Transcriptome analysis and Homology based non-coding RNA annotation of macronuclear genome of the Antarctic psychrophilic ciliate Euplotes focardii

The mechanisms of adaptation to low temperatures remain poorly understood, largely due to the limitations of traditional molecular approaches that focus on individual enzymes, e.g., lactate dehydrogenase; [...], cytoskeletal proteins [...], cellular organelles [...], etc. To optimally address temperature adaptation in eukaryotes, it is necessary to access not only to a subset of genes from cold adapted organisms, but to large sample sizes of sequences to enable evaluation via statistical and computational approaches. Only genome or transcriptome sequencing and analyses can effectively provide such data sets.\ud Up to now, the only transcriptomes from Antarctic organisms that have been unraveled are those from fishes and krill [...]. From these studies it resulted that these Antarctic organisms show increased expression in cellular chaperones, ubiquitination degradation proteins to remove cold denaturated proteins, and oxidative stress related proteins like glutathione S-transferase, superoxide dismutase and ferritin [...]. There is not much knowledge about cold adaptation of unicellular eukaryotic psychrophiles. With only very few range of unicellular psychrophilic transcriptome like Chaetoceros neogracile [...], Chlamydomonas subcaudata [...] and yeasts [...] being reported, my study aims to expand our existing knowledge on the existing cold adaptation of unicellular eukaryotic psychrophiles.\ud As single cell directly exposed to environmental cues, protozoa can represent excellent model organisms to unravel the full suite of cold stable function that allowed the ecological success of Antarctic organisms. In this context, I analyzed the transcriptome of the Antarctic ciliate Euplotes focardii with the purpose to obtain revealing insights into the cold adaption mechanisms.\ud My thesis is composed by two parts: in the first part I will report the result of the analysis at nucleotide level and gene annotation of the E. focardii transcriptome. In the second part I will describe the characterization of non-coding RNA focusing mainly on tRNAs that recognize the stop codon TGA