SRA

Plant genomes are often characterized by their high level of repetitiveness and their polyploid nature. As a direct consequence, genome assemblies of plant genomes are challenging. The introduction of short-reads technologies ten years ago, increased significantly the number of available plant genomes. Generally, these assemblies are incomplete and fragmented and only a few of them are at the chromosome-scale. Recently, Pacific Biosciences and Oxford Nanopore sequencing technologies were commercialized with the promise to sequence long DNA fragments (kilobases to megabases order) and then, by using efficient algorithms, provide assembly of high quality in terms of contiguity and completeness of the repetitive regions. However, even if genome assemblies based on long reads exhibits high contigs N50 (larger than 1Mb), there is still a lack in the knowledge of the genome organization at the chromosome-level. Here we described a strategy based on long reads (MinION and PromethION sequencers) and optical maps (Saphyr system) which can provide assemblies at the chromosome-level, and we demonstrated its applicability by sequencing de novo three plant genomes of two dicotyledons (Brassica rapa and Brassica oleracea) and one monocotyledon (Musa schizocarpa). All three assemblies show a contig N50 higher than 5Mb and contain scaffolds that represent entire chromosomes or chromosome arms.