Nucleotide and Structural Variation in Citrus Genomes: Resequencing and de novo Approaches

Citrus spp. is one of the most important fruit tree worldwide, mainly consumed as juice or fresh fruit. The origins of modern cultivated groups, such as sweet and sour oranges, lime, lemon, grapefruit remain not completely defined yet. However, it has been understood that three ancestral species, C. maxima, C. reticulata and C. medica, were the donor genotypes of today cultivated types. The genetic diversity within each modern group is the result of somatic mutations accumulated by asexual propagation by grafting or nucellar embryogenesis from the original hybrids obtained from the ancestral species. Most of this variability is currently uncharacterized, and therefore not exploitable, either to design reliable molecular markers for clone fingerprinting or to study the biological mechanisms underlying the varying phenotypes observed across clones, which are the basis of their consumption and market value. With the aim to describe the somatic mutation events in the sweet orange group we deep-sequenced 10 accessions by Illumina platform and leveraged several bioinformatics techniques to identify single nucleotide polymorphism, structural variants and large deletions that are specific to some clones. To this scope, we employed methods relying on paired-end read mapping, sequencing depth-of-coverage and allele frequencies analysis. Furthermore, in order to gain significant resolution in understanding the relative contribution of the three ancestral genomes we accomplished high-quality draft de novo assembly of a mandarin genotype, a pummelo type and a citron type. We are currently analyzing their sequences in order to acquire information on their structural differences.