Abstract
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.
Highlights
Tunicates are a group of several thousand species of marine non-vertebrate chordates, which recent phylogenetic studies based on molecular data place as the Vertebrate sister group [1]
In spite of the simplicity, small cell numbers and peculiar mode of development of ascidian embryos, some of their developmental processes and Gene Regulatory Networks (GRN) are shared with vertebrate embryos [6,7], though it currently remains uncertain whether this similarity reflects homology or convergence
This switch to Chado made it possible to extend the use of general ontologies
Summary
Tunicates are a group of several thousand species of marine non-vertebrate chordates, which recent phylogenetic studies based on molecular data place as the Vertebrate sister group [1]. Nucleic Acids Research, 2016, Vol 44, Database issue D809 gene expression data for the six species with highest quality genomes. The Developmental Browser (www.aniseed.cnrs.fr) formalizes, integrates and displays an extensive set of complementary and interrelated molecular and anatomical data for each species [48], which can be explored via four main menus giving access to functional annotations of genes and cis-regulatory sequences, to descriptions of anatomical entities, to gene expression data and to literature articles.
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
