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Analyzing the properties of duplicate genes during evolution is useful tounderstand the development of new cell functions. The yeast S. cerevisiae is auseful testing ground for this problem, because its duplicated genes withdifferent evolutionary birth and destiny are well distinguishable. Inparticular, there is a clear detection for the occurrence of a Whole GenomeDuplication (WGD) event in S. cerevisiae, and the genes derived from this event(WGD paralogs) are known. We studied WGD and non-WGD duplicates by two parallelanalysis based on structural protein domains and on Gene Ontology annotationscheme respectively. The results show that while a large number of``duplicable'' structural domains is shared in local and global duplications,WGD and non-WGD paralogs tend to have different functions. The reason for thisis the existence of WGD and non-WGD specific domains with largely differentfunctions. In agreement with the recent findings of Wapinski and collaborators(Nature 449, 2007), WGD paralogs often perform ``core'' cell functions, such astranslation and DNA replication, while local duplications associate with``peripheral'' functions such as response to stress. Our results also supportthe fact that domain architectures are a reliable tool to detect homology, asthe domains of duplicates are largely invariant with date and nature of theduplication, while their sequences and also their functions might migrate.

Identity and divergence of protein domain architectures after the Yeast Whole Genome Duplication event