Chromosome-scale genome assemblies of five different Brassica oleracea morphotypes provide insights in intraspecific diversification

Brassica oleracea is an economically important vegetable and fodder crop species that includes many morphotypes exhibiting enormous phenotypic variations. Previously, a pan-genome study based on short reads mapping approach has shown extensive structural variations between B. oleracea morphotypes. Here, to capture more complete genome sequences of B. oleracea, we report new chromosome-scale genome assemblies for five different morphotypes, namely broccoli, cauliflower, kale, kohlrabi and white cabbage, which were created by combining long-read sequencing data and Bionano DLS optical maps. The five assemblies are the most continuous and complete B. oleracea genomes to date (contig N50 > 10 Mb). Comparative analysis revealed both highly syntenic relationships and extensive structural variants among the five genomes. Dispensable and specific gene clusters accounted for ~38.19% of total gene clusters based on a pan-genome analysis including our five newly assembled genomes and four previously reported genomes. Using the pan-genome of B. oleracea and B. rapa, we revealed their different evolutionary dynamics of LTR-RTs. Furthermore, we inferred the ancestral genome of B. oleracea and the common ancestral genome of B. oleracea and B. rapa via a pan-genome approach. We observed faster WGT-derived gene loss in B. rapa than in B. oleracea before intraspecific diversification. We also revealed continuing gene loss bias during intraspecific diversification of the two species and a strong bias towards losing only one copy among the three paralogous genes. This study provides valuable genomic resources for B. oleracea improvement and insights towards understanding genome evolution during the intraspecific diversification of B. oleracea and B. rapa.