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

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.

Functions of the FGF signalling pathway in cephalochordates provide insight into the evolution of the prechordal plate

“…One hypothesis is that these cells were lost through an apoptotic process. In order to test this proposition, we performed a TUNEL assay in SU5402-treated and control embryos at six developmental stages from late gastrula to transition stage (from stage G6 to T0; Bertrand et al, 2021;Carvalho et al, 2021). In positive control embryos, obtained by using a DNase I treatment, all the nuclei were labelled from the surface to the most internal cells at all stages (Fig.…”

“…Ripe adults of Branchiostoma lanceolatum were collected at the Racou beach near Argeles-sur-Mer, France (latitude 42°32′ 53′′ N, longitude 3°0 3′ 27′′ E). Gametes were obtained by heat stimulation as previously described (Fuentes et al, 2007) and staging is as described previously (Bertrand et al, 2021;Carvalho et al, 2021). Before pharmacological treatment, embryos were transferred to scraped Petri dishes filled with filtered seawater to prevent the eggs from sticking to the plastic.…”

Exploring tissue morphodynamics using the photoconvertible Kaede protein in amphioxus embryos

“… The gastrula stage embryo (G4 stage) [ 13 , 14 ] was imaged before and after photoconversion (pre- and post-bleach, panels on the left). The same embryo was imaged at the late neurula stage (N4 stage) [ 13 , 14 ] (panels on the right). Gastrula stage pictures are blastopore views with dorsal to the top.…”

“…The embryo imaged at the late neurula stage showed expression in the ventral epidermis and in the somites (Fig 2). The same protocol was succesfully undertaken to trace the fate of the presumptive anterior somite [13,14] was imaged before and after photoconversion (pre-and post-bleach, panels on the left). The same embryo was imaged at the late neurula stage (N4 stage) [13,14]…”

Gene Regulatory Networks of Epidermal and Neural Fate Choice in a Chordate

“…Explants were then collected and either frozen for RNA extraction or directly processed for ATAC-seq. Staging is as proposed in Bertrand et al (2021) and Carvalho et al (2021) .…”