Comparative genome analyses of deuterostomes: Metabolism and base composities of tunicates, fish and mammals genomes

Zanotta, Luisa Berná (2011). Comparative genome analyses of deuterostomes: Metabolism and base composities of tunicates, fish and mammals genomes. PhD thesis The Open University.

DOI: https://doi.org/10.21954/ou.ro.0000edc8

Abstract

The hypothesis that the metabolic rate could affect the base composition of genomes, i.e. the GC content, was tested along the phylogenetic line of deuterostomes, in the classes of tunicates, fish and mammals, by different approaches dictated by available data. Significant differences were found between the GC content of the completely sequenced genomes of C.intestinalis and C.savignyi. Interestingly, the increment was higher in C.savignyi in coding and non-coding regions, and mainly at the third codon positions (7% GC3). Methylation process and substitution rate were checked if responsible of the observed differences. The frequencies of CpG, CpA and TpG were no different between the two tunicates, and (even if tunicates showed a substitution rate 50% faster than that of vertebrates) the base composition was not directly affected. Multivariate analysis on codon usages showed that: i) in both species selection acts on codon usage, shaping translationally preferred codons between highly and lowly expressed genes; and ii) gene expression level affects the GC content of the two tunicate genomes. Data on the metabolic rate and the average genomic GC content were available for more than 200 teleostean species. Analyzing data according to the habitats, significant differences were found, with polar fish characterized by the highest metabolic rate and by a high GC content. A significant correlation was found between the two variables. Finally, intra-genome analyses of functional classes in more than ten mammalian genomes, confirmed the link between metabolism and GC content. In each mammalian genome, indeed, the average GC3 level was higher in genes involved in "metabolic processes". The same genome organization was not found in amphibians and reptiles, characterized by lower metabolic rates than mammals. The various approaches converged towards a coherent picture, highlighting the importance of metabolic rate as a factor shaping the base composition of genomes