Milk thistle (Silybum marianum) belongs to the Asteraceae family and is a medicinal plant native to the Mediterranean Basin. Silymarin in achene is a widely used herbal product for chronic liver disease. There is growing interest in natural medicine using milk thistle in Korea, but the raw material completely relies on imports. Despite its economic importance, phenotypic evaluations of native resources of milk thistle in Korea have not been carried out. In addition, genomic research and molecular marker development are very limited in milk thistle. In this study, we evaluated 220 milk thistle resources consisting of 172 accessions collected from the domestic market, and 48 accessions isolated from 6 accessions distributed by the National Agrobiodiversity Center in Korea. Six plant characteristics (height, seed weight, number of flowers, seed weight per flower, spine length, and color at harvest) were measured, and six samples (M01–M06) were selected to represent the genetic diversity of the population for genomic research. To develop PCR-based and co-dominant insertion/deletion (InDel) markers, we performed genome-wide InDel detection by comparing the whole-genome resequencing data of the six selected accessions with the reference genome sequence (GCA_001541825). As a result, 177 InDel markers with high distinguishability and reproducibility were selected from the 30,845 InDel variants. Unknowingly imported alien plant resources could easily be genetically mixed, and jeopardized seed purity can cause continuous difficulties in the development of high value-added agricultural platforms utilizing natural products. The selected plant materials and 177 validated InDel markers developed via whole-genome resequencing analysis could be valuable resources for breeding, conservation, and ecological studies of natives to Korea, along with acceleration of Silybum marianum industrialization.

Perilla is a key component of Korean food. It contains several plant-specialized metabolites that provide medical benefits. In response to an increased interest in healthy supplement food from the public, people are focusing on the properties of Perilla. Nevertheless, unlike rice and soybeans, there are few studies based on molecular genetics on Perilla, so it is difficult to systematically study the molecular breed. The wild Perilla, Perilla citriodora ‘Jeju17’, was identified a decade ago on the Korean island of Jeju. Using short-reads, long-reads, and Hi-C, a chromosome-scale genome spanning 676 Mbp, with high contiguity, was assembled. Aligning the ‘Jeju17’ genome to the ‘PC002’ Chinese species revealed significant collinearity with respect to the total length. A total of 31,769 coding sequences were predicted, among which 3331 were ‘Jeju17’-specific. Gene enrichment of the species-specific gene repertoire highlighted environment adaptation, fatty acid metabolism, and plant-specialized metabolite biosynthesis. Using a homology-based approach, genes involved in fatty acid and lipid triacylglycerol biosynthesis were identified. A total of 22 fatty acid desaturases were found and comprehensively characterized. Expression of the FAD genes in ‘Jeju17’ was examined at the seed level, and hormone signaling factors were identified. The results showed that the expression of FAD genes in ‘Jeju17’ at the seed level was high 25 days after flowering, and their responses of hormones and stress were mainly associated with hormone signal transduction and abiotic stress via cis-elements patterns. This study presents a chromosome-level genome assembly of P. citriodora ‘Jeju17’, the first wild Perilla to be sequenced from the Korean island of Jeju. The analyses provided can be useful in designing ALA-enhanced Perilla genotypes in the future.

Cyst nematodes remain a major threat to global agricultural production, causing huge losses. To understand the parasitism of the cyst nematodes Heterodera trifolii (HT) and Heterodera schachtii (HS), we constructed whole-genome assemblies using short- and long-read sequencing technologies. The nematode genomes were 379 Mb and 183 Mb in size, with the integrated gene models predicting 40,186 and 18,227 genes in HT and HS, respectively. We found more than half of the genes predicted in HT (64.7%) and HS (53.2%) were collinear to their nearest neighbor H. glycines (HG). Large-scale duplication patterns in HT and segmental duplications of more than half of the orthologous genes indicate that the genome of HT is polyploid in nature. Functional analysis of the genes indicated that 65.6% of the HG genes existed within the HT genome. Most abundant genes in HT and HS were involved in gene regulation, DNA integration, and chemotaxis. Differentially expressed genes showed upregulation of cuticle structural constituent genes during egg and female stages and cytoskeletal motor activity-related genes in juvenile stage 2 (J2). Horizontal gene transfer analyses identified four new vitamin biosynthesis genes, pdxK, pdxH, pdxS, and fabG, of bacterial origin, to be first reported in HT and HS. Mitogenomes of HT, HS, and HG showed similar structure, composition, and codon usage. However, rates of substitution of bases in the gene nad4l were significantly different between HT and HS. The described genomes, transcriptomes, and mitogenomes of plant-parasitic nematodes HT and HS are potential bio-resources used to identify several strategies of control of the nematode.

Senna tora is a widely used medicinal plant. Its health benefits have been attributed to the large quantity of anthraquinones, but how they are made in plants remains a mystery. To identify the genes responsible for plant anthraquinone biosynthesis, we sequenced and annotated the genome of S. tora at the chromosome level with contig N50 and super-scaffold N50 of 4.03 Mb and 41.7 Mb. Comparison among related plant species showed that a chalcone synthase-like (CHS-L) gene family has lineage-specifically and rapidly expanded in S. tora . Combining genomics, transcriptomics, metabolomics, and biochemistry, we identified a CHS-L responsible for biosynthesis of anthraquinones, the first example in plants. The S. tora reference genome will accelerate the discovery of biologically active anthraquinone biosynthesis pathways in medicinal plants. One Sentence Summary: The chromosome-scale reference genome of a medicinal plant Senna tora , transcriptomics, metabolomics, and biochemical analysis provide new insights into anthraquinone biosynthesis in plants.