Insights from the first genome assembly of Onion (Allium cepa)

Abstract

Onion is an important vegetable crop with an estimated genome size of 16GB. We describe the de novo assembly and ab initio annotation of the genome of a doubled haploid onion line DHCU066619, which resulted in a final assembly of 14.9 Gb with a N50 of 461 Kb. Of which 2.2 Gb was ordered into 8 pseudomolecules using five genetic linkage maps. The remainder of the genome is available in 89.8 K scaffolds. Analysis of this genome shows that at least 72.4% of the genome is repetitive and consists, to a large extent, of (retro) transposons. Many (retro) transposons were already quite old as they had accumulated many mutations, facilitating their assembly, however, hampering their identification. The draft ab initio gene prediction indicated 540 925 putative gene models, which is far more than expected, possibly due to the presence of pseudogenes. 86,073 models showed similarity to published proteins (UNIPROT). No gene rich regions were found, genes are uniformly distributed over the genome. Analysis of synteny with A. sativum (garlic) showed collinearity but also major rearrangements between both species. Not-withstanding, this assembly is the first high-quality draft genome sequence available for the study of onion and will be a valuable resource for further research.

Genotyping-by-Sequencing Derived Genetic Linkage Map and Quantitative Trait Loci for Sugar Content in Onion (Allium cepa L.)

“…In the present study, we constructed a GBS-derived genetic linkage map and applied it to the QTL mapping for sugar content in onion. Until now, the reference genome of the bulb onion has not been available publicly [11]. However, we reported a reference-free GBS-SNP-based onion linkage map using 156 F 2 individuals comprising eight linkage groups (corresponding to the onion chromosomes) and successfully mapped four QTLs associated with sugar content in bulb onion.…”

“…This is why the high-quality whole genome sequencing of onion has not been completed yet. However, a recent study that describes the de novo assembly and created eight pseudomolecules with five genetic linkage maps using the doubled haploid onion line "DHCU066619" is the latest high-quality onion reference genome with 14.9 Gb size, though it has not yet been made public [11].…”