Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Kouhoku-ku, Yokohama, 223-8522, Japan.
Bioself Communication, 28 rue de la bibliotheque, 13001, Marseille, France.
Sci Rep. 2020 Oct 21;10(1):17916. doi: 10.1038/s41598-020-73544-9.
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 of vertebrates. In Ciona, a project on the ontology of both development and anatomy is ongoing for several years. Its goal is to standardize a resource relating each anatomical structure to developmental stages. Today, the ontology is codified until the hatching larva stage. Here, we present its extension throughout the swimming larva stages, the metamorphosis, until the juvenile stages. For standardizing 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 embryonic development. The new stages were grouped into four Periods named: Adhesion, Tail Absorption, Body Axis Rotation, and Juvenile. To build the anatomical ontology, 203 anatomical entities were identified, defined according to the literature, and annotated, taking advantage from the high resolution and the 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 on entity increase: in addition to the one occurring after fertilization, there is a second one during the Body Axis Rotation Period, when juvenile structures appear. Vice versa, one-third of anatomical entities associated with the embryo/larval life were significantly reduced at the beginning of metamorphosis. Data was finally integrated within the web-based resource "TunicAnatO", which includes a number of anatomical images and a dictionary with synonyms. This ontology will allow the standardization of data underpinning an accurate annotation of gene expression and the comprehension of mechanisms of differentiation. It will help in understanding the emergence of elaborated structures during both embryogenesis and metamorphosis, shedding light on tissue degeneration and differentiation occurring at metamorphosis.
海鞘（Ciona intestinalis 型 A）是生物学研究的模式生物，属于被囊动物门，是脊椎动物的近亲。几年来，海鞘一直在进行发育和解剖学本体论项目。其目标是标准化将每个解剖结构与发育阶段相关联的资源。如今，本体已经被编码到孵化幼虫阶段。在这里，我们展示了它在游泳幼虫阶段、变态期，直到幼体阶段的扩展。为了使发育本体标准化，我们从孵化幼虫阶段（受精后 17.5 小时）到幼体阶段（受精后 7 天）获取了不同的延时电影、共聚焦显微镜图像和组织学连续切片图像，用于每个发育事件。结合这些数据，我们定义了 12 个新的独特发育阶段（从第 26 阶段到第 37 阶段），除了之前定义的 26 个胚胎发育阶段。新的阶段被分为四个时期：黏附期、尾部吸收期、体轴旋转期和幼体期。为了构建解剖本体，我们根据文献定义了 203 个解剖实体，并进行了注释，利用共聚焦显微镜和组织学获得的高分辨率和互补信息。本体描述了从细胞水平（细胞谱系）到组织/器官水平的解剖实体的层次结构。比较发育过程中的实体数量，我们发现实体增加了两轮：除了受精后增加的一轮外，在体轴旋转期还增加了一轮，此时出现了幼体结构。相反，在变态开始时，与胚胎/幼虫生命相关的三分之一的解剖实体显著减少。最后，数据整合到基于网络的资源“TunicAnatO”中，该资源包括许多解剖图像和一个同义词词典。该本体将允许为准确注释基因表达和理解分化机制提供数据的标准化。它将有助于理解胚胎发生和变态过程中复杂结构的出现，并阐明变态过程中发生的组织退化和分化。
