Chromosome-scale genome assemblies of five differentBrassica oleraceamorphotypes provide insights in intraspecific diversification

Abstract

AbstractBrassica oleraceais 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 betweenB. oleraceamorphotypes. Here, to capture more complete genome sequences ofB. 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 completeB. oleraceagenomes 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 ofB. oleraceaandB. rapa, we revealed their different evolutionary dynamics of LTR-RTs. Furthermore, we inferred the ancestral genome ofB. oleraceaand the common ancestral genome ofB. oleraceaandB. rapavia a pan-genome approach. We observed faster WGT-derived gene loss inB. rapathan inB. oleraceabefore 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 forB. oleraceaimprovement and insights towards understanding genome evolution during the intraspecific diversification ofB. oleraceaandB. rapa.