Abstract
Draft Genome Assembly and Transcriptome Dataset for European Turnip (Brassica rapa L. ssp. rapifera), ECD4 Carrying Clubroot Resistance.
Highlights
The Brassica genus consists of economically important oil and leafy vegetable crops, which are cultivated worldwide
The protein sequences from turnip (AA) and diploid Brassica species, including Chinese cabbage (AA; reference genome v3.0), B. nigra (BB; v1.1), B. oleracea (CC; v1.1), Raphanus sativus (v1.1), and the outgroup species Arabidopsis thaliana were used to predict orthologous gene clusters
Syntenic blocks between the chromosomes of Chinese cabbage and contigs of European turnip were detected by using SyMAP (Soderlund et al, 2006) and are shown in a Circos plot. Genome rearrangement events such translocation between the two genomes were verified by using MUMmer (Delcher et al, 2003)
Summary
The Brassica genus consists of economically important oil and leafy vegetable crops, which are cultivated worldwide. 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. These data provide a valuable resource for studying the morphological diversity and evolution of turnips. We identified 709, 672, and 463 orthologous gene clusters specific to European turnip, yellow sarson, and Chinese cabbage, respectively (Supplementary Figure 9A). Three R genes homologous to Rcr, which is a clubroot resistance gene of TNL class identified in B. nigra (Chang et al, 2019), were identified in European turnip, but only one was identified in Chinese cabbage (Supplementary Table 9)
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