A de novo assembly for the 16GB Allium cepa genome, tears of joy

Onion (Allium cepa l.) has the largest genome of all vegetable crops (16GB). In terms of global production value, onion ranks second after tomato. In terms of genetics and genomics, knowledge on the onion genome is scarce compared to tomato. The purpose of the SEQUON project (http://www.oniongenome.net) is to sequence the onion nuclear DNA and provide an annotated de novo genome assembly of an onion doubled haploid line (DHCU066619). Initially, our strategy focussed on sequencing and de novo assembly the gene-space by making use of gene enrichment strategies. However, the introduction of the Illumina^® HiSeq 2500 made us reconsider our strategy and resulted in sequencing of the whole onion nuclear DNA instead, resulting in 1.03 Tb of raw sequencing reads from four TrueSeq sequencing libraries (230, 350, 500 and 700bp insert size). Assembly v1.0, using the MaSuRCA assembly pipeline, resulted in 10.8 Gb sequence in 6.2 M contigs (>500 bp) with a contig N50 of 2776 bp. Based on our results, and the corresponding insights in organisation of the onion genome, we hypnotize that long read sequencing will greatly improve these statistic.  The assembly was found to contain complete (full length) copies of 118 (48%) of the 248 core eukaryotic genes, with 203 (82%) being at least partially present using the CEGMA pipeline. The sequence information is extremely valuable for the identification of genes associated with important traits such as disease resistance and bulb quality, and for understanding the underlying mechanisms. The availability of the onion genome will speed up onion breeding twofold and will lead innovative new onion cultivars.