Structural and functional genomics of Fig (Ficus carica L.)

The fig tree is one of the first species cultivated by mankind (Kislev et al., 2006). The species of major commercial importance is certainly Ficus carica L., also known as common fig, constituted of numerous varieties with significant genetic heterogeneity and exceptional nutritional and pharmacological properties (Woodland, 1997; Salhi-Hannachi et al., 2006; Barolo et al., 2014). Ficus carica L. is a diploid species (2n = 2x = 26) with a genome size of about 0.36 pg/1C (Falistocco et al., 2009). The present thesis is dedicated to fill the existing gap of knowledge in the genomics of F. carica L., with reference to cultivar Dottato, which is the most widespread in Italy. This work is aimed to: increase knowledge of gene expression in responses to salinity in F. carica cv. Dottato, which is remarkably tolerant to salinity, but in which the molecular genetics of tolerance are largely unknown; increase the genomic resources available for this species, producing a first draft of the genome of the cv. Dottato; evaluate the existing variability between the Italian cv. Dottato and the Japanese cv. Horaishi predicted transcriptomes. Chapter I reports the analysis of response of F. carica L. plants grown under salinity conditions (0, 50, 100, 200 mM NaCl). It presents a transcriptome analysis of leaves of fig plants irrigated with NaCl after 24 and 48 days obtained with Illumina technology. It also describes the genes regulated at different times. It shows the gene regulation of functional pathways affected by salinity treatments comparing genes differentially expressed at 24 days with genes differentially expressed at 48 days. It also reports new genes which were not previously described as involved in response salinity. Chapter II details a comprehensive list and a critical description of genes differentially expressed in leaves of fig plants at early and late stages of irrigation with NaCl. Chapter III presents the first genome sequence of cv. Dottato and its annotation, obtained with a combination of Illumina paired-end HiSeq2000 reads and MiSeq long reads, which resulted composed for 70% of repeated sequences. Finally, chapter IV reports a comparative study between the cultivars Dottato and Horaishi predicted transcriptomes, specifically identifying genes occurring in one of the two cultivars and analysing their differences at functional genomics level. Overall, the data obtained in this work contribute to fill the existing gap of knowledge in the genomics of F. carica L., with reference to cultivar Dottato, at both structural and functional levels, extending the pan genome of this species.