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Clubroot, one of the most devastating diseases to the Brassicaceae family, is caused by the obligate biotrophic pathogen Plasmodiophora brassicae. However, studies of the molecular basis of disease resistance are still poor especially in quantitative resistance. In the present paper, two previously identified genotypes, a clubroot-resistant genotype (wild cabbage, B2013) and a clubroot-susceptible genotype (broccoli, 90196) were inoculated by P. brassicae for 0 (T0), 7 (T7), and 14 (T14) day after inoculation (DAI). Gene expression pattern analysis suggested that response changes in transcript level of two genotypes under P. brassicae infection were mainly activated at the primary stage (T7). Based on the results of DEGs functional enrichments from two infection stages, genes associated with cell wall biosynthesis, glucosinolate biosynthesis, and plant hormone signal transduction showed down-regulated at T14 compared to T7, indicating that defense responses to P. brassicae were induced earlier, and related pathways were repressed at T14. In addition, the genes related to NBS-LRR proteins, SA signal transduction, cell wall and phytoalexins biosynthesis, chitinase, Ca2+ signals and RBOH proteins were mainly up-regulated in B2013 by comparing those of 90196, indicating the pathways of response defense to clubroot were activated in the resistant genotype. This is the first report about comparative transcriptome analysis for broccoli and its wild relative during the different stages of P. brassicae infection and the results should be useful for molecular assisted screening and breeding of clubroot-resistant genotypes.

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BackgroundDue to its variegated and colorful leaves, ornamental kale (Brassica oleracea L. var. acephala) has become a popular ornamental plant. In this study, we report the fine mapping and analysis of a candidate purple leaf gene using a backcross population and an F2 population derived from two parental lines: W1827 (with white leaves) and P1835 (with purple leaves).ResultsGenetic analysis indicated that the purple leaf trait is controlled by a single dominant gene, which we named BoPr. Using markers developed based on the reference genome ‘02–12’, the BoPr gene was preliminarily mapped to a 280-kb interval of chromosome C09, with flanking markers M17 and BoID4714 at genetic distances of 4.3 cM and 1.5 cM, respectively. The recombination rate within this interval is almost 12 times higher than the usual level, which could be caused by assembly error for reference genome ‘02–12’ at this interval. Primers were designed based on ‘TO1000’, another B. oleracea reference genome. Among the newly designed InDel markers, BRID485 and BRID490 were found to be the closest to BoPr, flanking the gene at genetic distances of 0.1 cM and 0.2 cM, respectively; the interval between the two markers is 44.8 kb (reference genome ‘TO1000’). Seven annotated genes are located within the 44.8 kb genomic region, of which only Bo9g058630 shows high homology to AT5G42800 (dihydroflavonol reductase), which was identified as a candidate gene for BoPr. Blast analysis revealed that this 44.8 kb interval is located on an unanchored scaffold (Scaffold000035_P2) of ‘02–12’, confirming the existence of assembly error at the interval between M17 and BoID4714 for reference genome ‘02–12’.ConclusionsThis study identified a candidate gene for BoPr and lays a foundation for the cloning and functional analysis of this gene.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3613-x) contains supplementary material, which is available to authorized users.

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cabbage (Brassica oleracea var. capitata) is an important vegetable crop widely grown throughout the world, providing plentiful nutrients and health-promoting substances. To facilitate further genetics and genomic studies and crop improvement, we present here a high-quality reference genome for cabbage. We report a de novo genome assembly of the cabbage double-haploid line D134. A combined strategy of single-molecule real-time (SMRT) sequencing, 10× Genomics and chromosome conformation capture (Hi-c) produced a high quality cabbage draft genome. the chromosome-level D134 assembly is 529.92 Mb in size, 135 Mb longer than the current 02-12 reference genome, with scaffold N50 length being raised as high as 38 times. We annotated 44,701 high-quality protein-coding genes, and provided full-length transcripts for 45.59% of the total predicted gene models. Moreover, we identified novel genomic features like underrated TEs, as well as gene families and gene family expansions and contractions during B. oleracea evolution. The D134 draft genome is a cabbage reference genome assembled by SMRT long-read sequencing combined with the 10× Genomics and Hi-C technologies for scaffolding. This high-quality cabbage reference genome provides a valuable tool for improvement of Brassica crops. Brassica oleracea is an important vegetable species widely grown throughout the world. The species comprises several subspecies showing extensive morphological and phytochemical diversity. As a diploid species, B. oleracea underwent a whole-genome triplication (WGT) event 1 , followed by two whole-genome duplication (WGD) event 2,3 and a specific WGT 4 of the Brassiceae lineage, thus becoming a model for studies on polyploid genome evolution. Currently, two B. oleracea genomes based on next-generation sequencing (NGS) technology are available: the TO1000 (kale-like; B. oleracea var. alboglabra) assembly and the 02-12 (cabbage; B. oleracea var. capitata) assembly 5,6 , but their errors and gaps make them difficult to use for many studies 7-10. Recently, B. oleracea L. var. italica (broccoli) genome assembly was completed using long reads and optical maps 11. Broccoli and cabbage belong to Brassica species, however their growth, morphology and molecular levels is extremely variable, showing the importance of generating several genome assemblies for different morphotypes of B. oleracea. Up to now, there is still no high quality, comprehensive assembled cabbage (B. oleracea var. capitata) genome, which hinders greatly basic genetics and genomics research, as well as crop improvement. Thus generating an accurate cabbage genome assembly is crucial. To obtain a homozygous genome, the cabbage double-haploid (DH) line D134 was produced by microspore culture. We conducted whole-genome sequencing and de novo assembly for this line using single-molecule realtime (SMRT) cells on a PacBio Sequel platform combined with high-throughput chromosome conformation capture (Hi-C), next generation sequencing (NGS) and 10× Genomics technologies. This genome assembly is...

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