Species of the genusAlliumare well known for their large genomes.Allium cepais of great economic significance. Among vegetables, it ranks second after tomato in terms of the global production value. However, there is limited genomics information available onA.cepa. In this study, we sequenced theA. cepagenome at low-coverage and annotated repetitive sequences by using a combination of next-generation sequencing (NGS) and bioinformatics tools. Nearly 92% of 16 Gb haploid onion genome were defined as repetitive sequences, organized in 162 clusters of at least 0.01 percent of the genome. Of these, a proportion representing 40.5% of the genome were further analyzed in detail to obtain an overview of representative repetitive elements present in theA. cepagenome. Few representative satellite repeats were studied by fluorescencein situhybridization (FISH) and southern blotting. These results provided a basis for evolutionary cytogenomics within theAlliumgenus.
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