Milestones (M), Deliverables (D)
WP 1: DATA COLLECTION
M
I conducted extensive fieldwork in the Italian Western Alps cave systems, where I collected specimens for nine spider species of the genus Troglohyphantes, with the help of Dr. Marco Isaia. I specifically sampled species that inhabit different parts of the caves (entrance, shallow, and deep compartments, see figure 1 for a visual representation of compartment distribution) with different troglobitic phenotypic adaptations depending on the compartment.
D
My sampling design involved obtaining approximately 27 specimens representing 9 species, distributed as follows: three closely related species inhabiting each of the three main cave compartments.
WP 2: GENOMIC DATA GENERATION AND PROCESS
M
2.1. I extracted genomic DNA from Troglohyphantes pluto, a spider species inhabiting the entrance compartment of caves, to generate a high quality reference genome. A de novo Cantata Bio Hi-C sequencing approach was used to generate the genome assembly. Transcriptomic data was also retrieved from the same species to functionally annotate the genome.
2.2. I also generated whole-genome sequencing data from all the samples mentioned in WP1.
D
2.1. I generate a chromosome level reference genome with functional annotations, which will serve as a valuable resource for future studies in arthropod and particularly troglobitic fauna evolution.
2.2. I produced a genomic database of Troglohyphantes species, the most diverse spider genus in European caves, that will help to outgrow the knowledge on cave adaptation from this project and in future projects with new data being produced with collaborators.
WP 3 to 5: THE GENOMIC BASIS OF REPEATED ADAPTATION TO CAVES
M
3.2. Following a phylogenomic approach, I identified putative orthologs involved in the adaptation to the cave environment. I studied the role of natural selection in promoting independent evolution, specifically how the relaxation of selection on specific genes determined the evolution of cave-dwelling spiders.
3.3. Following a comparative structural variant detection approach, I determined that deletions and duplications play a key role in shaping the genetic diversity of cave-dwelling spiders.
D
3.2. The study revealed a set of genes that are under similar selective pressures in the species with total phenotipic adaptations to caves (from the deep cave environment).
3.3. I obtained a database of genes with deletions and genes with duplication in regions that could be affecting the expression of the genes, facilitating troglobitic adaptation.
WP 6: RESULTS DISSEMINATION AND OUTREACH ACTIVITIES
Based on the results obtained during the development of this action, a research paper is in preparation. I attended one national conference, and I will attend one national and one international conference during this and next year to disseminate our findings to a wider audience.
I gave two talks in high schools during the International Day of Women and Girls in Science in Barcelona and Montpellier. I was selected to present my research at an international conference in Uruguay, but unfortunately, I couldn't go for personal reasons. I was also selected to participate as a student at the EMBO "Hands-on course in genome sequencing, assembly, and downstream analyses" course (
https://meetings.embo.org/event/22-gen-seq-analysis(odnośnik otworzy się w nowym oknie)) in 2022, to improve my skills in genome assembly and annotation, where I also had the opportunity to network with other researchers in the field.
