Genome-complexity in terms of gene amplification: intriguing issues from reference species

Gene duplication (GD) and alternative splicing (AS) have emerged as two major processes supporting the functional diversification of the genes. My research project is mainly focused on the genome-scale analysis of these two important and complex mechanisms. Using comparative approaches and bioinformatics strategies I focused on the analysis of intragenome duplications, specifically focusing on Transcription Factors gene families in Plants and Homo sapiens. In particular, to investigate on gene duplication in Plants, the A.thaliana genome was used as a reference. The Arabidopsis genome underwent ancient whole genome duplication events (WGDs), followed by gene reduction and diploidization [Blanc G. et al 2000; Vision TJ, et al 2000; Simillion C. et al 2002; Cui L. et al., 2006; reviewed in Van de Peer and Meyer, 2005]. However, what dramatically increases its complexity are the extended genome rearrangements (i.e. deletions, inversions, translocations), which relocated and split up the retained portions around the genome [Tang H. et al., 2008], together with probable chromosome reductions within the Brassicaceae [Conner, J.A., et al., 1998]. Under the classical model for the evolution the duplicated genes may go for loss of function, neofunctionalization and subfunctionalization. In the first case, one member of the duplicated pair usually degenerates by accumulating deleterious mutations, while the other copy retains the original function. In the case of neofunctionalization, one duplicate may acquire a new adaptive function and the result is the preservation of both members of the pair, one with presenting the new function and the other retaining the old one. Functional divergence can occur even by subfunctionalization, that is the two copies act with a complementary effect to accomplish the functionalities of the ancestral gene. Duplicated genes also may interact through inter-locus recombination, gene conversion, or concerted evolution. In particular, we designed a bioinformatics pipeline to detect duplicated and singleton genes, taking into account several issues related to the computational methods applied. The implemented pipeline can provide a reference as tool for the detection of paralogy relationships in other genomes. Moreover, set of genes sharing one or more paralogs were organized in networks made available to the scientific community for small and large scale analyses, while single copy genes were deeply investigated since their presence represents an intriguing aspect in a so highly duplicated genome. A web accessible database (available at http://biosrv.cab.unina.it/athparalogs/main/index) allows access to the network organization, and the relevance of this resource either for evolutionary investigation or gene family analyses is here presented. In addition, our analysis underlines the need of a more accurate annotation process for the Arabidopsis genome and stirs up intriguing evolutionary issues related to the presence of single copy genes in a highly duplicated genome. Since the release 10 of the Arabidopsis genome [The Arabidopsis Information Resource, 2010] was recently made public, we confirmed and briefly described the main results concerning the TAIR9 also for this newest version. Transcription factor gene families (TFs) were analyzed considering the collection of networks obtained from A. thaliana. Due to their key roles in gene regulation, TFs are among the best examples of dosage-sensitive genes. This work provides support to the classification of transcription factors in A.thaliana and represents a step forward to understand TF families organization and evolution. Transcription factors were also analyzed in terms of alternative splicing. To further investigate on the impact of alternative splicing on transcriptional regulation, a genome-wide study of alternative splicing of TFs was also considered in the human genome, providing insights into the dynamic usage of splice isoforms and their regulatory impact in different cell types.