Expression of 20 SCPP genes during tooth and bone mineralization in Senegal bichir

The African bichir (Polypterus senegalus) is a living representative of Polypteriformes. P. senegalus possesses teeth composed of dentin covered by an enameloid cap and a layer of collar enamel on the tooth shaft, as in lepisosteids. A thin layer of enamel matrix can also be found covering the cap enameloid after its maturation and during the collar enamel formation. Teleosts fish do not possess enamel; teeth are protected by cap and collar enameloid, and inversely in sarcopterygians, where teeth are only covered by enamel, with the exception of the cap enameloid in teeth of larval urodeles. The presence of enameloid and enamel in the teeth of the same organism is an opportunity to solve the evolutionary history of the presence of enamel/enameloid in basal actinopterygians. In silico analyses of the jaw transcriptome of a juvenile bichir provided twenty SCPP transcripts. They included enamel, dentin, and bone-specific SCPPs known in sarcopterygians and several actinopterygian-specific SCPPs. The expression of these 20 genes was investigated by in situ hybridizations on jaw sections during tooth and dentary bone formation. A spatiotemporal expression patterns were established and compared with previous studies of SCPP gene expression during enamel/enameloid and bone formation. Similarities and differences were highlighted, and several SCPP transcripts were found specifically expressed during tooth or bone formation suggesting either conserved or new functions of these SCPPs.

Ancient fish lineages illuminate toll-like receptor diversification in early vertebrate evolution

Since its initial discovery over 50 years ago, understanding the evolution of the vertebrate RAG- mediated adaptive immune response has been a major area of research focus for comparative geneticists. However, how the evolutionary novelty of an adaptive immune response impacted the diversity of receptors associated with the innate immune response has received considerably less attention until recently. Here, we investigate the diversification of vertebrate toll-like receptors (TLRs), one of the most ancient and well conserved innate immune receptor families found across the Tree of Life, integrating genomic data that represent all major vertebrate lineages with new transcriptomic data from Polypteriformes, the earliest diverging ray-finned fish lineage. Our analyses reveal TLR sequences that reflect the 6 major TLR subfamilies, TLR1, TLR3, TLR4, TLR5, TLR7, and TLR11, and also currently unnamed, yet phylogenetically distinct TLR clades. We additionally recover evidence for a pulse of gene gain coincident with the rise of the RAG-mediated adaptive immune response in jawed vertebrates, followed by a period of rapid gene loss during the Cretaceous. These gene losses are primarily concentrated in marine teleost fish and synchronous with the mid Cretaceous anoxic event, a period of rapid extinction for marine species. Finally, we reveal a mismatch between phylogenetic placement and gene nomenclature for up to 50% of TLRs found in clades such as ray-finned fishes, cyclostomes, amphibians, and elasmobranchs. Collectively, these results provide an unparalleled perspective of TLR diversity and offer a ready framework for testing gene annotations in non-model species.

Comparative iTRAQ proteomics revealed proteins associated with lobed fin regeneration in Bichirs

Background

Polypterus senegalus can fully regenerate its pectoral lobed fins, including a complex endoskeleton, with remarkable precision. However, despite the enormous potential of this species for use in medical research, its regeneration mechanisms remain largely unknown.

Methods

To identify the differentially expressed proteins (DEPs) during the early stages of lobed fin regeneration in P. senegalus, we performed a differential proteomic analysis using isobaric tag for relative and absolute quantitation (iTRAQ) approach based quantitative proteome from the pectoral lobed fins at 3 time points. Furthermore, we validated the changes in protein expression with multiple-reaction monitoring (MRM) analysis.

Results

The experiment yielded a total of 3177 proteins and 15,091 unique peptides including 1006 non-redundant (nr) DEPs. Of these, 592 were upregulated while 349 were downregulated after lobed fin amputation when compared to the original tissue. Bioinformatics analyses showed that the DEPs were mainly associated with Ribosome and RNA transport, metabolic, ECM-receptor interaction, Golgi and endoplasmic reticulum, DNA replication, and Regulation of actin cytoskeleton.

Conclusions

To our knowledge, this is the first proteomic research to investigate alterations in protein levels and affected pathways in bichirs’ lobe-fin/limb regeneration. In addition, our study demonstrated a highly dynamic regulation during lobed fin regeneration in P. senegalus. These results not only provide a comprehensive dataset on differentially expressed proteins during the early stages of lobe-fin/limb regeneration but also advance our understanding of the molecular mechanisms underlying lobe-fin/limb regeneration.

Locomotion in elongate fishes: A contact sport

Despite the physical differences between water and air, a number of fish lineages are known to make terrestrial excursions on land. Many of these fishes exhibit an elongate body plan. Elongation of the body can occur in several ways, the most common of which is increasing the number of vertebrae in one or both regions of the axial skeleton--precaudal and/or caudal. Elongate species are often found in three-dimensionally complex habitats. It has been hypothesized that elongate fishes use this structure to their locomotor advantage. In this study, we consider how elongation and differences in vertebral regionalization correspond with the use of wooden pegs, which are provided as analogs to vertically oriented substrate, structures that protrude above the ground. We compare aquatic and terrestrial locomotor behaviors of Polypterus senegalus, Erpetoichthys calabaricus, and Gymnallabes typus as they move through a peg array. When considering axial elongation we find that the highly elongate species, E. calabaricus and G. typus, contact more pegs but on average move slower in both environments than P. senegalus. When considering axial regionalization, we find that the precaudally elongate species, P. senegalus and E. calabaricus, differ in the patterns of peg contact between the two environments whereas the caudally elongate species, G. typus, exhibits similar peg contact between the two environments. Our study highlights the importance of incorporating body shape and vertebral regionalization to understand how elongate fishes move in water and on land.

A study of the relict fish fauna of northern Chad, with the first records of a polypterid and a poeciliid in the Sahara desert

Seventeen species and sub-species of fishes belonging to four families (Cyprinidae, Clariidae, Aplocheilidae, Cichlidae) were known to occur in perennial bodies of water in the Sahara desert. The study of fishes collected in Lake Boukou near Ounianga Serir (Borkou, northern Chad) shows, for the first time, the occurrence in the Sahara desert of relict populations of Polypterus senegalus (Polypteridae) and Poropanchax normani (Poeciliidae). The Cichlidae Tilapia zilli was also collected in this lake. With these new records, the relict fish fauna currently known in lakes and gueltas of the Borkou plateaus comprises six species. In the Ennedi Mountains, where the specific status of Barbus populations was unclear, B. macrops was collected in Bachikere guelta. The toad Amietophrynus regularis was collected in Ounianga Kebir.