La genomica e la trascrittomica comparativa rivelano le basi genetiche dell'adattamento del pinguino Imperatore (A. forsteri) all'estremo ambiente antartico

The eco-evolutionary history of penguins is profoundly influenced by their shift from temperate to cold environments. Breeding only in Antarctica during the winter, the Emperor penguin appears as an extreme outcome of this process, with unique features related to insulation, heat production and energy management. However, whether this species actually diverged from a less cold-adapted ancestor, thus more similar in ecology to its sister species, the King penguin, is still an open question. As the Antarctic niche shift likely resulted in vast changes in selective pressure experienced by the Emperor penguin, the identification and relative quantification of the genomic signatures of selection, unique to each of these sister species, could answer this question. Applying a suite of phylogeny-based methods on 7,651 orthologous gene alignments of 7 penguins and 13 other birds, we identified a set of candidate genes showing significantly different selection regimes either in the Emperor or in the King penguin lineage. Among the candidate genes under selection in the Emperor penguin, 161 genes can be assigned to functional pathways relevant to cold adaptation (cardiovascular system, lipid, fatty acid and glucose metabolism, insulation, among the others). In order to detect signatures of more recent selection in the two penguin species of the Aptenodytes genus, we also performed genome-wide analyses of selection, through the application of haplotype-based methods, on 48 individuals of Emperor and King penguins. Both the selection analyses applied, over short and long evolutionary time, revealed a more pervasive selective shift in the Emperor penguin, supporting the hypothesis that its extreme cold adaptation is a derived state from a more King penguin-like ecology. Moreover, also the haplotype-based methods detected genetic traits, associated to positively selected regions, that are potentially involved in the Emperor penguin adaptation to the extreme cold conditions (e.g., adipose tissue and lipid metabolism, cold-induced thermogenesis and cardiovascular functions). When a population colonizes a new environment, gene expression becomes crucial in guaranteeing population persistence and contributes to adaptive divergence. To investigate the relevance of gene expression changes in adaptation to the extreme cold Antarctic environment, we explored transcriptomic differences at intraspecific and interspecific levels by analyzing QuantSeq 3’mRNA-Seq data from a large number of tissue samples (100 samples from 5 tissues of 10 individuals from natural populations of each species). Specifically, our analyses concerned tissues that could exhibit the major genetic differences for cold adaptation comparing the two species: skin (thermal insulation), liver (lipid and fatty-acid metabolism), brain (cold tolerance), muscle (thermogenesis) and kidney (osmoregulation). In general, the expression profiles revealed a characterizing tissue-clustered pattern and a number of differentially expressed genes which, in the Emperor penguin, could be the candidates underlying its relevant adaptations to the Antarctic lifestyle. We especially focused on the transcriptional profile of the muscle given its critical role in whole body energy metabolism and temperature homeostasis in birds. Our findings on the most up-regulated differentially expressed genes in the muscle, together with the enrichment of GO terms and KEGG pathways, confirm a thermogenic role of this tissue in both the Aptenodytes penguins but probably involving different biological pathways. Moreover, we used total mRNA-Seq data from 5 tissues of 3 individuals per species to de novo assemble the first reference transcriptome of the Emperor and the King penguin. Our findings suggest both the transcriptomes cover a wide range of protein-coding sequences, encompassing more than 84% of genes in the Aves orthologs database.