The Ontology of the Amphioxus Anatomy and Life Cycle (AMPHX).

Stephanie Bertrand,Vladimir Daric,Jr-Kai Yu,Nicolas Matentzoglu,Delphine Dauga,Michael Schubert,João E Carvalho,Hector Escrivá

doi:10.3389/fcell.2021.668025

Abstract

An ontology is a computable representation of the different parts of an organism and its different developmental stages as well as the relationships between them. The ontology of model organisms is therefore a fundamental tool for a multitude of bioinformatics and comparative analyses. The cephalochordate amphioxus is a marine animal representing the earliest diverging evolutionary lineage of chordates. Furthermore, its morphology, its anatomy and its genome can be considered as prototypes of the chordate phylum. For these reasons, amphioxus is a very important animal model for evolutionary developmental biology studies aimed at understanding the origin and diversification of vertebrates. Here, we have constructed an amphioxus ontology (AMPHX) which combines anatomical and developmental terms and includes the relationships between these terms. AMPHX will be used to annotate amphioxus gene expression patterns as well as phenotypes. We encourage the scientific community to adopt this amphioxus ontology and send recommendations for future updates and improvements.

Highlights

Cephalochordates are a group of benthic marine filter feeding animals which live buried in the sand of shallow coastal environments in most temperate and tropical seas
In the amphioxus ontology (AMPHX) ontology, we have described the anatomy and development, from the oocyte to the adult, of the cephalochordate amphioxus
In order for our data to be consistent with the FAIR principle7, we submitted the AMPHX ontology to the FAIRsharing repository (Sansone et al, 2019), which approved our entry8

Summary

Introduction

Cephalochordates (i.e., amphioxus) are a group of benthic marine filter feeding animals which live buried in the sand of shallow coastal environments in most temperate and tropical seas. There are only about thirty species and three genera (Branchiostoma, Epigonichthys, and Asymmetron), this chordate subphylum attracts the attention of numerous researchers because of its key phylogenetic position, representing the earliest diverging evolutionary lineage within chordates, and for its extraordinary morphological, anatomical, and genomic conservation with the last common ancestor of all chordates, including vertebrates (Bertrand and Escriva, 2011; Escriva, 2018) Some of these conserved morphological characters include a dorsal hollow neural tube and a dorsal notochord, pharyngeal slits, segmented muscles, and gonads as well as organs homologous to those of vertebrates, such as the pronephric kidney or an endostyle. The Ontology of Amphioxus the amphioxus genome shows simplified 3D structure and genetic regulation when compared to vertebrate genomes (Acemel et al, 2016; Marletaz et al, 2018)

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