Advances in Eggplant Genome Sequencing

Abstract

Thanks to the recent development of NGS technologies, draft genomes are at present available for many crops. However, most of the genome sequences are incomplete and highly fragmented because they rely on the alignment of billions of short-sequence reads and do not comprehensively report on genomic elements such as highly variable regions and DNA repeats that are difficult to map using short reads. The Italian Eggplant Genome Consortium (IEGC) has recently developed a high-quality and anchored genome assembly of the eggplant line 67/3, which is the male parent of an F6 RIL (Recombinant Inbred Line) mapping population. The hybrid assembly, obtained by merging the sequence assembly obtained with SOAPdenovo2 and the optical map, covered 1.22 Gb. The newly developed eggplant genome sequence represents an improvement in respect to the previous one published in 2104 by Hirakawa and co-authors, both in terms of projected genome size and lower number of larger scaffolds (N50 of 2.0 Mb in respect to 64.5 Kb). Optical mapping demonstrated the ability to facilitate the assembly of super-scaffolds and made it possible to correct misassembly and scaffolding errors. The female parent of the RIL mapping population (inbred line ‘305E40’) was also sequenced (coverage of 34×), and following the low-coverage resequencing (coverage 1×) of the F6 RIL population, the genome assembly was anchored to the 12 chromosomes by applying the SoiLoCo pipeline. Recently, the complete chloroplast (cp) genome of S. melongena has been also assembled and characterized. It exhibited a circular DNA molecule of 154,289 bp and displayed a typical quadripartite structure including a pair of inverted repeats (IR) as well as one large single-copy (LSC) and one small single-copy (SSC) region for a whole of 125 unique functional genes.