Abstract
Brassica rapa comprises several important cultivated vegetables and oil crops. Current reference genome assemblies of Brassica rapa are quite fragmented and not highly contiguous, thereby limiting extensive genetic and genomic analyses. Here, we report an improved assembly of the B. rapa 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 B. rapa 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 B. rapa genome. The B. rapa genome v3.0 will serve as an important community resource for future genetic and genomic studies in B. rapa. This resource will facilitate breeding efforts in B. rapa, as well as comparative genomic analysis with other Brassica species.
Highlights
Introduction The genusBrassica comprises various economically important species, many of which are extensively cultivated around the world as oil crops and vegetables
We note that PacBio reads tend to provide excellent results to fill gaps in assemblies stemming from short reads, as demonstrated by our current assembly and other studies[14,24]
Using the high-density genetic map derived from cross B. rapa lines with the same morphotype, we could accurately compare the quality of v3.0 with that of previous assemblies, indicating that our novel assembly achieved the highest contiguity and quality among the three assemblies
Summary
Introduction The genusBrassica comprises various economically important species, many of which are extensively cultivated around the world as oil crops and vegetables. The Brassica genomes underwent an additional whole-genome triplication event after. The B. rapa genome was the first to be sequenced among the Brassica species[2]. The first released genome draft, B. rapa genome v1.5, was created using a wholegenome shotgun strategy with Illumina short reads and facilitated genome assemblies of other Brassica species[3,4,5]. A more recent release, B. rapa genome v2.0 (ref.6), resulted from iterative updates with additional short read data. It was further updated to the B. rapa genome v2.5 after improving the scaffold order (http://brassicadb.org/ brad/datasets/pub/Genomes/Brassica_rapa/V2.0/V2.5/). Since 2011, both genetic and comparative genomic studies in Brassica species have benefited from the B. rapa draft sequences.
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