Draft Genome Assembly and Transcriptome Dataset for European Turnip (Brassica rapa L. ssp. rapifera), ECD4 Carrying Clubroot Resistance.

The Brassica genus consists of economically important oil and leafy vegetable crops, which are cultivated worldwide. The Brassica species represent as the “U's triangle” (Nagahara, 1935), which includes the three basic diploid species Brassica rapa (A genome), Brassica nigra (B genome), and Brassica oleracea (C genome), as well as the three amphidiploid species Brassica juncea (A and B genomes), Brassica napus (A and C genomes), and Brassica carinata (B and C genomes). Brassica rapa (2n = 2x = 20) has been cultivated for specific phenotypic characteristics such as heading (i.e., ssp. pekinensis; Chinese cabbage) and non-heading (i.e., ssp. chinesis; pak choi) leafy vegetables, tuberized hypocotyl/roots (i.e., ssp. rapifera; turnip), and oil rich seedpods (i.e., ssp. trilocularis; yellow sarson) in the oil crops. Although the genomes of its subspecies are very similar (Lin et al., 2014), B. rapa demonstrates extreme morphological diversity. Because of the economical value and scientific interest in phenotypic diversity, the genome sequence of mesopolyploid B. rapa ssp. pekinensis Chiifu, a Chinese cabbage, was the first published B. rapa reference genome, and revealed that B. rapa evolved via a two-step whole-genome triplication and, as a result, has three syntenic subgenomes (Wang et al., 2011). The polyploidization is hypothesized to have facilitated the diversification of genes as well as gene fractionation, and as a consequence led to the evolution of different morphotypes within and between related Brassica species. The study of intraspecific diversity in B. rapa offers opportunities to advance our understanding of plant growth, development, and phenotypic evolution (Paterson et al., 2001). Over the last few years, the genome assembly of B. rapa (version 3.0) has been improved using single-molecule sequencing, optical mapping, and chromosome conformation capture technologies (Hi-C), resulting in an approximately 30-fold improvement with a contig N50 size of 1.45 Mb compared with that of previous references (Zhang et al., 2018). The assembly refined the syntenic relationship of genome blocks and centromere locations in the genome, and identified a greater number of annotated transposable elements (TEs) than in previous assemblies. In addition to the whole-genome sequence of Chinese cabbage, chromosome-level genome sequences of other B. rapa subspecies, including yellow sarson (Belser et al., 2018) and pak choi (Li P. et al., 2020; Li Y. et al., 2020), have been recently reported. The studies provide insight to the understanding of genetic drivers underlying the morphological variation among B. rapa subspecies. Moreover, a pangenome from Chinese cabbage, rapid-cycling Brassica, and Japanese vegetable turnip was constructed using Illumina short-read data (Lin et al., 2014), identifying genomic determinants of morphological variation, especially copy number differences in peroxidases associated with the phenylpropanoid biosynthetic pathway in turnip. Turnip (B. rapa L. ssp. rapifera) represent one of the morphotypes in B. rapa that forms tubers (hypocotyl/taproot tubers), produces lobed leaves with long petioles, and can be used to study the genetics underlying storage organ formation (Zhang et al., 2014). Brassica species are susceptible to clubroot disease, caused by Plasmodiophora brassicae (Schwelm et al., 2015), and forms galls (clubs) on infected root tissues with abnormal proliferation, preventing water and nutrient uptake and retarding the normal growth and development of plants, resulting in significantly reduced yield and quality. Sources of known clubroot resistance genes are derived from European turnip, carrying strong resistance to this disease (Matsumoto et al., 1998; Hirani et al., 2018). The resistance genes of European turnip have been introduced into other Brassica crops including vegetables and oilseed rape. In particular, European clubroot differential (ECD) turnips, that exhibited high levels of resistance to clubroot and that consist of four accessions (ECD1–ECD4), were developed and have been helpful for discovering dominant loci conferring clubroot resistance genes including CRa, CRb, and CRc for marker-assisted selection in canola and other Brassica species (Hirani et al., 2018). Here, we report the draft genome assembly of a European turnip, ECD4, which has strong clubroot resistance, that was generated by PacBio single-molecule long-read sequencing technology. This draft genome assembly coupled with transcriptome data derived from various leaf and root tissues will support the discovery of disease resistance genes (R genes) especially clubroot resistance genes, enabling the development of allele-specific markers for marker-assisted selection in Brassica breeding. Moreover, these data provide a valuable resource for studying the morphological diversity and evolution of turnips. For the genome assembly of European turnip (ECD4), a total of 70.63 Gb of PacBio long reads (an average sequencing coverage of 136.36x) and 72.16 Gb of Illumina short reads (139.3x) were generated (Supplementary Table 1). Based on k-mer analysis (k = 21), the estimated genome size of European turnip is approximately 518 Mbp (Figure 1A). The genome assembly resulted in a 315.8 Mb draft genome with 655 contigs (contig N50 length of 1.45 Mb; the longest contig length was 21.92 Mb) (Table 1). Our assembly data covered about 61% of the genome of European turnip, being predicted as mostly euchromatins. The assembly coverage is slightly low compared with those reported in Chinese cabbage (353 Mb) (Zhang et al., 2018), pak choi (370 Mb) (Li P. et al., 2020; Li Y. et al., 2020), and yellow sarson (402 Mb) (Belser et al., 2018). Whole-genome sequences of Chinese cabbage, pak choi, and yellow sarson were assembled at the chromosome-level by using chromosome conformation capture (Hi-C) technology [Chinese cabbage (reference genome version 3.0) and pak choi] and/or BioNano...