| The Brassica genus belongs to the Brassicaceae family,including oil and vegetable crops with high economic value that are widely cultivated all over the world.The Brassica genus includes three diploid species of Brassica rapa,Brassica oleracea,and Brassica nigra,as well as three allopolyploid species of Brassica napus,Brassica juncea,and Brassica carinata.During intraspecific diversification,B.rapa accumulates abundant phenotypic variants.For example,during the B.rapa intraspecific diversification,different subspecies and varieties such as Chinese cabbage,turnip,oil types,pak choi,and Caixin are formed.Therefore,identifying the comprehensive variants for B.rapa is of great significance to the study of intraspecific diversification and breeding.In the present study,we de novo assembled 16 representative B.rapa genomes and constructed a pan-genome of the B.rapa species.Based on the pan-genome and 524 resequencing accessions,we constructed a variation dataset of B.rapa,and identified candidate genes related to the domestication of different B.rapa morphotypes.Additionally,based on the pan-genome,we explored the evolutionary characteristics of gene fractionation in the mesopolyploid B.rapa genome during intraspecific differentiation.The main results are as follows:1.We de novo assembled 16 different B.rapa genomes,combined with the two published B.rapa reference genomes,we constructed a B.rapa pan-genome consisting of 18 representative B.rapa genomes.The B.rapa pan-genome includes 47,107 gene families,of which 55.74%,25.00%,17.80%,and 1.46% of the genes have been identified as core,softcore,dispensable,and private genes.2.We obtained resequencing reads of 524 B.rapa genomes,combined with the pan-genome,we identified 3.97 M SNPs,1.14 M In Dels,and 57,877 polymorphic structural variants in the 524 B.rapa genomes.Notably,we identified 4 Mb-level inversions among different B.rapa genomes.3.We built an integrated graph-based genome with SVs,and investigated SV landscape in 524 B.rapa genomes.We found that structural variants were associated with B.rapa morphotype domestication.Furthermore,we identified four candidate genes,named Br PIN3.3,Br MYB95.3,Br FL5.1,and Br SAL4.2,which might be related to the formation of leafy head in B.rapa.4.We found that 13.42% of the genes that were syntenic with Arabidopsis thaliana were fractionated in different genomes.We denoted such genes as being “FSG(Flexible syntenic gene)”.We found that the FSGs accumulated more transposable elements and non-synonymous mutations.Further analysis revealed that gene flexibility is associated with individual genome adaptation.5.We found that the proportion of FSGs in the MF subgenomes was significantly higher than that of the LF subgenome,revealing the continuing influence of the dominant subgenome on intraspecific diversification in B.rapa.Our results illustrated that in addition to the “two-step” evolution of B.rapa,genome composition also contributed to subgenome dominance.Based on the B.rapa pan-genome constructed from representative B.rapa accessions,we demonstrated the important role of structural variation on the domestication of different B.rapa morphotypes,and illustrated the significant impact of ancient polyploidization on intraspecific diversification of B.rapa.Collectively,our work serves as a rich resource for genomic analysis and breeding of B.rapa. |
