The Draft Genome of
            <i>Ciona intestinalis</i>
            : Insights into Chordate and Vertebrate Origins

Dehal, Paramvir; Satou, Yutaka; Campbell, R. Keith; Chapman, Jarrod; Degnan, Bernard M.; Tomaso, Anthony De; Davidson, Brad; Gregorio, Anna Di; Gelpke, Maarten D. Sollewijn; Goodstein, David; Harafuji, Naoe; Hastings, Kenneth E.M.; Ho, Isaac; Hotta, Kohji; Huang, Wayne; Kawashima, Takeshi; Lemaire, Patrick; Martínez, Diego; Meinertzhagen, Ian A.; Necula, Simona; Nonaka, Masaru; Putnam, Nicholas H.; Rash, Sam; Saiga, Hidetoshi; Satake, Masanobu; Terry, Astrid; Yamada, Lixy; Wang, Hong Gang; Awazu, Satoko; Azumi, Kaoru; Boore, Jeffrey L.; Branno, Margherita; Chin-Bow, Stephen T.; DeSantis, Rosaria; Doyle, Sharon A.; Francino, M. Pilar; Keys, David; Haga, Shinobu; Hayashi, Hiroko; Hino, Kyosuke; Imai, Kaoru S.; Inaba, Kazuo; Kano, Shungo; Kobayashi, Kenji; Kobayashi, Mari; Lee, Ki Young; Makabe, Kazuhiro W.; Manohar, Chitra F.; Matassi, Giorgio; Medina, Mónica; Mochizuki, Yasuaki; Mount, Stephen M.; Morishita, Tomomi; Miura, Sachiko; Nakayama, Aki; Nishizaka, Satoko; Nomoto, Hisayo; Ohta, Fumiko; Oishi, Kazuko; Rigoutsos, Isidore; Sano, Masako; Sasaki, Akane; Sasakura, Yasunori; Shoguchi, Eiichi; Shin-I, Tadasu; Spagnuolo, Antonietta; Stainier, Didier Y. R.; Suzuki, Miho; Tassy, Olivier; Takatori, Naohito; Tokuoka, Miki; Yagi, Keisuke; Yoshizaki, Fumiko; Wada, Shinpei; Zhang, Cindy; Hyatt, P. Douglas; Larimer, Frank W.; Detter, Chris; Doggett, Norman A.; Glavina, Tijana; Hawkins, Trevor; Richardson, Paul M.; Lucas, Susan; Kohara, Yuji; Levine, Michael; Satoh, Nori; Rokhsar, Daniel S.

doi:10.1126/science.1080049

Cited by 1,528 publications

(1,211 citation statements)

References 82 publications

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“…In addition, 64% of the insertion sites occurred at two or more tandem repeats of the TA dinucleotides. Because the C. intestinalis genome has been estimated to contain approximately 65% T and A nucleotides (Dehal et al, 2002), the probability of the appearance of another TA dinucleotide adjacent to the TA sites targeted by SB should be approximately 21%, a value that is lower than the value observed in the present analysis. This suggests that SB is preferably inserted in the tandem repeats of TA in C. intestinalis.…”

Section: The Tendency Of the Sb Insertion Sites In The C Intestinalicontrasting

confidence: 68%

Germline transgenesis of the chordate Ciona intestinalis with hyperactive variants of sleeping beauty transposable element

Hozumi

Mita

Miskey

et al. 2012

Developmental Dynamics

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Background: Transposon-mediated transgenesis is an excellent method for creating stable transgenic lines and insertional mutants. In the chordate Ciona intestinalis, Minos is the only transposon that has been used as the tool for germline transformation. Adding another transposon system in this organism enables us to conduct genetic techniques which can only be realized with the use of two transposons. Results: In the present study, we found that another Tc1/mariner superfamily transposon, sleeping beauty (SB), retains sufficient activity for germline transformation of C. intestinalis. SB shows efficiencies of germline transformation, insertion into gene coding regions, and enhancer detection comparable to those of Minos. We have developed a system for the remobilization of SB copies in the C. intestinalis genome by using transgenic lines expressing SB transposase in the germ cells. With this system, we examined the manner of SB mobilization in the C. intestinalis genome. SB shows intrachromosomal transposition more frequently than Minos. Conclusions: SB-based germline transformation and the establishment of a new method that uses its frequent intrachromosomal transposition will result in breakthroughs in genetic approaches that use C. intestinalis together with Minos. Developmental Dynamics 242:30-43, 2013. V C 2012 Wiley Periodicals, Inc.Key words: ascidian; Ciona intestinalis; transposon; Tc1; mariner; sleeping beauty; Minos Key findings:In C. intestinalis, Minos is the only transposon that has been used as a tool for germline transformation. We found that another transposon, sleeping beauty (SB), retains sufficient activity for the germline transformation of C. intestinalis. SB-based germline transformation will result in breakthroughs in genetic approaches that use C. intestinalis together with Minos.

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Section: The Tendency Of the Sb Insertion Sites In The C Intestinalicontrasting

confidence: 68%

Germline transgenesis of the chordate Ciona intestinalis with hyperactive variants of sleeping beauty transposable element

Hozumi

Mita

Miskey

et al. 2012

Developmental Dynamics

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“…A rigorous genomebased search for homologues of the genes encoding these molecules in Ciona intestinalis (a solitary protochordate) was unsuccessful 141 . It is not yet possible to search whole genomes in the two orders of extant jawless vertebrates, the lampreys and hagfish; however, several molecular genetic searches have failed to detect the presence of MHC class I or class II molecules in these species.…”

Section: Box 1 Alternative Mediators Of Histocompatibilitymentioning

confidence: 99%

Reconstructing immune phylogeny: new perspectives

2005

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Numerous studies of the mammalian immune system have begun to uncover profound interrelationships, as well as fundamental differences, between the adaptive and innate systems of immune recognition. Coincident with these investigations, the increasing experimental accessibility of non-mammalian jawed vertebrates, jawless vertebrates, protochordates and invertebrates has provided intriguing new information regarding the likely patterns of emergence of immune-related molecules during metazoan phylogeny, as well as the evolution of alternative mechanisms for receptor diversification. Such findings blur traditional distinctions between adaptive and innate immunity and emphasize that, throughout evolution, the immune system has used a remarkably extensive variety of solutions to meet fundamentally similar requirements for host protection.The evolutionary development of the METAZOANS was associated with the diversification of a wide range of specialized cell-surface molecules that mediate key metabolic processes, as well as provide crucial contact interfaces and carry out a broad range of other essential functions. It is not unexpected that some of these molecules also came to function as barriers to pathogenic invasion and, in doing so, began to carry out dedicated innate immune protective functions. Whereas the simplest form of protection, barrier formation, is essentially mechanical in nature, relentless pressure from genetic variation in pathogens probably drove the evolution of such innate immune protective molecules towards diversification and, in parallel, towards integration of signalling pathways to regulate cellular responses to external stimulation. However, despite the sophistication that such innate immune mediators achieved over time, their biological complexity, by definition, would be limited by genome space, so with increasing complexity of body plan and/or increasing pathogen sophistication, they could be overwhelmed. NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author ManuscriptMore than 500 million years ago, a TRANSPOSITION event, probably involving a recombinationactivating gene (RAG)-bearing element, might have given rise to the predecessors of the rearranging antigen-binding receptors of the jawed vertebrates, which encompass the vertebrate radiations that extend from the cartilaginous fish through to humans. This is considered the defining point in the emergence of RAG-mediated (conventional) adaptive immunity 1,2 , which has evolved to create a mechanism for deriving almost limitless variation from very few genes. Studies in traditional and non-traditional animal models, such as sharks, bony fish and birds, have brought this event and its ramifications for host defence into sharper focus. We can now predict much about how these rearranging antigenbinding receptors probably arose, what alternative pathways of immune-receptor gene evolution have occurred, what relationships exist between B-and T-cell-mediated immunity and natural killer (NK)-cell function, how complex immune ...

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“…Metamorphosis of C. intestinalis can be induced by exogenous THs and inhibited by goitrogens known to block TH synthesis in vertebrates (Patricolo et al, 1981(Patricolo et al, , 2001). However, the molecular pathways triggered by THs remain elusive since the only TR of C. intestinalis (Dehal et al, 2002) does not bind any iodinated tyrosine derivative tested (Carosa et al, 1998;Paris et al, 2008). The urochordates are particularly interesting regarding the evolution of metamorphosis because of the diversity of their postembryonic developmental strategies.…”

Section: Evolution Of Metamorphosis In Other Vertebrates: Why Direct mentioning

confidence: 99%

The history of a developmental stage: Metamorphosis in chordates

Paris

Laudet

2008

Genesis

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Summary: Metamorphosis displays a striking diversity in chordates, a deuterostome phylum that comprises vertebrates, urochordates (tunicates), and cephalochordates (amphioxus). In anuran amphibians, the tadpole loses its tail, develops limbs, and undergoes profound changes at the behavioral, physiological, biochemical, and ecological levels. In ascidian tunicates, the tail is lost and the head tissues are drastically remodeled into the adult animal, whereas in amphioxus, the highly asymmetric larva transforms into a relatively symmetric adult. This wide diversity has led to the proposal that metamorphosis evolved several times independently in the different chordate lineages during evolution. However, the molecular mechanisms involved in metamorphosis are largely unknown outside amphibians and teleost fishes, in which metamorphosis is regulated by the thyroid hormones (TH) T 3 and T 4 binding to their receptors (thyroid hormone receptors). In this review, we compare metamorphosis in chordates and then propose a unifying definition of the larva-to-adult transition, based on the conservation of the role of THs and some of their derivatives as the main regulators of metamorphosis. According to this definition, all chordates (if not, all deuterostomes) have a homologous metamorphosis stage during their postembryonic development. The intensity and the nature of the morphological remodeling varies extensively among taxa, from drastic remodeling like in some ascidians or amphibians to more subtle events, as in mammals. genesis 46:657-672,

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The Draft Genome of Ciona intestinalis : Insights into Chordate and Vertebrate Origins

Cited by 1,528 publications

References 82 publications

Germline transgenesis of the chordate Ciona intestinalis with hyperactive variants of sleeping beauty transposable element

Germline transgenesis of the chordate Ciona intestinalis with hyperactive variants of sleeping beauty transposable element

Reconstructing immune phylogeny: new perspectives

The history of a developmental stage: Metamorphosis in chordates

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