PT - JOURNAL ARTICLE AU - Kohji Hotta AU - Delphine Dauga AU - Lucia Manni TI - The comprehensive ontology of the anatomy and development of the solitary ascidian <em>Ciona</em>: the swimming larva and its metamorphosis AID - 10.1101/2020.06.09.140640 DP - 2020 Jan 01 TA - bioRxiv PG - 2020.06.09.140640 4099 - http://biorxiv.org/content/early/2020/06/10/2020.06.09.140640.short 4100 - http://biorxiv.org/content/early/2020/06/10/2020.06.09.140640.full AB - Background Ciona robusta (Ciona intestinalis type A), a model organism for biological studies, belongs to ascidians, the main class of tunicates, which are the closest relatives to vertebrates. In Ciona, a project on the ontology of both development and anatomy has been developing for several years. Its goal is to standardize a resource relating each anatomical structure to developmental stages. Today, the ontology is codified up to the hatching larva stage. Here, we present its extension throughout the swimming larva stages and the metamorphosis, up to the juvenile stages.Results To standardize the developmental ontology, we acquired different time-lapse movies, confocal microscope images, and histological serial section images for each developmental event from the hatching larva stage (17.5 h post-fertilization) to the juvenile stage (7 days post-fertilization). Combining these data, we defined 12 new distinct developmental stages (from Stage 26 to Stage 37), in addition to the previously defined 26 stages, referred to as embryonic development. The new stages were grouped into four Periods named: Adhesion, Tail Absorption, Body Axis Rotation, and Juvenile.In building the anatomical ontology, 204 anatomical entities were identified, defined according to the literature, and annotated, taking advantage of the high resolution and complementary information obtained from confocal microscopy and histology. The ontology describes the anatomical entities in hierarchical levels, from the cell level (cell lineage) to the tissue/organ level. Comparing the number of entities during development, we found two rounds of entity increase: In addition to the one occurring after fertilization, a second one occurred during the Body Axis Rotation Period, when juvenile structures appear. On the other hand, a high number of anatomical entities (related to the larva life) are significantly reduced at the beginning of metamorphosis. Data were finally integrated within the web-based resource “TunicAnatO”, which includes several anatomical images and a dictionary with synonyms.Conclusions This ontology will allow for the standardization of data underpinning an accurate annotation of gene expression and the comprehension of the mechanisms of differentiation. It will help create an understanding of the emergence of elaborated structures during both embryogenesis and metamorphosis, shedding light on tissue degeneration and differentiation occurring at metamorphosis.Competing Interest StatementThe authors have declared no competing interest.ADOAnatomical Developmental OntologyAOAnatomical OntologyASNETAscidian Dendritic Network in TunicCLSMConfocal Scanning Laser MicroscopyDCENDorsal Caudal Epidermal NeuronsDODevelopmental OntologyIDIdentificationOBOOpen Biological and Biomedical OntologiesRTENRostral Tail Epidermal NeuronsTunicAnatOTunicate Anatomical developmental OntologyVCENVentral Caudal Epidermal Neurons