Takeshi Kawashima

Publications of Takeshi Kawashima

• A genomewide survey of bHLH transcription factors in the coral Acropora digitifera identifies three novel orthologous families, pearl, amber, and peridot.

  Authors: Fuki Gyoja, Takeshi Kawashima, Nori Satoh

  Development genes and evolution. 03/2012;

  Decoding the genome of the coral, Acropora digitifera, enabled us to characterize a nearly full set of 70 basic helix-loop-helix (bHLH) transcription factors in this organism. This number isDecoding the genome of the coral, Acropora digitifera, enabled us to characterize a nearly full set of 70 basic helix-loop-helix (bHLH) transcription factors in this organism. This number is comparable to 68 bHLH genes in the sea anemone, Nematostella vectensis, and larger than those in most other invertebrate metazoans. The 70 bHLH genes were assigned to 29 orthologous families previously reported. In addition, we identified three novel HLH orthologous families, which we designated pearl, amber, and peridot, increasing the number of orthologous families to 32. Pearl and amber orthologues were found in genomes and expressed sequenced tags (ESTs) of Mollusca and Annelida in addition to Cnidaria. Peridot orthologues were found in genomes and ESTs of Cephalochordata and Hemichordata in addition to Cnidaria. These three genes were likely lost in the clades of Drosophila melanogaster, Caenorhabditis elegans, and Homo sapiens during animal evolution.

• Draft Genome of the Pearl Oyster Pinctada fucata: A Platform for Understanding Bivalve Biology.

  Authors: Takeshi Takeuchi, Takeshi Kawashima, Ryo Koyanagi, Fuki Gyoja, Makiko Tanaka, Tetsuro Ikuta, Eiichi Shoguchi, Mayuki Fujiwara, Chuya Shinzato, Kanako Hisata [......] Takashi Ishikawa, Tetsuji Masaoka, Atushi Fujiwara, Kazuyoshi Endo, Hirotoshi Endo, Hiromichi Nagasawa, Shigeharu Kinoshita, Shuichi Asakawa, Shugo Watabe, Nori Satoh

  DNA research : an international journal for rapid publication of reports on genes and genomes. 02/2012;

  The study of the pearl oyster Pinctada fucata is key to increasing our understanding of the molecular mechanisms involved in pearl biosynthesis and biology of bivalve molluscs. We sequenced ∼1150-MbThe study of the pearl oyster Pinctada fucata is key to increasing our understanding of the molecular mechanisms involved in pearl biosynthesis and biology of bivalve molluscs. We sequenced ∼1150-Mb genome at ∼40-fold coverage using the Roche 454 GS-FLX and Illumina GAIIx sequencers. The sequences were assembled into contigs with N50 = 1.6 kb (total contig assembly reached to 1024 Mb) and scaffolds with N50 = 14.5 kb. The pearl oyster genome is AT-rich, with a GC content of 34%. DNA transposons, retrotransposons, and tandem repeat elements occupied 0.4, 1.5, and 7.9% of the genome, respectively (a total of 9.8%). Version 1.0 of the P. fucata draft genome contains 23 257 complete gene models, 70% of which are supported by the corresponding expressed sequence tags. The genes include those reported to have an association with bio-mineralization. Genes encoding transcription factors and signal transduction molecules are present in numbers comparable with genomes of other metazoans. Genome-wide molecular phylogeny suggests that the lophotrochozoan represents a distinct clade from ecdysozoans. Our draft genome of the pearl oyster thus provides a platform for the identification of selection markers and genes for calcification, knowledge of which will be important in the pearl industry.

• Using the Acropora digitifera genome to understand coral responses to environmental change.

  Authors: Chuya Shinzato, Eiichi Shoguchi, Takeshi Kawashima, Mayuko Hamada, Kanako Hisata, Makiko Tanaka, Manabu Fujie, Mayuki Fujiwara, Ryo Koyanagi, Tetsuro Ikuta, Asao Fujiyama, David J Miller, Nori Satoh

  Nature. 08/2011; 476(7360):320-3.

  Despite the enormous ecological and economic importance of coral reefs, the keystone organisms in their establishment, the scleractinian corals, increasingly face a range of anthropogenic challengesDespite the enormous ecological and economic importance of coral reefs, the keystone organisms in their establishment, the scleractinian corals, increasingly face a range of anthropogenic challenges including ocean acidification and seawater temperature rise. To understand better the molecular mechanisms underlying coral biology, here we decoded the approximately 420-megabase genome of Acropora digitifera using next-generation sequencing technology. This genome contains approximately 23,700 gene models. Molecular phylogenetics indicate that the coral and the sea anemone Nematostella vectensis diverged approximately 500 million years ago, considerably earlier than the time over which modern corals are represented in the fossil record (∼240 million years ago). Despite the long evolutionary history of the endosymbiosis, no evidence was found for horizontal transfer of genes from symbiont to host. However, unlike several other corals, Acropora seems to lack an enzyme essential for cysteine biosynthesis, implying dependency of this coral on its symbionts for this amino acid. Corals inhabit environments where they are frequently exposed to high levels of solar radiation, and analysis of the Acropora genome data indicates that the coral host can independently carry out de novo synthesis of mycosporine-like amino acids, which are potent ultraviolet-protective compounds. In addition, the coral innate immunity repertoire is notably more complex than that of the sea anemone, indicating that some of these genes may have roles in symbiosis or coloniality. A number of genes with putative roles in calcification were identified, and several of these are restricted to corals. The coral genome provides a platform for understanding the molecular basis of symbiosis and responses to environmental changes.

• The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications.

  Authors: Toshiaki Katayama, Mark D Wilkinson, Rutger Vos, Takeshi Kawashima, Shuichi Kawashima, Mitsuteru Nakao, Yasunori Yamamoto, Hong-Woo Chun, Atsuko Yamaguchi, Shin Kawano [......] Martin Senger, Jessica Severin, Yasumasa Shigemoto, Hideaki Sugawara, James Taylor, Oswaldo Trelles, Chisato Yamasaki, Riu Yamashita, Noriyuki Satoh, Toshihisa Takagi

  Journal of biomedical semantics. 08/2011; 2:4.

  ABSTRACT: The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperabilityABSTRACT: The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively deployed, end-user applications need to be aware of, and support, best practices and standards. Here, we report on an initiative in which software developers and genome biologists came together to explore and raise awareness of these issues: BioHackathon 2009. Developers in attendance came from diverse backgrounds, with experts in Web services, workflow tools, text mining and visualization. Genome biologists provided expertise and exemplar data from the domains of sequence and pathway analysis and glyco-informatics. One goal of the meeting was to evaluate the ability to address real world use cases in these domains using the tools that the developers represented. This resulted in i) a workflow to annotate 100,000 sequences from an invertebrate species; ii) an integrated system for analysis of the transcription factor binding sites (TFBSs) enriched based on differential gene expression data obtained from a microarray experiment; iii) a workflow to enumerate putative physical protein interactions among enzymes in a metabolic pathway using protein structure data; iv) a workflow to analyze glyco-gene-related diseases by searching for human homologs of glyco-genes in other species, such as fruit flies, and retrieving their phenotype-annotated SNPs. Beyond deriving prototype solutions for each use-case, a second major purpose of the BioHackathon was to highlight areas of insufficiency. We discuss the issues raised by our exploration of the problem/solution space, concluding that there are still problems with the way Web services are modeled and annotated, including: i) the absence of several useful data or analysis functions in the Web service "space"; ii) the lack of documentation of methods; iii) lack of compliance with the SOAP/WSDL specification among and between various programming-language libraries; and iv) incompatibility between various bioinformatics data formats. Although it was still difficult to solve real world problems posed to the developers by the biological researchers in attendance because of these problems, we note the promise of addressing these issues within a semantic framework.

• The genome of the Western clawed frog Xenopus tropicalis.

  Authors: Uffe Hellsten, Richard M Harland, Michael J Gilchrist, David Hendrix, Jerzy Jurka, Vladimir Kapitonov, Ivan Ovcharenko, Nicholas H Putnam, Shengqiang Shu, Leila Taher [......] Dan Wells, Andrea Wills, Richard K Wilson, Lyle B Zimmerman, Aaron M Zorn, Robert Grainger, Timothy Grammer, Mustafa K Khokha, Paul M Richardson, Daniel S Rokhsar

  Science (New York, N.Y.). 04/2010; 328(5978):633-6.

  The western clawed frog Xenopus tropicalis is an important model for vertebrate development that combines experimental advantages of the African clawed frog Xenopus laevis with more tractableThe western clawed frog Xenopus tropicalis is an important model for vertebrate development that combines experimental advantages of the African clawed frog Xenopus laevis with more tractable genetics. Here we present a draft genome sequence assembly of X. tropicalis. This genome encodes more than 20,000 protein-coding genes, including orthologs of at least 1700 human disease genes. Over 1 million expressed sequence tags validated the annotation. More than one-third of the genome consists of transposable elements, with unusually prevalent DNA transposons. Like that of other tetrapods, the genome of X. tropicalis contains gene deserts enriched for conserved noncoding elements. The genome exhibits substantial shared synteny with human and chicken over major parts of large chromosomes, broken by lineage-specific chromosome fusions and fissions, mainly in the mammalian lineage.

• The dynamic genome of Hydra.

  Authors: Jarrod A Chapman, Ewen F Kirkness, Oleg Simakov, Steven E Hampson, Therese Mitros, Thomas Weinmaier, Thomas Rattei, Prakash G Balasubramanian, Jon Borman, Dana Busam [......] J Craig Venter, Ulrich Technau, Bert Hobmayer, Thomas C G Bosch, Thomas W Holstein, Toshitaka Fujisawa, Hans R Bode, Charles N David, Daniel S Rokhsar, Robert E Steele

  Nature. 03/2010; 464(7288):592-6.

  The freshwater cnidarian Hydra was first described in 1702 and has been the object of study for 300 years. Experimental studies of Hydra between 1736 and 1744 culminated in the discovery of asexualThe freshwater cnidarian Hydra was first described in 1702 and has been the object of study for 300 years. Experimental studies of Hydra between 1736 and 1744 culminated in the discovery of asexual reproduction of an animal by budding, the first description of regeneration in an animal, and successful transplantation of tissue between animals. Today, Hydra is an important model for studies of axial patterning, stem cell biology and regeneration. Here we report the genome of Hydra magnipapillata and compare it to the genomes of the anthozoan Nematostella vectensis and other animals. The Hydra genome has been shaped by bursts of transposable element expansion, horizontal gene transfer, trans-splicing, and simplification of gene structure and gene content that parallel simplification of the Hydra life cycle. We also report the sequence of the genome of a novel bacterium stably associated with H. magnipapillata. Comparisons of the Hydra genome to the genomes of other animals shed light on the evolution of epithelia, contractile tissues, developmentally regulated transcription factors, the Spemann-Mangold organizer, pluripotency genes and the neuromuscular junction.

• Domain shuffling and the evolution of vertebrates.

  Authors: Takeshi Kawashima, Shuichi Kawashima, Chisaki Tanaka, Miho Murai, Masahiko Yoneda, Nicholas H Putnum, Daniel S Rokhsar, Minoru Kanehisa, Nori Satoh, Hiroshi Wada

  Genome research. 06/2009;

  The evolution of vertebrates was driven by a number of important events, including the development of cartilage, the immune system, and complicated craniofacial structures. Here we examine domainThe evolution of vertebrates was driven by a number of important events, including the development of cartilage, the immune system, and complicated craniofacial structures. Here we examine domain shuffling as an alternative mechanism for the contribution of novel genetic material required for vertebrate evolution. We mapped domain-shuffling events during the evolution of deuterostomes with a focus on how domain shuffling contributed to the evolution of vertebrate- and chordate-specific characteristics. We identified approximately 1,000 new domain pairs in the vertebrate lineage, including approximately 100 that were shared by all seven of the vertebrate species examined. Some of these pairs occur in the protein components of vertebrate-specific structures, such as cartilage and the inner ear, suggesting that domain shuffling made a marked contribution to the evolution of vertebrate-specific characteristics. The evolutionary history of the domain pairs is traceable; for example, the Xlink domain of aggrecan, one of the major components of cartilage, was originally utilized as a functional domain of a surface molecule of blood cells in protochordate ancestors, and it was recruited by the protein of the matrix component of cartilage in the vertebrate ancestor. We also identified genes that were created as a result of domain shuffling in ancestral chordates. Some of these are involved in the functions of chordate structures, such as the endostyle, Reissner's fiber of the neural tube, and the notochord. Our analyses shed new light on the evolutionary role of domain shuffling, especially in the evolution of vertebrates and chordates.

• [Decoding of amphioxus genome and evolution of chordates]

  Authors: Noriyuki Satoh, Takeshi Kawashima, Eiichi Shoguchi

  Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme. 02/2009; 54(1):20-8.

• The Trichoplax genome and the nature of placozoans.

  Authors: Mansi Srivastava, Emina Begovic, Jarrod Chapman, Nicholas H Putnam, Uffe Hellsten, Takeshi Kawashima, Alan Kuo, Therese Mitros, Asaf Salamov, Meredith L Carpenter [......] Maria A Moreno, Kai Kamm, Jane Grimwood, Jeremy Schmutz, Harris Shapiro, Igor V Grigoriev, Leo W Buss, Bernd Schierwater, Stephen L Dellaporta, Daniel S Rokhsar

  Nature. 09/2008; 454(7207):955-60.

  As arguably the simplest free-living animals, placozoans may represent a primitive metazoan form, yet their biology is poorly understood. Here we report the sequencing and analysis of theAs arguably the simplest free-living animals, placozoans may represent a primitive metazoan form, yet their biology is poorly understood. Here we report the sequencing and analysis of the approximately 98 million base pair nuclear genome of the placozoan Trichoplax adhaerens. Whole-genome phylogenetic analysis suggests that placozoans belong to a 'eumetazoan' clade that includes cnidarians and bilaterians, with sponges as the earliest diverging animals. The compact genome shows conserved gene content, gene structure and synteny in relation to the human and other complex eumetazoan genomes. Despite the apparent cellular and organismal simplicity of Trichoplax, its genome encodes a rich array of transcription factor and signalling pathway genes that are typically associated with diverse cell types and developmental processes in eumetazoans, motivating further searches for cryptic cellular complexity and/or as yet unobserved life history stages.

• The amphioxus genome illuminates vertebrate origins and cephalochordate biology.

  Authors: Linda Z Holland, Ricard Albalat, Kaoru Azumi, Elia Benito-Gutiérrez, Matthew J Blow, Marianne Bronner-Fraser, Frederic Brunet, Thomas Butts, Simona Candiani, Larry J Dishaw [......] Fumiko Yoshizaki, Jr-Kai Yu, Qing Zhang, Christian M Zmasek, Pieter J de Jong, Kazutoyo Osoegawa, Nicholas H Putnam, Daniel S Rokhsar, Noriyuki Satoh, Peter W H Holland

  Genome research. 08/2008; 18(7):1100-11.

  Cephalochordates, urochordates, and vertebrates evolved from a common ancestor over 520 million years ago. To improve our understanding of chordate evolution and the origin of vertebrates, weCephalochordates, urochordates, and vertebrates evolved from a common ancestor over 520 million years ago. To improve our understanding of chordate evolution and the origin of vertebrates, we intensively searched for particular genes, gene families, and conserved noncoding elements in the sequenced genome of the cephalochordate Branchiostoma floridae, commonly called amphioxus or lancelets. Special attention was given to homeobox genes, opsin genes, genes involved in neural crest development, nuclear receptor genes, genes encoding components of the endocrine and immune systems, and conserved cis-regulatory enhancers. The amphioxus genome contains a basic set of chordate genes involved in development and cell signaling, including a fifteenth Hox gene. This set includes many genes that were co-opted in vertebrates for new roles in neural crest development and adaptive immunity. However, where amphioxus has a single gene, vertebrates often have two, three, or four paralogs derived from two whole-genome duplication events. In addition, several transcriptional enhancers are conserved between amphioxus and vertebrates-a very wide phylogenetic distance. In contrast, urochordate genomes have lost many genes, including a diversity of homeobox families and genes involved in steroid hormone function. The amphioxus genome also exhibits derived features, including duplications of opsins and genes proposed to function in innate immunity and endocrine systems. Our results indicate that the amphioxus genome is elemental to an understanding of the biology and evolution of nonchordate deuterostomes, invertebrate chordates, and vertebrates.

• The amphioxus genome and the evolution of the chordate karyotype.

  Authors: Nicholas H Putnam, Thomas Butts, David E K Ferrier, Rebecca F Furlong, Uffe Hellsten, Takeshi Kawashima, Marc Robinson-Rechavi, Eiichi Shoguchi, Astrid Terry, Jr-Kai Yu [......] Tatjana Sauka-Spengler, Jeremy Schmutz, Tadasu Shin-I, Atsushi Toyoda, Marianne Bronner-Fraser, Asao Fujiyama, Linda Z Holland, Peter W H Holland, Nori Satoh, Daniel S Rokhsar

  Nature. 07/2008; 453(7198):1064-71.

  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 the highlyLancelets ('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 the highly polymorphic approximately 520-megabase genome of the Florida lancelet Branchiostoma floridae, and analyse it in the context of chordate evolution. Whole-genome comparisons illuminate the murky relationships among the three chordate groups (tunicates, lancelets and vertebrates), and allow not only reconstruction of the gene complement of the last common chordate ancestor but also partial reconstruction of its genomic organization, as well as a description of two genome-wide duplications and subsequent reorganizations in the vertebrate lineage. These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution.

• The transcription/migration interface in heart precursors of Ciona intestinalis.

  Authors: Lionel Christiaen, Brad Davidson, Takeshi Kawashima, Weston Powell, Hector Nolla, Karen Vranizan, Michael Levine

  Science (New York, N.Y.). 07/2008; 320(5881):1349-52.

  Gene regulatory networks direct the progressive determination of cell fate during embryogenesis, but how they control cell behavior during morphogenesis remains largely elusive. Cell sorting,Gene regulatory networks direct the progressive determination of cell fate during embryogenesis, but how they control cell behavior during morphogenesis remains largely elusive. Cell sorting, microarrays, and targeted molecular manipulations were used to analyze cardiac cell migration in the ascidian Ciona intestinalis. The heart network regulates genes involved in most cellular activities required for migration, including adhesion, cell polarity, and membrane protrusions. We demonstrated that fibroblast growth factor signaling and the forkhead transcription factor FoxF directly upregulate the small guanosine triphosphatase RhoDF, which synergizes with Cdc42 to contribute to the protrusive activity of migrating cells. Moreover, RhoDF induces membrane protrusions independently of other cellular activities required for migration. We propose that transcription regulation of specific effector genes determines the coordinated deployment of discrete cellular modules underlying migration.

• The amphioxus genome and the evolution of the chordate karyotype

  Authors: Nicholas H. Putnam, Thomas Butts, David E. K. Ferrier, Rebecca F. Furlong, Uffe Hellsten, Takeshi Kawashima, Marc Robinson-Rechavi, Eiichi Shoguchi, Astrid Terry, Jr-Kai Yu [......] Tatjana Sauka-Spengler, Jeremy Schmutz, Tadasu Shin-I, Atsushi Toyoda, Marianne Bronner-Fraser, Asao Fujiyama, Linda Z. Holland, Peter W. H. Holland, Nori Satoh, Daniel S. Rokhsar

  Nature. 01/2008; 453:1064-1071.

• Gene expression profile during the life cycle of the urochordate Ciona intestinalis.

  Authors: Kaoru Azumi, Sorin V Sabau, Manabu Fujie, Takeshi Usami, Ryo Koyanagi, Takeshi Kawashima, Shigeki Fujiwara, Michio Ogasawara, Masanobu Satake, Masaru Nonaka, Hong-Gang Wang, Yutaka Satou, Nori Satoh

  Developmental biology. 09/2007; 308(2):572-82.

  Recent whole-genome studies and in-depth expressed sequence tag (EST) analyses have identified most of the developmentally relevant genes in the urochordate, Ciona intestinalis. In this study, weRecent whole-genome studies and in-depth expressed sequence tag (EST) analyses have identified most of the developmentally relevant genes in the urochordate, Ciona intestinalis. In this study, we made use of a large-scale oligo-DNA microarray to further investigate and identify genes with specific or correlated expression profiles, and we report global gene expression profiles for about 66% of all the C. intestinalis genes that are expressed during its life cycle. We succeeded in categorizing the data set into 5 large clusters and 49 sub-clusters based on the expression profile of each gene. This revealed the higher order of gene expression profiles during the developmental and aging stages. Furthermore, a combined analysis of microarray data with the EST database revealed the gene groups that were expressed at a specific stage or in a specific organ of the adult. This study provides insights into the complex structure of ascidian gene expression, identifies co-expressed gene groups and marker genes and makes predictions for the biological roles of many uncharacterized genes. This large-scale oligo-DNA microarray for C. intestinalis should facilitate the understanding of global gene expression and gene networks during the development and aging of a basal chordate.

• Comparative pair-wise domain-combinations for screening the clade specific domain-architectures in metazoan genomes.

  Authors: Shuichi Kawashima, Takeshi Kawashima, Nicholas H Putnam, Daniel S Rokhsar, Hiroshi Wada, Minoru Kanehisa

  Genome informatics. International Conference on Genome Informatics. 02/2007; 19:50-60.

  In the evolution of the eukaryotic genome, exon or domain shuffling has produced a variety of proteins. On the assumption that each fusion event between two independent protein-domains occurred onlyIn the evolution of the eukaryotic genome, exon or domain shuffling has produced a variety of proteins. On the assumption that each fusion event between two independent protein-domains occurred only once in the evolution of metazoans, we can roughly estimate when the fusion events were happened. For this purpose, we made phylogenetic profiles of pair-wise domain-combinations of metazoans. The phylogenetic profiles can be expected to reflect the protein evolution of metazoan. Interestingly, the phylogenetic tree of metazoans, derived from the profiles, supported the "Ecdysozoa hypothesis" that is one of the major hypotheses for metazoan evolution. Further, the phylogenetic profiles showed the candidates of genes that were required for each clade-specific features in metazoan evolution. We propose that comparative proteome analysis focusing on pair-wise domain-combinations is a useful strategy for researching the metazoan evolution. Additionally, we found that the extant ecdysozoans share only fourteen domain-combinations in our profiles. Such a small number of ecdysozoan-specific domain-combinations is consistent with the extensive gene-losses through the evolution of ecdysozoans.

• Further EST analysis of endocrine genes that are preferentially expressed in the neural complex of Ciona intestinalis: receptor and enzyme genes associated with endocrine system in the neural complex.

  Authors: Toshio Sekiguchi, Takeshi Kawashima, Yutaka Satou, Nori Satoh

  General and comparative endocrinology. 02/2007; 150(2):233-45.

  Identification of orthologs of vertebrate neuropeptides and hypothalamic hormones in the neural complex of ascidians suggests integral roles of the ascidian neural complex in the endocrine system. InIdentification of orthologs of vertebrate neuropeptides and hypothalamic hormones in the neural complex of ascidians suggests integral roles of the ascidian neural complex in the endocrine system. In the present study, we investigated endocrine-related genes expressed in the neural complex of Ciona intestinalis. Comprehensive analyses of 3'-end sequences of the neural complex cDNAs placed 10,029 clones into 4051 independent clusters or genes, 1524 of them being expressed preferentially in this organ. Comparison of the 1524 genes with the human proteome databank demonstrated that 476 matched previously identified human proteins with distinct functions. Further analyses of sequence similarity of the 476 genes demonstrated that 21 genes are candidates for those involved in the endocrine system. Although we cannot detect hormone or peptide candidates, we found 21 genes such as receptors for peptide ligands, receptor-modulating proteins, and processing enzymes. We then characterized the Ciona prohormone convertase 2 (Ci-PC2) and carboxypeptidase E (Ci-CPE), which are associated with endoproteolytic processing of peptide hormone precursors. Furthermore, genes encoding these transcripts are expressed specifically in the neural complex of young adult ascidians. These data provide the molecular basis for further functional studies of the endocrine role of the neural complex of ascidians.

• Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis.

  Authors: Eiichi Shoguchi, Takeshi Kawashima, Yutaka Satou, Makoto Hamaguchi, Tadasu Sin-I, Yuji Kohara, Nik Putnam, Daniel S Rokhsar, Nori Satoh

  Genome research. 03/2006; 16(2):297-303.

  The draft genome ( approximately 160 Mb) of the urochordate ascidian Ciona intestinalis has been sequenced by the whole-genome shotgun method and should provide important insights into the origin andThe draft genome ( approximately 160 Mb) of the urochordate ascidian Ciona intestinalis has been sequenced by the whole-genome shotgun method and should provide important insights into the origin and evolution of chordates as well as vertebrates. However, because this genomic data has not yet been mapped onto chromosomes, important biological questions including regulation of gene expression at the genome-wide level cannot yet be addressed. Here, we report the molecular cytogenetic characterization of all 14 pairs of C. intestinalis chromosomes, as well as initial large-scale mapping of genomic sequences onto chromosomes by fluorescent in situ hybridization (FISH). Two-color FISH using 170 bacterial artificial chromosome (BAC) clones and construction of joined scaffolds using paired BAC end sequences allowed for mapping of up to 65% of the deduced 117-Mb nonrepetitive sequence onto chromosomes. This map lays the foundation for future studies of the protochordate C. intestinalis genome at the chromosomal level.

• [Recent advances in developmental genomics of the ascidian Ciona intestinalis]

  Authors: Takeshi Kawashima, Eiichi Shoguchi, Yutaka Satou, Noriyuki Satoh

  Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme. 01/2006; 50(16 Suppl):2153-9.

• An integrated database of the ascidian, Ciona intestinalis: towards functional genomics.

  Authors: Yutaka Satou, Takeshi Kawashima, Eiichi Shoguchi, Akie Nakayama, Nori Satoh

  Zoological science. 09/2005; 22(8):837-43.

  An integrated genome database is essential for future studies of functional genomics. In this study, we update cDNA and genomic resources of the ascidian, Ciona intestinalis, and provide anAn integrated genome database is essential for future studies of functional genomics. In this study, we update cDNA and genomic resources of the ascidian, Ciona intestinalis, and provide an integrated database of the genomic and cDNA data by extending a database published previously. The updated resources include over 190,000 ESTs (672,396 in total together with the previous ESTs) and over 1,000 full-insert sequences (6,773 in total). In addition, results of mapping information of the determined scaffolds onto chromosomes, ESTs from a full-length enriched cDNA library for indication of precise 5'-ends of genes, and comparisons of SNPs and indels among different individuals are integrated into this database, all of these results being reported recently. These advances continue to increase the utility of Ciona intestinalis as a model organism whilst the integrated database will be useful for researchers in comparative and evolutionary genomics.

• Molecular cytogenetic characterization of Ciona intestinalis chromosomes.

  Authors: Eiichi Shoguchi, Takeshi Kawashima, Chizuko Nishida-Umehara, Yoichi Matsuda, Nori Satoh

  Zoological science. 06/2005; 22(5):511-6.

  The compact genome of the ascidian Ciona intestinalis has been sequenced. Chromosome karyotype and mapping of the genome sequence information on each of the 14 pairs of chromosomes are essential forThe compact genome of the ascidian Ciona intestinalis has been sequenced. Chromosome karyotype and mapping of the genome sequence information on each of the 14 pairs of chromosomes are essential for genome-wide studies of gene expression and function in this basal chordate. Although the small chromosome size (most pairs measuring less than 2 mum) complicates accurate chromosome pairing based on morphology alone, the present results suggest that 20 chromosomes are metacentric and 8 are submetacentric or subtelocentric, and two pairs of large chromosomes (#1 and #2) were defined. The characterization of chromosomes by FISH and staining with propidium iodide indicated that 18S/28S ribosomal gene repeats are present in the short arms of three pairs of chromosomes and that the short arms of these pairs show remarkable size polymorphism. In addition, each chromosome was characterized molecular cytogenetically by mapping representative BAC clones with FISH. The present study is therefore a first step in expanding the karyotype analysis and entire physical mapping of the genome sequence of Ciona intestinalis.