Uncovering the Citrus Genome and its Applications

Elucidation of genomic sequences is an essential and necessary first step to identify genetic variants associated with agronomic traits of interest. We have sequenced the genomes of 150 citrus varieties with the Illumina platform at an average coverage higher than 60x. Paired end genomic DNA libraries were constructed and average readings of (2x) 100 bp length with an average insert size of 500 bp were performed. For each variety, useful total average readings were higher than 220 million and total mapped readings approached 212 million. The haploid genome of Citrus clementine www.phytozome.com, as reference genome, we used. Sequencing statistics indicate an average representation of the reference genome higher than 92% with coverage ≥15x. For sequencing, 150 Citrus including members of the 3 ancestral taxa, many varieties (mandarins, oranges, lemons, grapefruits and limes) and rootstocks were selected. Storage and analysis of genomic sequences required the construction of a prototype web portal, implementing bioinformatics tools to process the readings, retrieve associations and detect structural variants and genomic changes. The portal allows searching and sequence comparison among millions of gene variants and billions of base pairs reads. Initial analyses suggest that the stored information can help unravel fundamental aspects of biological and evolutionary interest such as the mechanism of generation of spontaneous varieties. From the commercial standpoint this information may help to authenticate varieties, to identify markers for breeding and to identify genes of mayor agronomic interest. Ongoing and new breeding programs have been included in the project to provide source material for GWAS and CBS analyses

This work was conducted with funding of projects: PSE-060000-2009-8 and IPT-010000-2010-43