Biology subjects

Gairin, E.

Publications and source records attributed to Gairin, E..

3 recordsLinked to original sources

bioRxiv2024

The genome of the sapphire damselfish Chrysiptera cyanea: a new resource to support further investigation of the evolution of Pomacentrids

The number of high-quality genomes is rapidly growing across taxa. However, it remains limited for coral reef fish of the Pomacentrid family, with most research focused on anemonefish. Here, we present the first assembly for a Pomacentrid of the genus Chrysiptera. Using PacBio long-read sequencing with a coverage of 94.5x, the genome of the Sapphire Devil, Chrysiptera cyanea was assembled and annotated. The final assembly consisted of 896 Mb pairs across 91 contigs, with a BUSCO completeness of 97.6%. 28,173 genes were identified. Comparative analyses with available chromosome-scale assemblies for related species identified contig-chromosome correspondences. This genome will be useful to use as a comparison to study the specific adaptations linked to symbiosis life of the closely related anemonefish. Furthermore, this species is present in most tropical coastal areas in the Indo-West Pacific and could become a model for environmental monitoring. This work will allow to expand coral reef research efforts and highlights the power of long-read assemblies to retrieve high quality genomes.

genomics↗

bioRxiv2022

Validation of a novel fully immersive Virtual Reality setup with a behavioural study of freely-moving fish

Virtual Reality (VR) enables standardised stimuli to invoke behavioural responses in animals, however, in fish studies VR has been limited to either basic virtual stimulation projected below the bowl for freely-swimming individuals or a simple virtual arena rendered over a large field-of-view for head-restrained individuals. We developed a novel immersive VR setup with real-time rendering of animated 3D scenarios, validated in a proof of concept study on the behaviour of coral reef post-larval fish. Fish use a variety of cues to select a habitat during the recruitment stage, and to recognize conspecifics and predators, but which visual cues are used remains unknown. We measured behavioural responses of groups of five convict surgeonfish (Acanthurus triostegus) to simulations of habitats, static or moving shoals of conspecifics, predators, and non-aggressive heterospecifics. Post-larval fish were consistently attracted to virtual corals and conspecifics presented statically, but repulsed by their predators (bluefin jacks, Caranx melampygus). When simulated shoals passed nearby repeatedly, they were again attracted by conspecifics showing a tendency to follow the shoal, whereas they moved repeatedly to the back of the passing predator shoal. They also discriminated between species of similar sizes: they were attracted more to conspecifics than butterflyfish (Forcipiger longirostris), and repulsed more by predators than parrotfish (Scarus psittacus). The quality of visual simulations was high enough to identify between visual cues - size, body shape, colour pattern - used by post-larval fish in species recognition. Despite a tracking technology limited to fish 2D positions in the aquarium, preventing the real-time updating of the rendered viewpoint, we could show that VR and modern tracking technologies offer new possibilities to investigate fish behaviour through the quantitative analysis of their physical reactions to highly-controlled scenarios.

animal behavior and cognition↗

bioRxiv2022

The chromosome-scale genome assembly of the yellowtail clownfish Amphiprion clarkii provides insights into melanic pigmentation of anemonefish

Anemonefish are an emerging group of model organisms for studying genetic, ecological, evolutionary, and developmental traits of coral reef fish. The yellowtail clownfish Amphiprion clarkii possesses species-specific characteristics such as inter-species co-habitation, high intra-species color variation, no anemone specificity, and a broad geographic distribution, that can increase our understanding of anemonefish evolutionary history, behavioral strategies, fish-anemone symbiosis, and color pattern evolution. Despite its position as an emerging model species, the genome of A. clarkii is yet to be published. Using PacBio long-read sequencing and Hi-C chromatin capture technology, we generated a high-quality chromosome-scale genome assembly initially comprised of 1,840 contigs with an N50 of 1,203,211 bp. These contigs were successfully anchored into 24 chromosomes of 843,582,782 bp and annotated with 25,050 protein-coding genes encompassing 97.0 % of conserved actinopterygian genes, making the quality and completeness of this genome the highest amongst all published anemonefish genomes to date. Transcriptomic analysis identified tissue-specific gene expression patterns, with the brain and optic lobe having the largest number of expressed genes. Further analyses revealed higher copy numbers of erbb3b (a gene involved in melanophore development) in A. clarkii compared to other anemonefish, thus suggesting a possible link between erbb3b and the natural melanism polymorphism observed in A. clarkii. The publication of this high-quality genome, along with A. clarkiis many unique traits, position this species as an ideal model organism for addressing scientific questions across a range of disciplines.

genomics↗