Domain shuffling and the evolution of vertebrates (2009)
Kawashima, Takeshi, Kawashima, Shuichi, Tanaka, Chisaki, Murai, Miho, Yoneda, Masahiko, Putnam, Nicholas H., ...
The evolution of vertebrates has included a number of important events: the development of cartilage, the immune system, and complicated craniofacial structures. Here, we examine domain shuffling as...
David S. Johnson, Qing Zhou, Kasumi Yagi, Nori Satoh, Wing Wong, Arend Sidow
De novo discovery of a tissue-specific gene
The amphioxus genome and the evolution of the chordate karyotype (2008)
Putnam, Nicholas H., Butts, Thomas, Ferrier, David E. K., Furlong, Rebecca F., Hellsten, Uffe, Kawashima, Takeshi, ...
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 highly...
Transposon mediated transgenesis in a marine invertebrate chordate: Ciona intestinalis (2007)
Sasakura, Yasunori, Oogai, Yuichi, Matsuoka, Terumi, Satoh, Nori, Awazu, Satoko
Abstract Achievement of transposon mediated germline transgenesis in a basal chordate, Ciona intestinalis , is discussed. A Tc1 / mariner superfamily transposon, Minos , has excision and...
Transposon mediated transgenesis in a marine invertebrate chordate: Ciona intestinalis (2007)
Sasakura, Yasunori, Oogai, Yuichi, Matsuoka, Terumi, Satoh, Nori, Awazu, Satoko
Achievement of transposon mediated germline transgenesis in a basal chordate, Ciona intestinalis, is discussed. A Tc1/mariner superfamily transposon, Minos, has excision and transposition activities...
DNA methylation is an important epigenetic factor that participates in silencing genes. Genomic approaches to studying DNA methylation promise to be particularly fruitful, since DNA methylation is...
Ushimaru, Yuji, Konno, Aru, Kaizu, Maiko, Ogawa, Kazuo, Satoh, Nori, Inaba, Kazuo
We previously identified a 66 kDa axonernal protein (Ci-Axp66.0) in sperm of the ascidian Ciona intestinalis. Here we found that Ci-Axp66.0 shows sequence similarity to the DC2 subunit of the...
Primary genetic linkage maps of the ascidian, Ciona intestinalis (2006)
Kano, Shungo, Satoh, Nori, Sordino, Paolo
For whole-genome analysis in a basal chordate (protochordate), we used F1 pseudo-testcross mapping strategy and amplified fragment length polymorphism (AFLP) markers to construct primary linkage maps...
Genomic overview of mRNA 5'-leader trans-splicing in the ascidian Ciona intestinalis (2006)
Satou, Yutaka, Hamaguchi, Makoto, Takeuchi, Keisuke, Hastings, Kenneth E. M., Satoh, Nori
Although spliced leader (SL) trans-splicing in the chordates was discovered in the tunicate Ciona intestinalis there has been no genomic overview analysis of the extent of trans-splicing or the...
Ogasawara, Michio, Nakazawa, Noriko, Azumi, Kaoru, Yamabe, Eiji, Satoh, Nori, Satake, Masanobu
The innate immunity of ascidian hemocytes is considered to be a prototype of that in vertebrates. In this study, we identified as many transcripts as possible that were expressed specifically in...
Ogasawara, Michio, Nakazawa, Noriko, Azumi, Kaoru, Yamabe, Eiji, Satoh, Nori, Satake, Masanobu
The innate immunity of ascidian hemocytes is considered to be a prototype of that in vertebrates. In this study, we identified as many transcripts as possible that were expressed specifically in...
An integrated database of the ascidian, Ciona intestinalis: Towards functional genomics (2005)
Satou, Yutaka, Kawashima, Takeshi, Shoguchi, Eiichi, Nakayama, Akie, Satoh, Nori
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 an...
Takeuchi, Keisuke, Satou, Yutaka, Yamamoto, Hiroaki, Satoh, Nori
The draft genome sequence and a large quantity of EST and cDNA information are now available for the ascidian Ciona intestinalis. In the present study, genes involved in pigment synthesis pathways...
Molecular cytogenetic characterization of Ciona intestinalis chromosomes (2005)
Shoguchi, Eiichi, Kawashima, Takeshi, Nishida-Umehara, Chizuko, Matsuda, Yoichi, Satoh, Nori
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 for...
Tissue-specific profile of DNA replication in the swimming larvae of Ciona intestinalis (2005)
Nakayama, Akie, Satoh, Nori, Sasakura, Yasunori
The cell cycle is strictly regulated during development and its regulation is essential for organ formation and developmental timing. Here we observed the pattern of DNA replication in swimming...
De novo discovery of a tissue-specific gene regulatory module in a chordate (2005)
Johnson, David S., Zhou, Qing, Yagi, Kasumi, Satoh, Nori, Wong, Wing, Sidow, Arend
We engage the experimental and computational challenges of de novo regulatory module discovery in a complex and largely unstudied metazoan genome. Our analysis is based on the comprehensive...
Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis (2005)
Shoguchi, Eiichi, Kawashima, Takeshi, Satou, Yutaka, Hamaguchi, Makoto, Sin-I, Tadasu, Kohara, Yuji, ...
The draft genome (∼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...
De novo discovery of a tissue-specific gene regulatory module in a chordate (2005)
Johnson, David S., Zhou, Qing, Yagi, Kasumi, Satoh, Nori, Wong, Wing, Sidow, Arend
We engage the experimental and computational challenges of de novo regulatory module discovery in a complex and largely unstudied metazoan genome. Our analysis is based on the comprehensive...
Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi (2005)
Vinson, Jade P., Jaffe, David B., O'Neill, Keith, Karlsson, Elinor K., Stange-Thomann, Nicole, Anderson, Scott, ...
Whole-genome assembly is now used routinely to obtain high-quality draft sequence for the genomes of species with low levels of polymorphism. However, genome assembly remains extremely challenging...
Surfing with the tunicates into the post-genome era (2005)
This year is the centenary of Edward G. Conklin's signal findings in embryology: the elucidation of complete cell lineages and the discovery of localized maternal determinants. Conklin used ascidian...
Development of Ciona intestinalis juveniles (Through 2nd ascidian stage) (2004)
Chiba, Shota, Sasaki, Akane, Nakayama, Akie, Takamura, Katsumi, Satoh, Nori
Following the reading of its draft genome sequence and the collection of a large quantity of cDNA information, Ciona intestinalis is now becoming a model organism for whole-genome analyses of the...
Fluorescent in situ hybridization to ascidian chromosomes (2004)
Shoguchi, Eiichi, Ikuta, Tetsuro, Yoshizaki, Fumiko, Satou, Yutaka, Satoh, Nori, Asano, Katsutoshi, ...
The draft genome of the ascidian Ciona intestinalis has been sequenced. Mapping of the genome sequence to the Ciona 14 haploid chromosomes is essential for future studies of the genome-wide control...
Wakoh, Takeshi, Ikeda, Makoto, Uchino, Ryuji, Azumi, Kaoru, Nonaka, Masaru, Kohara, Yuji, ...
The immunity provided by ascidian hemocytes represents one prototype of innate immune function in vertebrates. However, there are currently no molecular markers of ascidian hemocytes. We accumulated...
Construction of a cDNA microarray derived from the ascidian Ciona intestinalis (2003)
Azumi, Kaoru, Takahashi, Hiroki, Miki, Yasufumi, Fujie, Manabu, Usami, Takeshi, Ishikawa, Hisayoshi, ...
A cDNA microarray was constructed from a basal chordate, the ascidian Ciona intestinalis. The draft genome of Ciona has been read and inferred to contain similar to16,000 protein-coding genes, and...
Novel endostyle-specific genes in the ascidian Ciona intestinalis (2003)
Sasaki, Akane, Miyamoto, Yuki, Satou, Yutaka, Satoh, Nori, Ogasawara, Michio
The endostyle is a pharyngeal organ of Urochordata, Cephalochordata and larval Cyclostomata. This organ secretes mucus-proteins for internal filter feeding, a feeding system that must have developed...
Ishibashi, Tomoko, Nakazawa, Masumi, Ono, Hiroaki, Satoh, Nori, Gojobori, Takashi, Fujiwara, Shigeki
Yagi, Kasumi, Satou, Yatuka, Mazet, Francoise, Shimeld, Sebastian M., Degnan, Bernard M., Rokhsar, Daniel S., ...
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...
Yagi, Kasumi, Satou, Yatuka, Mazet, Francoise, Shimeld, Sebastian M., Degnan, Bernard M., Rokhsar, Daniel S., ...
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...
Yagi, Kasumi, Satou, Yatuka, Mazet, Francoise, Shimeld, Sebastian M., Degnan, Bernard M., Rokhsar, Daniel S., ...
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...
Cleto, Cynthia L., Vandenberghe, Amanda E., MacLean, Darren W., Pannunzio, Pierre, Tortorelli, Christine, Meedel, Thomas H., ...
Ascidians are protochordates related to vertebrate ancestors. The ascidian larval tail, with its notochord, dorsal nerve cord, and flanking rows of sarcomeric muscle cells, exhibits the basic...
Cleto, Cynthia L., Vandenberghe, Amanda E., MacLean, Darren W., Pannunzio, Pierre, Tortorelli, Christine, Meedel, Thomas H., ...
Ascidians are protochordates related to vertebrate ancestors. The ascidian larval tail, with its notochord, dorsal nerve cord, and flanking rows of sarcomeric muscle cells, exhibits the basic...
Cleto, Cynthia L., Vandenberghe, Amanda E., MacLean, Darren W., Pannunzio, Pierre, Tortorelli, Christine, Meedel, Thomas H., ...
Ascidians are protochordates related to vertebrate ancestors. The ascidian larval tail, with its notochord, dorsal nerve cord, and flanking rows of sarcomeric muscle cells, exhibits the basic...
Harada, Yoshito, Shoguchi, Eiichi, Taguchi, Shunsuke, Okai, Noko, Humphreys, Tom, Tagawa, Kunifumi, ...
The auricularia larva of sea cucumbers and tornaria larva of acorn worms share striking developmental and morphological similarities. They are regarded as not only an archetype of the nonchordate...
Taguchi, Shunsuke, Tagawa, Kunifumi, Humphreys, Tom, Satoh, Nori
We have identified and characterized the sequence and expression of two Group B Sox genes in the acorn worm, Ptychodera flava. One sequence represents a Group B1 Sox gene and is designated Pf-SoxB1;...
EST analysis of genes that are expressed in the neural complex of Ciona intestinalis adults. (2001)
Takamura, Katsumi, Oka, Nobuo, Akagi, Akiko, Okamoto, Kenji, Okada, Taro, Fukuoka, Takuya, ...
A subtractive cDNA library was made corresponding to mRNAs expressed in the neural complex relative to those expressed in the pharynx of adults of the ascidian Ciona intestinalis. Determination and...
Murakami, Yasunori, Ogasawara, Michio, Sugahara, Fumiaki, Hirano, Shigeki, Satoh, Nori, Kuratani, Shigeru
The Pax6 gene plays a developmental role in various metazoans as the master regulatory gene for eye patterning. Pax6 is also spatially regulated in particular regions of the neural tube. Because the...
Trunk lateral cell-specific genes of the ascidian Halocynthia roretzi (2001)
Takahashi, Hiroki, Satoh, Nori
Cell lineage analysis of the ascidian Halocynthia roretzi demonstrated that a pair of cells situated on the right and left sides of 64-cell stage embryos, termed the A7.6 cells, give rise to trunk...
Embryonic expression of a hemichordate distal-less gene (2001)
Harada, Yoshito, Okai, Noko, Taguchi, Shunsuke, Shoguchi, Eiichi, Tagawa, Kunifumi, Humphreys, Tom, ...
Hemichordates occupy a critical phylogenetic position among deuterostomes because they exhibit echinoderm-like larval morphology and chordate-like adult morphology. Analyses of the expression and...
Ogasawara, Michio, Di Lauro, Roberto, Satoh, Nori
The endostyle is a special organ in the pharynx of urochordates, cephalochordates and cyclostomes. During evolution of the primitive chordates, the endostyle was organized in their common ancestor(s)...
Michio Ogasawara, Roberto Di Lauro, Nori Satoh
The endostyle is a special organ in the pharynx of urochordates, cephalochordates and cyclostomes. During evolution of the primitive chordates, the endostyle was organized in their common ancestor(s)...
Brachyury downstream notochord differentiation in the ascidian embryo (1999)
Takahashi, Hiroki, Hotta, Kohji, Erives, Albert, Di Gregorio, Anna, Zeller, Robert W., Levine, Michael, ...
Germ-line transgenesis of the Tc1/mariner superfamily transposon Minos in Ciona intestinalis
Sasakura, Yasunori, Awazu, Satoko, Chiba, Shota, Satoh, Nori
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...
Brachyury downstream notochord differentiation in the ascidian embryo
Takahashi, Hiroki, Hotta, Kohji, Erives, Albert, Di Gregorio, Anna, Zeller, Robert W., Levine, Michael, ...
The ascidian tadpole represents the most simplified chordate body plan. It contains a notochord composed of just 40 cells, but as in vertebrates Brachyury is essential for notochord differentiation....
Ikuta, Tetsuro, Yoshida, Natsue, Satoh, Nori, Saiga, Hidetoshi
Ascidians, belonging to the subphylum Urochordata, the earliest branch from the lineage to the vertebrates, exhibit a prototypical morphogenesis of chordates in the larval development, although they...
Satouh, Yuhkoh, Padma, Potturi, Toda, Toshifusa, Satoh, Nori, Ide, Hiroyuki, Inaba, Kazuo
Members of the heat-shock protein (HSP)40 regulate the protein folding activity of HSP70 proteins and help the functional specialization of this molecular chaperone system in various types of...
Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi
Vinson, Jade P., Jaffe, David B., O'Neill, Keith, Karlsson, Elinor K., Stange-Thomann, Nicole, Anderson, Scott, ...
Whole-genome assembly is now used routinely to obtain high-quality draft sequence for the genomes of species with low levels of polymorphism. However, genome assembly remains extremely challenging...
De novo discovery of a tissue-specific gene regulatory module in a chordate
Johnson, David S., Zhou, Qing, Yagi, Kasumi, Satoh, Nori, Wong, Wing, Sidow, Arend
We engage the experimental and computational challenges of de novo regulatory module discovery in a complex and largely unstudied metazoan genome. Our analysis is based on the comprehensive...
Surfing with the tunicates into the post-genome era
This year is the centenary of Edward G. Conklin's signal findings in embryology: the elucidation of complete cell lineages and the discovery of localized maternal determinants. Conklin used ascidian...
Sasakura, Yasunori, Nakashima, Keisuke, Awazu, Satoko, Matsuoka, Terumi, Nakayama, Akie, Azuma, Jun-ichi, ...
Tunicates are the only animals that perform cellulose biosynthesis. The tunicate gene for cellulose synthase, Ci-CesA, was likely acquired by horizontal transfer from bacteria and was a key...
Genomic overview of mRNA 5′-leader trans-splicing in the ascidian Ciona intestinalis
Satou, Yutaka, Hamaguchi, Makoto, Takeuchi, Keisuke, Hastings, Kenneth E. M., Satoh, Nori
Although spliced leader (SL) trans-splicing in the chordates was discovered in the tunicate Ciona intestinalis there has been no genomic overview analysis of the extent of trans-splicing or the...
Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis
Shoguchi, Eiichi, Kawashima, Takeshi, Satou, Yutaka, Hamaguchi, Makoto, Sin-I, Tadasu, Kohara, Yuji, ...
The draft genome (∼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...
Wada, Shuichi, Hamada, Mayuko, Satoh, Nori
Molecular chaperones play crucial roles in various aspects of the biogenesis and maintenance of proteins in the cell. The heat shock protein 70 (HSP70) chaperone system, in which HSP70 proteins act...
Germ-line transgenesis of the Tc1/mariner superfamily transposon Minos in Ciona intestinalis
Sasakura, Yasunori, Awazu, Satoko, Chiba, Shota, Satoh, Nori
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...
Brachyury downstream notochord differentiation in the ascidian embryo
Takahashi, Hiroki, Hotta, Kohji, Erives, Albert, Di Gregorio, Anna, Zeller, Robert W., Levine, Michael, ...
The ascidian tadpole represents the most simplified chordate body plan. It contains a notochord composed of just 40 cells, but as in vertebrates Brachyury is essential for notochord differentiation....
Ikuta, Tetsuro, Yoshida, Natsue, Satoh, Nori, Saiga, Hidetoshi
Ascidians, belonging to the subphylum Urochordata, the earliest branch from the lineage to the vertebrates, exhibit a prototypical morphogenesis of chordates in the larval development, although they...
Satouh, Yuhkoh, Padma, Potturi, Toda, Toshifusa, Satoh, Nori, Ide, Hiroyuki, Inaba, Kazuo
Members of the heat-shock protein (HSP)40 regulate the protein folding activity of HSP70 proteins and help the functional specialization of this molecular chaperone system in various types of...
Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi
Vinson, Jade P., Jaffe, David B., O'Neill, Keith, Karlsson, Elinor K., Stange-Thomann, Nicole, Anderson, Scott, ...
Whole-genome assembly is now used routinely to obtain high-quality draft sequence for the genomes of species with low levels of polymorphism. However, genome assembly remains extremely challenging...
De novo discovery of a tissue-specific gene regulatory module in a chordate
Johnson, David S., Zhou, Qing, Yagi, Kasumi, Satoh, Nori, Wong, Wing, Sidow, Arend
We engage the experimental and computational challenges of de novo regulatory module discovery in a complex and largely unstudied metazoan genome. Our analysis is based on the comprehensive...
Surfing with the tunicates into the post-genome era
This year is the centenary of Edward G. Conklin's signal findings in embryology: the elucidation of complete cell lineages and the discovery of localized maternal determinants. Conklin used ascidian...
Sasakura, Yasunori, Nakashima, Keisuke, Awazu, Satoko, Matsuoka, Terumi, Nakayama, Akie, Azuma, Jun-ichi, ...
Tunicates are the only animals that perform cellulose biosynthesis. The tunicate gene for cellulose synthase, Ci-CesA, was likely acquired by horizontal transfer from bacteria and was a key...
Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis
Shoguchi, Eiichi, Kawashima, Takeshi, Satou, Yutaka, Hamaguchi, Makoto, Sin-I, Tadasu, Kohara, Yuji, ...
The draft genome (∼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...
Wada, Shuichi, Hamada, Mayuko, Satoh, Nori
Molecular chaperones play crucial roles in various aspects of the biogenesis and maintenance of proteins in the cell. The heat shock protein 70 (HSP70) chaperone system, in which HSP70 proteins act...
Genomic overview of mRNA 5′-leader trans-splicing in the ascidian Ciona intestinalis
Satou, Yutaka, Hamaguchi, Makoto, Takeuchi, Keisuke, Hastings, Kenneth E. M., Satoh, Nori
Although spliced leader (SL) trans-splicing in the chordates was discovered in the tunicate Ciona intestinalis there has been no genomic overview analysis of the extent of trans-splicing or the...
Transposon mediated transgenesis in a marine invertebrate chordate: Ciona intestinalis
Sasakura, Yasunori, Oogai, Yuichi, Matsuoka, Terumi, Satoh, Nori, Awazu, Satoko
Achievement of transposon mediated germline transgenesis in a basal chordate, Ciona intestinalis, is discussed. A Tc1/mariner superfamily transposon, Minos, has excision and transposition activities...