A chromosome-level reference genome of non-heading Chinese cabbage [Brassica campestris (syn. Brassica rapa) ssp. chinensis

Ying Li,Li-Ming Ma,Chang-Wei Zhang,Dong Xiao,Hong-Kun Zheng,Xi-Lin Hou,Tong-Kun Liu,Fei Chen,Gao-Feng Liu

doi:10.1038/s41438-020-00449-z

Abstract

Non-heading Chinese cabbage (NHCC) is an important leafy vegetable cultivated worldwide. Here, we report the first high-quality, chromosome-level genome of NHCC001 based on PacBio, Hi-C, and Illumina sequencing data. The assembled NHCC001 genome is 405.33 Mb in size with a contig N50 of 2.83 Mb and a scaffold N50 of 38.13 Mb. Approximately 53% of the assembled genome is composed of repetitive sequences, among which long terminal repeats (LTRs, 20.42% of the genome) are the most abundant. Using Hi-C data, 97.9% (396.83 Mb) of the sequences were assigned to 10 pseudochromosomes. Genome assessment showed that this B. rapa NHCC001 genome assembly is of better quality than other currently available B. rapa assemblies and that it contains 48,158 protein-coding genes, 99.56% of which are annotated in at least one functional database. Comparative genomic analysis confirmed that B. rapa NHCC001 underwent a whole-genome triplication (WGT) event shared with other Brassica species that occurred after the WGD events shared with Arabidopsis. Genes related to ascorbic acid metabolism showed little variation among the three B. rapa subspecies. The numbers of genes involved in glucosinolate biosynthesis and catabolism were higher in NHCC001 than in Chiifu and Z1, due primarily to tandem duplication. The newly assembled genome will provide an important resource for research on B. rapa, especially B. rapa ssp. chinensis.

Highlights

Introduction TheBrassica genus comprises various economically important crops, many of which are extensively cultivated worldwide as oil crops and leafy vegetables
Our newly assembled B. rapa genome achieves a high level of continuity and completeness
De novo genome assembly The size of the B. rapa NHCC001 genome estimated by k-mer analysis was 477.76 Mb, larger than that of the B. rapa Chiifu genome, which was estimated to be 442.90 Mb (Supplementary Figure S1)

Summary

Introduction

Introduction TheBrassica genus comprises various economically important crops, many of which are extensively cultivated worldwide as oil crops and leafy vegetables. Single-molecule sequencing, referred to as third-generation sequencing, aims to meet the demand for high-quality plant genome assembly[7], and PacBio and Oxford Nanopore Technology (ONT) sequencing have been used to assemble new, high-quality reference genomes for maize and tomato[8,9]. The Brassica genus provides a good opportunity to study genome evolution in polyploids. The first B. rapa genome draft published in 2011 was assembled using a whole-genome shotgun strategy with Illumina short reads[10]. The recently released B. rapa Chiifu genome v3.0 based on PacBio sequencing lacked nearly 20% of the expected genome content (353.14 of 442.9 Mb), and the assembly was highly fragmented (contig N50 1.45 Mb)[11]. The genome of a new morphotype, B. rapa Z1, was assembled using Nanopore sequencing with a contig N50 of 5.51 Mb12. Current sequencing technologies are evolving rapidly, and the development of improved technologies enables the production of higher quality genomes

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Discussion

Conclusion