Brozovic M.,Montpellier University |
Martin C.,Montpellier University |
Dantec C.,Montpellier University |
Dauga D.,Aix - Marseille University |
And 27 more authors.
Nucleic Acids Research | Year: 2016
Ascidians belong to the tunicates, the sister group of vertebrates and are recognized model organisms in the field of embryonic development, regeneration and stem cells. ANISEED is the main information system in the field of ascidian developmental biology. This article reports the development of the system since its initial publication in 2010. Over the past five years, we refactored the system from an initial custom schema to an extended version of the Chado schema and redesigned all user and back end interfaces. This new architecture was used to improve and enrich the description of Ciona intestinalisembryonic development, based on an improved genome assembly and gene model set, refined functional gene annotation, and anatomical ontologies, and a new collection of full ORF cDNAs. The genomes of nine ascidian species have been sequenced since the release of the C. intestinalisgenome. In ANISEED 2015, all nine new ascidian species can be explored via dedicated genome browsers, and searched by Blast. In addition, ANISEED provides full functional gene annotation, anatomical ontologies and some gene expression data for the six species with highest quality genomes. ANISEED is publicly available at: http://www.aniseed.cnrs.fr. © The Author(s) 2015.
PubMed | Kochi University, 620 University Road, Montpellier University, New York University and 9 more.
Type: Journal Article | Journal: Nucleic acids research | Year: 2016
Ascidians belong to the tunicates, the sister group of vertebrates and are recognized model organisms in the field of embryonic development, regeneration and stem cells. ANISEED is the main information system in the field of ascidian developmental biology. This article reports the development of the system since its initial publication in 2010. Over the past five years, we refactored the system from an initial custom schema to an extended version of the Chado schema and redesigned all user and back end interfaces. This new architecture was used to improve and enrich the description of Ciona intestinalis embryonic development, based on an improved genome assembly and gene model set, refined functional gene annotation, and anatomical ontologies, and a new collection of full ORF cDNAs. The genomes of nine ascidian species have been sequenced since the release of the C. intestinalis genome. In ANISEED 2015, all nine new ascidian species can be explored via dedicated genome browsers, and searched by Blast. In addition, ANISEED provides full functional gene annotation, anatomical ontologies and some gene expression data for the six species with highest quality genomes. ANISEED is publicly available at: http://www.aniseed.cnrs.fr.
Jacobs M.W.,Woods Hole Oceanographic Institution |
Jacobs M.W.,620 University Road |
Jacobs M.W.,McDaniel College |
Sherrard K.M.,620 University Road |
Sherrard K.M.,University of Chicago
Ecology | Year: 2010
The presumed trade-off between offspring size and quality predicted by life history theory is often invoked to explain the wide range of propagule sizes observed in animals and plants. This trade-off is broadly supported by intraspecific studies but has been difficult to test in an interspecific context, particularly in animals. We tested the fitness consequences of offspring size both intra- and interspecifically for seven species of ascidians (sessile, suspension-feeding, marine invertebrates) whose offspring volumes varied over three orders of magnitude. We measured two major components of fitness, juvenile growth rates and survival, in laboratory and field experiments encompassing several food conditions. Contrary to the predictions of life history theory, larger offspring size did not result in higher rates of growth or survival, and large offspring did not perform better under nutritional stress, either intraspecifically or interspecifically. In fact, two of the four species with small offspring grew rapidly enough to catch up in size to the species with large offspring in as little as eight weeks, under wild-type food conditions. Trade-offs between growth potential and defense may overwhelm and obscure any trade-offs between offspring size and survival or growth rate. While large initial size may still confer a competitive advantage, we failed to detect any consequences of interspecific variation in initial size. This implies that larger offspring in these species, far from being inherently superior in growth or survival, require compensation in other aspects of life history if reproductive effort is to be efficient. Our results suggest that the importance of initial offspring size is context dependent and often overestimated relative to other life history traits. © 2010 by the Ecological Society of America.
Stolfi A.,New York University |
Sasakura Y.,University of Tsukuba |
Chalopin D.,CNRS Lyon Institute of Functional Genomics |
Satou Y.,Kyoto University |
And 11 more authors.
Genesis | Year: 2015
Tunicates are invertebrate members of the chordate phylum, and are considered to be the sister group of vertebrates. Tunicates are composed of ascidians, thaliaceans, and appendicularians. With the advent of inexpensive high-throughput sequencing, the number of sequenced tunicate genomes is expected to rise sharply within the coming years. To facilitate comparative genomics within the tunicates, and between tunicates and vertebrates, standardized rules for the nomenclature of tunicate genetic elements need to be established. Here we propose a set of nomenclature rules, consensual within the community, for predicted genes, pseudogenes, transcripts, operons, transcriptional cis-regulatory regions, transposable elements, and transgenic constructs. In addition, the document proposes guidelines for naming transgenic and mutant lines. genesis 53:65-78, 2015. © 2014 Wiley Periodicals, Inc.
Sherrard K.,620 University Road |
Robin F.,French National Center for Scientific Research |
Lemaire P.,French National Center for Scientific Research |
Munro E.,620 University Road
Current Biology | Year: 2010
Background: Epithelial invagination is a fundamental morphogenetic behavior that transforms a flat cell sheet into a pit or groove. Previous studies of invagination have focused on the role of actomyosin-dependent apical contraction; other mechanisms remain largely unexplored. Results: We combined experimental and computational approaches to identify a two-step mechanism for endoderm invagination during ascidian gastrulation. During Step 1, which immediately precedes invagination, endoderm cells constrict their apices because of Rho/Rho-kinase-dependent apical enrichment of 1P-myosin. Our data suggest that endoderm invagination itself occurs during Step 2, without further apical shrinkage, via a novel mechanism we call collared rounding: Rho/Rho-kinase- independent basolateral enrichment of 1P-myosin drives apico-basal shortening, whereas Rho/Rho-kinase-dependent enrichment of 1P and 2P myosin in circumapical collars is required to prevent apical expansion and for deep invagination. Simulations show that boundary-specific tension values consistent with these distributions of active myosin can explain the cell shape changes observed during invagination both in normal embryos and in embryos treated with pharmacological inhibitors of either Rho-kinase or Myosin II ATPase. Indeed, we find that the balance of strong circumapical and basolateral tension is the only mechanism based on differential cortical tension that can explain ascidian endoderm invagination. Finally, simulations suggest that mesectoderm cells resist endoderm shape changes during both steps, and we confirm this prediction experimentally. Conclusions: Our findings suggest that early ascidian gastrulation is driven by the coordinated apposition of circumapical and lateral endoderm contraction, working against a resisting mesectoderm. We propose that similar mechanisms may operate during other invaginations. © 2010 Elsevier Ltd. All rights reserved.
Maliska M.E.,University of Washington |
Maliska M.E.,620 University Road |
Maliska M.E.,Michigan State University |
Pennell M.W.,Michigan State University |
And 5 more authors.
Biology Letters | Year: 2013
Ascidian species (Tunicata: Ascidiacea) usually have tailed, hatching tadpole larvae. In several lineages, species have evolved larvae that completely lack any tail tissues and are unable to disperse actively. Some tailless species hatch, but some do not hatch before going through metamorphosis. We show here that ascidian species with the highest speciation rates are those with the largest range sizes and tailed hatching larval development. We use methods for examining diversification in binary characters across a posterior distribution of trees, and show that mode of larval development predicts geographical range sizes. Conversely, we find that species with the least dispersive larval development (tailless, non-hatching) have the lowest speciation rates and smallest geographical ranges. Our speciation rate results are contrary to findings from sea urchins and snails examined in the fossil record, and further work is necessary to reconcile these disparate results. © 2013 The Author(s) Published by the Royal Society.