NGS applications to understand invertebrate biodiversity of Antarctica and mechanisms of gene expression involved in climatic changes

Human activities, such as greenhouse emissions and pollution, are leading to global warming, environmental changes and biodiversity reduction. Pristine environments such as those of Antarctica are not immune to these phenomena, as is noticeable from the temperature shifts and ice-melting registered within the continent in recent decades. To date, many scientists focused on how marine species react to these changes but no molecular data are currently available for continental terrestrial invertebrates and in particular for Collembola (=springtails). Therefore, part of my PhD project was to study the transcriptomic response of the endemic Antarctic springtail Cryptopygus terranovus following a mid-term exposure of 20 days at 18°C. Expression data were compared with wild specimens sampled in native environment. Although individual plasticity in transcript modulation was recorded, several pathways appear to be differentially modulated: protein catabolism, fatty acid metabolism and a sexual response characterized by spermatid development were induced, while lipid catabolism was downregulated in treated samples. Moreover, the temperature experienced by these micro-invertebrates is a pivotal parameter to understand these animals' ecology and physiology. However, at present, detailed knowledge of microhabitat physical conditions in Antarctica is limited and biased towards sub-Antarctic and maritime Antarctic regions. To better understand these temperature conditions, it was analysed a year-round temperature data in ponds and soils in an area of the Victoria Land coast, comparing these measurements with air temperatures from the closest automatic weather station. Important difference in temperature dynamics between the air, soil and pond datasets was registered. Ponds were the warmest sites overall, mostly differing with the air temperatures due to their greater thermal capacity, which also influenced their patterns of freeze-thaw cycles and mean daily thermal excursion. Furthermore, to better understand the biodiversity of Collembola two new mitochondrial genomes of Antarctic springtails were sequenced and analysed. They were employed to revise the entire systematic of the class, its nucleotide composition and genome arrangement by comparing them to all the available sequences deposited in Genbank. In the phylogenetic analysis, with minor exceptions, it was confirmed the monophyly of Poduromorpha and Symphypleona sensu stricto (the latter recovered as the most basal group in the springtail phylogenetic tree), whereas monophyly of Neelipleona and Entomobryomorpha was only supported when some critical taxa in these two lineages were excluded. The genome arrangement review allowed to identify four new gene orders (one from the newly sequenced Tullbergia mixta), for a total of 16 models. Finally, nucleotide composition analyses confirmed the low AT bias in Collembola mitochondrial DNA respect to other Hexapoda, and that third codon position is inclined to mutation accumulation, especially in 4-fold amino-amino acids. To ease the process of mitochondrial genome analyses, it was created a web resource named EZmito, a free web server useful to analyse mitochondrial genomes. It is composed of five main tools: (i) EZsplit, useful to download and format sequences directly from the NCBI database; (ii) EZpipe, a pipeline designed to format mitochondrial sequences before the phylogenetic analysis; (iii) EZskew, which helps users to calculate nucleotide biases; (iv) EZcodon, a fast tool which calculates the Relative Synonym Codon Usage of different mtDNA species and (v) EZmix, which recognizes areas of inter molecular similarity indicative of the assembly of chimeric mitochondrial genomes. Interestingly, to date, the most used tool within the hub is EZcodon, followed by EZsplit and EZpipe.