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

A near-complete genome assembly of Brassica rapa provides new insights into the evolution of centromeres

Brassica rapa comprises many important cultivated vegetables and oil crops. However, Chiifu v3.0, the current B. rapa reference genome, still contains hundreds of gaps. Here, we presented a near-complete genome assembly of B. rapa Chiifu v4.0, which was 424.59 Mb with only two gaps, using Oxford Nanopore Technology (ONT) ultralong-read sequencing and Hi-C technologies. The new assembly contains 12 contigs, with a contig N50 of 38.26 Mb. Eight of the ten chromosomes were entirely reconstructed in a single contig from telomere to telomere. We found that the centromeres were mainly invaded by ALE and CRM long terminal repeats (LTRs). Moreover, there is a high divergence of centromere length and sequence among B. rapa genomes. We further found that centromeres are enriched for Copia invaded at 0.14 MYA on average, while pericentromeres are enriched for Gypsy LTRs invaded at 0.51 MYA on average. These results indicated the different invasion mechanisms of LTRs between the two structures. In addition, a novel repetitive sequence PCR630 was identified in the pericentromeres of B. rapa. Overall, the near-complete genome assembly, B. rapa Chiifu v4.0, offers valuable tools for genomic and genetic studies of Brassica species and provides new insights into the evolution of centromeres.

Differences in pseudogene evolution contributed to the contrasting flavors of turnip and Chiifu, two Brassica rapa subspecies

Pseudogenes are important resources for investigation of genome evolution and genomic diversity because they are nonfunctional but have regulatory effects that influence plant adaptation and diversification. However, few systematic comparative analyses of pseudogenes in closely related species have been conducted. Here, we present a turnip (Brassica rapa ssp. rapa) genome sequence and characterize pseudogenes among diploid Brassica species/subspecies. The results revealed that the number of pseudogenes was greatest in Brassica oleracea (CC genome), followed by B. rapa (AA genome) and then Brassica nigra (BB genome), implying that pseudogene differences emerged after species differentiation. In Brassica AA genomes, pseudogenes were distributed asymmetrically on chromosomes because of numerous chromosomal insertions/rearrangements, which contributed to the diversity among subspecies. Pseudogene differences among subspecies were reflected in the flavor-related glucosinolate (GSL) pathway. Specifically, turnip had the highest content of pungent substances, probably because of expansion of the methylthioalkylmalate synthase-encoding gene family in turnips; these genes were converted into pseudogenes in B. rapa ssp. pekinensis (Chiifu). RNA interference-based silencing of the gene encoding 2-oxoglutarate-dependent dioxygenase 2, which is also associated with flavor and anticancer substances in the GSL pathway, resulted in increased abundance of anticancer compounds and decreased pungency of turnip and Chiifu. These findings revealed that pseudogene differences between turnip and Chiifu influenced the evolution of flavor-associated GSL metabolism-related genes, ultimately resulting in the different flavors of turnip and Chiifu.

What Can We Learn from -Omics Approaches to Understand Clubroot Disease?

Clubroot is one of the most economically significant diseases worldwide. As a result, many investigations focus on both curing the disease and in-depth molecular studies. Although the first transcriptome dataset for the clubroot disease describing the clubroot disease was published in 2006, many different pathogen-host plant combinations have only recently been investigated and published. Articles presenting -omics data and the clubroot pathogen Plasmodiophora brassicae as well as different host plants were analyzed to summarize the findings in the richness of these datasets. Although genome data for the protist have only recently become available, many effector candidates have been identified, but their functional characterization is incomplete. A better understanding of the life cycle is clearly required to comprehend its function. While only a few proteome studies and metabolome analyses were performed, the majority of studies used microarrays and RNAseq approaches to study transcriptomes. Metabolites, comprising chemical groups like hormones were generally studied in a more targeted manner. Furthermore, functional approaches based on such datasets have been carried out employing mutants, transgenic lines, or ecotypes/cultivars of either Arabidopsis thaliana or other economically important host plants of the Brassica family. This has led to new discoveries of potential genes involved in disease development or in (partial) resistance or tolerance to P. brassicae. The overall contribution of individual experimental setups to a larger picture will be discussed in this review.