An Eggplant (Solanum melongena L.) High Quality Genome Draft

Eggplant (Solanum melongenaL. 2n = 2x = 24, projected genome size 1.1Gbp) is the third most important Solanaceous crop after potato and tomato. Its world production is about 46 Mt (FAOSTAT 2012), and Italy is the first European producer. Despite this, eggplant still remains a “genomic orphan species”, while genome sequences of potato and tomato have been recently published and so far, its genome organization has been investigated merely by inspecting reduced-complexity libraries. Unlike tomato and potato, which belong to the subgenus Potatoe, eggplant belongs to the subgenus Leptostemonum and thus represents a unique member for comparative genomic analyses within the genus Solanum.

A reference genome was produced by sequencing the inbred eggplant line ‘67/3’, which is the parent, together with the line ‘305E40’, of a mapping population composed of 167 F6 RILs. Illumina libraries with different insert sizes (from 270bp to 10kb) were sequenced using Illumina Hiseq1000 technology, producing approximately a 155 X coverage, and assembled using SOAPDENOVO 2. The draft eggplant genome includes 396,807 contigs (1. 39 Gbp, N50= 16,262) and 35,799 scaffolds (1.21 Gbp, N50=405,352).

Strand-specific RNA-Seq data, for a total of 74 Gb, were produced from 19 tissues to facilitate annotation. A preliminary analysis with the Maker pipeline allowed to annotate about 35,000 putative protein-coding genes. Each individual of the RIL mapping population was sequenced at about 1X coverage generating approximately a total of 150 Gbp of sequence data. Analysis of the data is in progress with the aim to generate a dense genetic map to anchor and orient the genomic assembly. Our efforts will extend the current knowledge of the genome organization of eggplant, produce new tools and markers for accelerating eggplant breeding, as well as accelerate comparative genomic analyses.