Anthocyanins are a group of flavonoid compounds. As a group of important secondary metabolites, they perform several key biological functions in plants. Anthocyanins also play beneficial health roles as potentially protective factors against cancer and heart disease. To elucidate the anthocyanin biosynthetic pathway in Brassica rapa, we conducted comparative genomic analyses between Arabidopsis thaliana and B. rapa on a genome-wide level. In total, we identified 73 genes in B. rapa as orthologs of 41 anthocyanin biosynthetic genes in A. thaliana. In B. rapa, the anthocyanin biosynthetic genes (ABGs) have expanded and most genes exist in more than one copy. The anthocyanin biosynthetic structural genes have expanded through whole genome and tandem duplication in B. rapa. More structural genes located upstream of the anthocyanin biosynthetic pathway have been retained than downstream. More negative regulatory genes are retained in the anthocyanin biosynthesis regulatory system of B. rapa. These results will promote an understanding of the genetic mechanism of anthocyanin biosynthesis, as well as help the improvement of the nutritional quality of B. rapa through the breeding of high anthocyanin content varieties.

Summary: Brassica rapacomprises many important cultivated vegetables and oil crops. However, Chiifu v3.0, the currentB. rapareference genome, still contains hundreds of gaps. Here, we presented a near‐complete genome assembly ofB. rapaChiifu 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 byALEandCRMlong terminal repeats (LTRs). Moreover, there is a high divergence of centromere length and sequence amongB. rapagenomes. We further found that centromeres are enriched forCopiainvaded at 0.14 MYA on average, while pericentromeres are enriched forGypsyLTRs 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 sequencePCR630was identified in the pericentromeres ofB. rapa. Overall, the near‐complete genome assembly,B. rapaChiifu v4.0, offers valuable tools for genomic and genetic studies ofBrassicaspecies and provides new insights into the evolution of centromeres.

Summary: Transposable element (TE) is prevalent in plant genomes. However, studies on their impact on phenotypic evolution in crop plants are relatively rare, because systematically identifying TE insertions within a species has been a challenge. Here, we present a novel approach for uncovering TE insertion polymorphisms (TIPs) using pan‐genome analysis combined with population‐scale resequencing, and we adopt this pipeline to retrieve TIPs in a Brassica rapa germplasm collection. We found that 23% of genes within the reference Chiifu‐401‐42 genome harbored TIPs. TIPs tended to have large transcriptional effects, including modifying gene expression levels and altering gene structure by introducing new introns. Among 524 diverse accessions, TIPs broadly influenced genes related to traits and acted a crucial role in the domestication of B. rapa morphotypes. As examples, four specific TIP‐containing genes were found to be candidates that potentially involved in various climatic conditions, promoting the formation of diverse vegetable crops in B. rapa. Our work reveals the hitherto hidden TIPs implicated in agronomic traits and highlights their widespread utility in studies of crop domestication.

Energy and food source crop demand claims to be vulnerable to climate change impacts. The new and orphan crops, which in the past have received only limited research attention but are sustainable to environmental systems, are needed. In this review, we summarize the available literature about Ethiopian mustard as an alternative energy source and its sustainable economic importance as a new promising Brassicacea crop for new opportunities in the face of producing sustainable environment and energy development. Ethiopian mustard has many advantages and can be adopted to replace crops that are susceptible to adverse environmental conditions. Ethiopian mustard is becoming a new promising Brassicaceae crop with the current global energy demand increases. However, researchers have only focused on energy source production which has resulted in developing high erucic acid varieties. This results partly in limited studies on developing Ethiopian mustard edible oil varieties. The adoption and scaling-up of this promising crop as an oilseed crop in developing countries and Mediterranean conditions can sustain the impact of climate change with the demand for food and energy debate concepts. Indeed, further agronomic, quality and genomic studies on oilseed nutritional traits for efficient breeding and utilization are needed.