Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies

<i>Brassica rapa</i> comprises several important cultivated vegetables and oil crops. Current reference genome assemblies of <i>Brassica rapa</i> are quite fragmented and not highly contiguous, thereby limiting extensive genetic and genomic analyses. Here, we report an improved assembly of the <i>B. rapa</i> genome (v3.0) using single-molecule sequencing, optical mapping, and chromosome conformation capture technologies (Hi-C). Relative to the previous reference genomes, our assembly features a contig N50 size of 1.45 Mb, representing a ~30-fold improvement. We also identified a new event that occurred in the <i>B. rapa</i> genome ~1.2 million years ago, when a long terminal repeat retrotransposon (LTR-RT) expanded. Further analysis refined the relationship of genome blocks and accurately located the centromeres in the <i>B. rapa</i> genome. The <i>B. rapa</i> genome v3.0 will serve as an important community resource for future genetic and genomic studies in <i>B. rapa</i>. This resource will facilitate breeding efforts in <i>B. rapa</i>, as well as comparative genomic analysis with other <i>Brassica</i> species.