DOI: 10.5061/dryad.ht76hdrfp
title: Loricarioid catfish evolved skin denticles that recapitulate teeth at the structural, developmental, and genetic levels (raw RNAseq reads)

description: The first vertebrate mineralized skeleton was an external bony armor
 coated with dental structures. The subsequent emergence of a mineralized
 endoskeleton and of teeth are considered key innovations in the
 diversification of vertebrates. Although time clouds our understanding of
 the initial evolution of these mineralized structures, recent
 re-emergences may shed light on the underlying processes. Loricarioid
 catfishes are a lineage that, much like the ancestral vertebrates, bear
 denticle-clad bony armor from head to tail. Loricarioid denticles (LDs)
 and oral teeth are very similar in superstructure. We show here that other
 extra-oral dental structures are found as ancestral characters only in
 lineages that are distantly related to loricarioids such as sharks or
 coelacanth, indicating that LDs have independently re-emerged in
 loricarioid catfishes. We investigate whether the similarities between LDs
 and teeth extend to their developmental and genetic context, and how their
 development compares to that of other vertebrate integument structures.
 Our detailed study of the development of LDs, and gene expression analyses
 through in situ hybridization confirm that all 12 genes from the
 tooth-forming gene regulatory network (oGRN) are expressed in developing
 LDs in a similar way as they are expressed in developing teeth. We then
 compare the developmental, structural, and genetic aspects of LD and teeth
 with that of other integument appendages such as fish scales, shark dermal
 denticles, feathers and hairs. We find that LDs share all developmental
 cues with teeth and, to a lesser extent, with the other vertebrate
 integument structures. Taken together, our results indicate that denticles
 have re-emerged on the trunk of loricarioid catfishes through the ectopic
 co-option of the oGRN rather than the resurrection of an ancestral
 trunk-specific denticle genetic pathway.
description: <i><b>Sample fixation</b></i>
 All
 embryos were collected directly from the aquarium in which they were laid,
 at the desired age (2-6 dpf). Unhatched embryos (younger than 5 dpf) were
 dechorionated by hand, with forceps. All embryos were euthanized in a tank
 containing a lethal concentration (400g/ml) of tricaine methanesulfonate
 (MS-222), then fixed in 4% paraformaldehyde (PFA) pH 7.42 for at least 24
 h at 4° C. Then, they were dehydrated in a series of methanol solutions
 and stored in 100% methanol at -20° C.
 <i><b>Sequencing and assembly of the embryonic
 transcriptome of </b></i><b>A.
 triradiatus</b> Two embryos of 3, 4, and 5 dpf of
 Ancistrus triradistus were collected, pooled and their total RNA was
 extracted using the Trizol reagent. The mRNA was then purified using the
 Oligotex mRNA Mini Kit (Qiagen 70022). Library preparation, quality
 control and Illumina NGS sequencing was performed by the Genomics Platform
 of the University of Geneva
 (http://www.ige3.unige.ch/genomics-platform.php). Sequencing was performed
 on a HiSeq 2500 (Illumina) which generated 60 million single reads of
 200bp.
description: Raw data still have Illumina adapters and low quality bases. A
 cleanup with Cutadapt (Martin and Wang 2011) is recommended.