs targeting the Ciona transcriptome. We also describe a one-step cloning-free protocol for the assembly of sgRNA expression cassettes. These cassettes can be directly electroporated as unpurified PCR products into Ciona embryos for sgRNA expression in vivo, resulting in high frequency of CRISPR/Cas9-mediated mutagenesis in somatic cells of electroporated embryos. We found a strong correlation between the frequency of an Ebf loss-of-function phenotype and the mutagenesis efficacies of individual Ebf-targeting sgRNAs tested using this method. We anticipate that our approach can be scaled up to systematically design and deliver highly efficient sgRNAs for the tissue-specific investigation of gene functions in Ciona.

  • tissue specific genome editing in ciona embryos by crispr cas9
    Development, 2014
    Co-Authors: Alberto Stolfi, Shashank Gandhi, Farhana Salek, Lionel Christiaen
    Abstract:

    The CRISPR/Cas9 system has ushered in a new era of targeted genetic manipulations. Here, we report the use of CRISPR/Cas9 to induce double-stranded breaks in the genome of the sea squirt Ciona intestinalis. We use electroporation to deliver CRISPR/Cas9 components for tissue-specific disruption of the Ebf (Collier/Olf/EBF) gene in hundreds of synchronized Ciona embryos. Phenotyping of transfected embryos in the ‘F0’ generation revealed that endogenous Ebf function is required for specification of Islet-expressing motor ganglion neurons and atrial siphon muscles. We demonstrate that CRISPR/Cas9 is sufficiently effective and specific to generate large numbers of embryos carrying mutations in a targeted gene of interest, which should allow for rapid screening of gene function in Ciona.

  • genetic and genomic toolbox of the chordate ciona intestinalis
    Genetics, 2012
    Co-Authors: Alberto Stolfi, Lionel Christiaen
    Abstract:

    The experimental malleability and unique phylogenetic position of the sea squirt Ciona intestinalis as part of the sister group to the vertebrates have helped establish these marine chordates as model organisms for the study of developmental genetics and evolution. Here we summarize the tools, techniques, and resources available to the Ciona geneticist, citing examples of studies that employed such strategies in the elucidation of gene function in Ciona. Genetic screens, germline transgenesis, electroporation of plasmid DNA, and microinjection of morpholinos are all routinely employed, and in the near future we expect these to be complemented by targeted mutagenesis, homologous recombination, and RNAi. The genomic resources available will continue to support the design and interpretation of genetic experiments and allow for increasingly sophisticated approaches on a high-throughput, whole-genome scale.

D. Rosell - One of the best experts on this subject based on the ideXlab platform.

  • excavating and endolithic sponge species porifera from the mediterranean species descriptions and identification key
    Organisms Diversity & Evolution, 2002
    Co-Authors: D. Rosell
    Abstract:

    Abstract The present study is a review of the excavating and endolithic sponges present in the Mediterranean. A dichotomic key to 22 species is presented. Detailed species descriptions are provided based on newly collected material and previous descriptions from the literature. In the case of Cliona viridis (Schmidt, 1862), an in-depth histological study has also been performed. Discussions on problematic taxonomic issues are also included. Dotona pulchella Carter, 1880 subspecies mediterranea subsp. n. is described. The previously enacted synonymy between Pione vastifica Hancock, 1849 and Pione lampa (de Laubenfels, 1950) is restricted to those specimens identified as “forma occulta”. Cliona amplicavata Rutzler, 1974 is recorded for the first time in the Mediterranean. Cliona cretensis Pulitzer-Finali, 1983 is proposed to be synonymous to Cliona thoosina Topsent, 1887. Cliona copiosa Sara, 1959 and Cliona tremitensis Sara, 1961 are considered synonymous to C. viridis . The spicule complement of Scantilletta levispira (Topsent, 1898), D. pulchella and C. amplicavata is enlarged, and some spicule types are better described based on light microscopy and SEM observation. Pione vastifica shows great variability in the microrhabds, seemingly related to depth. Regarding excavating patterns, several species appear to selectively excavate particular substrate types, whereas others are not selective among calcareous materials. A. labyrinthica, P. vastifica , Cliona janitrix Topsent, 1932, C. viridis and C. lobata Hancock, 1849 have asexual reproduction. Excavating ability, bud production and the way the sponge grows inside the substrate are biological features common to distant taxa such as Clionidae and Aka spp. that may constitute convergent (analogous) characters. Access to colour pictures of some of the species described at http://atlantis.ceab.csic.es/~dani/clionids.html .

  • Phylogenetic Relationships within the Excavating Hadromerida (Porifera), with a Systematic Revision
    Cladistics, 1997
    Co-Authors: D. Rosell, M.j. Uriz
    Abstract:

    Abstract This study was performed to ascertain the relationships among clionid and spirastrellid species from the Mediterranean Sea, based on phylogenetic criteria. A matrix of 34 taxa and 20 characters was analysed. Cladistic analysis using PAUP produced 12 equally parsimonious trees of 54 steps (CI=0.648, RI=0.865). Resolution was high in all parts of the strict consensus tree except in those which involved relationships among the most characteristic clionid species: those having only tylostyles as megascleres and, if microscleres are present, these being spirasters. Six monophyletic groups, three of them represented by monospecific clades, appear in the totally resolved part of the trees, which supports their separation into different genera. On the basis of the results obtained, the species at present within the genus Cliona have been allocated to five different genera: Scantilletta , Pione , Volzia , Bernatia and Cliona , while Dotona and Cliothosa are maintained as separate genera. Scantilletta and Pione are genera erected by de Laubenfels (1936 Pap. Tortugas Lab. 30 , 1–225) and Gray (1867 Proc. Zool. Soc. Lond. XXXII , 492–558) respectively, and whose diagnoses are amended here. Volzia and Bernatia are proposed as new genera to include Cliona albicans and Cliona rovignensis , and Cliona vermifera , respectively. Thus, the genus Cliona clearly appears in our analysis as a polyphyletic group. It is only maintained provisionally to harbour species whose position cannot be clearly ascertained from the information at hand. Skeletal characters such as spicule types and skeletal arrangement have proven to be useful in discriminating some genera and families but they do not completely resolve the phylogeny of this group of species. Biochemical, genetic, cytological or reproductive information, when available, may help in the resolution of the phylogenetic tree.

Yasunori Sasakura - One of the best experts on this subject based on the ideXlab platform.

  • The nervous system of the adult ascidian Ciona intestinalis Type A (Ciona robusta): Insights from transgenic animal models - Fig 1
    2017
    Co-Authors: Tomohiro Osugi, Yasunori Sasakura, Honoo Satake
    Abstract:

    (A) Superimposed image of the dorsal view of the transgenic Ciona. Major organs locating at the dorsal region and Kaede-positive nerves are shown. Four images taken by the fluorescence stereo microscope were merged. A large arrow indicates the direction of the oral siphon. The atrial siphon was removed to better visualize the cerebral ganglion and the orange-pigmented organ (OPO). (B) Dark field image of the dorsal view of the transgenic Ciona. Four images taken by the fluorescence stereo microscope were merged. A large arrow indicates the direction of the oral siphon. The trajectory from the cerebral ganglion to the ovary is indicated by open and closed arrowheads. Note that the banded pattern in the trajectory (open arrowheads) was caused by the contraction of the body muscle. Nerves to the body muscles are indicated by double arrowheads. (C) Schematic of an adult Ciona. The key anatomical parts of an adult Ciona are indicated. AS, atrial siphon; CG, cerebral ganglion; Gd, gonoduct; Int, intestine; NG, neural gland; Od; oviduct, OPO, orange-pigmented organ; OS, oral siphon; Ov, ovary; Ph, pharynx; Rec, rectum; Sd, spermiduct; St, stomach; T, testis; Te, tentacle. Scale bars indicate 2.5 mm.

  • crispr cas9 mediated gene knockout in the ascidian ciona intestinalis
    Development Growth & Differentiation, 2014
    Co-Authors: Haruka Sasaki, Akiko Hozumi, Keita Yoshida, Yasunori Sasakura
    Abstract:

    Knockout of genes with CRISPR/Cas9 is a newly emerged approach to investigate functions of genes in various organisms. We demonstrate that CRISPR/Cas9 can mutate endogenous genes of the ascidian Ciona intestinalis, a splendid model for elucidating molecular mechanisms for constructing the chordate body plan. Short guide RNA (sgRNA) and Cas9 mRNA, when they are expressed in Ciona embryos by means of microinjection or electroporation of their expression vectors, introduced mutations in the target genes. The specificity of target choice by sgRNA is relatively high compared to the reports from some other organisms, and a single nucleotide mutation at the sgRNA dramatically reduced mutation efficiency at the on-target site. CRISPR/Cas9-mediated mutagenesis will be a powerful method to study gene functions in Ciona along with another genome editing approach using TALE nucleases.

  • high throughput enhancer trap by remobilization of transposon minos in ciona intestinalis
    Genesis, 2007
    Co-Authors: Terumi Matsuoka, Satoko Awazu, Nori Satoh, Kazuo Inaba, Yasunori Sasakura
    Abstract:

    The enhancer trap approach utilizing transposons yields us information about gene functions and gene expression patterns. In the ascidian Ciona intestinalis, transposon-based transgenesis and insertional mutagenesis were achieved with a Tc1/mariner transposon Minos. We report development of a novel technique for enhancer trap in C. intestinalis. This technique uses remobilization of Minos in the Ciona genome. A Minos vector for enhancer trap was constructed and a tandem array insertion of the vector was introduced into the Ciona genome to create a mutator line. Minos was remobilized in Ciona chromosomes to create new insertions by providing transposases. These transposase-introduced animals were crossed with wild-type animals. Nearly 80% of F1 families showed novel GFP expression patterns. This high-throughput enhancer trap screen will be useful to create new marker transgenic lines showing reporter gene expression in specific tissues and to identify novel patterns of gene expression.

  • Minos transposon causes germline transgenesis of the ascidian Ciona savignyi.
    Development Growth & Differentiation, 2004
    Co-Authors: Terumi Matsuoka, Satoko Awazu, Yasunori Sasakura
    Abstract:

    An ascidian, Ciona savignyi, is regarded as a good experimental animal for genetics because of its small and compact genome for which a draft sequence is available, its short generation time and its interesting phylogenic position. ENU-based mutagenesis has been carried out using this animal. However, insertional mutagenesis using transposable elements (transposons) has not yet been introduced. Recently, one of the Tc1/mariner superfamily transposons, Minos, was demonstrated to cause germline transgenesis in the related species Ciona intestinalis. In this report, we show that Minos has the ability to transpose from DNA to DNA in Ciona savignyi in transposition assays. Although the activity was slightly weaker than in Ciona intestinalis, Minos still caused germline transgenesis in Ciona savignyi. In addition, one insertion seemed to have caused an enhancer trapping. These results indicate that Minos provides a potential tool for transgenic techniques such as insertional mutagenesis in Ciona savignyi.

  • germ line transgenesis of the tc1 mariner superfamily transposon minos in ciona intestinalis
    Proceedings of the National Academy of Sciences of the United States of America, 2003
    Co-Authors: Yasunori Sasakura, Satoko Awazu, Shota Chiba
    Abstract:

    The tadpole larva of the basal chordate Ciona intestinalis has the most simplified, basic body-plan of chordates. Because it has a compact genome with a complete draft sequence, a large quantity of EST/cDNA information, and a short generation time, Ciona is a suitable model for future genetics. We establish here a transgenic technique in Ciona that uses the Tc1/mariner superfamily transposon Minos. Minos was integrated efficiently into the genome of germ cells and transmitted stably to subsequent generations. In addition, an enhancer-trap line was obtained. This is a demonstration of efficient, Minos-mediated transgenesis in marine invertebrates.