Genomes of Meniocus linifolius and Tetracme quadricornis reveal the ancestral karyotype and genomic features of core Brassicaceae.

Brassicaceae represents an important plant family from both a scientific and economic perspective. However, genomic features related to the early diversification of this family have not been fully characterized, especially upon the uplift of the Tibetan Plateau, which was followed by increasing aridity in the Asian interior, intensifying monsoons in Eastern Asia, and significantly fluctuating daily temperatures. Here, we reveal the genomic architecture that accompanied early Brassicaceae diversification by analyzing two high-quality chromosome-level genomes for Meniocus linifolius (Arabodae; clade D) and Tetracme quadricornis (Hesperodae; clade E), together with genomes representing all major Brassicaceae clades and the basal Aethionemeae. We reconstructed an ancestral core Brassicaceae karyotype (CBK) containing 9 pseudochromosomes with 65 conserved syntenic genomic blocks and identified 9702 conserved genes in Brassicaceae. We detected pervasive conflicting phylogenomic signals accompanied by widespread ancient hybridization events, which correlate well with the early divergence of core Brassicaceae. We identified a successive Brassicaceae-specific expansion of the class I TREHALOSE-6-PHOSPHATE SYNTHASE 1 (TPS1) gene family, which encodes enzymes with essential regulatory roles in flowering time and embryo development. The TPS1s were mainly randomly amplified, followed by expression divergence. Our results provide fresh insights into historical genomic features coupled with Brassicaceae evolution and offer a potential model for broad-scale studies of adaptive radiation under an ever-changing environment.

Glucosinolates in cancer prevention and treatment: experimental and clinical evidence.

Glucosinolates are naturally occurring ß-d-thioglucosides that mainly exist in the Brassicaceae family. The enzyme myrosinase hydrolyzes glucosinolates to form isothiocyanates, which are chemical protectors. Phenethyl isothiocyanate, sulforaphane, and benzyl isothiocyanate are potential isothiocyanate with efficient anti-cancer effects as a protective or treatment agent. Glucosinolate metabolites exert the cancer-preventive activity through different mechanisms, including induction of the Nrf2 transcription factor, inhibition of expression of tumor necrosis factor-α (TNFα) and interleukin-1ß (IL-1ß), induction of apoptosis through inhibiting phase I enzymes and inducting phase II enzymes, interruption of caspase pathways, STAT1/STAT2, inhibition of sulfotransferases. Moreover, glucosinolates and their metabolites are effective in cancer treatment by inhibiting angiogenesis, upregulating natural killers, increasing expression of p53, p21, caspase 3 and 9, and modulating NF-κB. Despite the mentioned cancer-preventing effects, some isothiocyanates can increase the risk of tumors. So, further studies are needed to obtain an accurate and effective dose for each glucosinolates to treat different types of tumors.

A comparison of phylogenetic and distance-based approaches for the distinction of genetically closed species, Draba rimarum (Rech.f.) A.R. Khosravi & A. Eslami-Farouji, and Draba aucheri Boiss. (Brassicaceae) as a case study.

Circumscribing species boundries is necessary in systematic plant biology. Even a mistake in delimiting taxa may lead to incorrect scientific interpretations. Draba rimarum (Rech.f.) A.R. Khosravi & A. Eslami-Farouji is an endemic Iranian species with a narrow geographic distribution, and is genetically close to D. aucheri. The present study provided a phylogenetic review, time divergence, and planar network of both species to unravel the distinct position of both species along with the prediction of any conflicting or ambiguous signals. Regarding this purpose, here we represent that phylogenetic trees may fail to show reliable results toward the distinct position of genetically close species.

Phytochemical Constituents from the Seeds of Capsella bursa-pastoris and Their Antioxidant Activities.

Phytochemical investigation of 70% EtOH extract of the seeds of Capsella bursa-pastoris led to the isolation of a new cyclobutane organic acid (1), and fourteen known compounds, including two organosulfur compounds (2, 3), two quinonoids (4, 5), five flavonoids (6-10), three sterols (11-13) and two other types (14, 15). The structures of the compounds were elucidated by extensive spectroscopic analyses as well as comparison of their spectroscopic data with those reported in the literature. The antioxidant capacities of all compounds and extractive fractions were evaluated by the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical-scavenging test and ferric reducing antioxidant power (FRAP) assay. Then the antioxidative substances were evaluated for their neuroprotective effects against H2O2-induced HT22 cell injury. The results indicated the strong scavenging ability to free radical of the extractive fractions and compounds 1-3, 8-10 and 13, and the ferric reducing antioxidant power of the extractive fractions and compounds 1-3, 8 and 10, which were close to or higher than that of the positive control trolox. The EtOAc fraction, n-BuOH fraction, and compounds 1, 3 and 8 can protect HT-22 cells from oxidative damage.

Analysis of WAK Genes in Nine Cruciferous Species with a Focus on Brassica napus L.

The wall-associated kinase family contributes to plant cell elongation and pathogen recognition. Nine Cruciferous species were studied for identification and molecular evolution of the WAK gene family. Firstly, 178 WAK genes were identified. A phylogenetic tree was constructed of the Cruciferous WAK proteins into four categories, of which the Brassica rapa, Brassica oleracea and Brassica napus genes in the U's triangle were more closely related. The WAK gene family was unevenly distributed in B. napus chromosomal imaging, with the largest number of BnWAK genes located on chromosome C08. In the expression analysis, the expression patterns of the WAK gene family varied under different stress treatments, and some members of BnWAKs were significantly different under stress treatments. This study lays a foundation for further revealing the functional mechanisms of the WAK gene family in Brassica napus.

The evolution of the hypotetraploid Catolobus pendulus genome - the poorly known sister species of Capsella.

The establishment of Arabidopsis as the most important plant model has also brought other crucifer species into the spotlight of comparative research. While the genus Capsella has become a prominent crucifer model system, its closest relative has been overlooked. The unispecific genus Catolobus is native to temperate Eurasian woodlands, from eastern Europe to the Russian Far East. Here, we analyzed chromosome number, genome structure, intraspecific genetic variation, and habitat suitability of Catolobus pendulus throughout its range. Unexpectedly, all analyzed populations were hypotetraploid (2n = 30, ~330 Mb). Comparative cytogenomic analysis revealed that the Catolobus genome arose by a whole-genome duplication in a diploid genome resembling Ancestral Crucifer Karyotype (ACK, n = 8). In contrast to the much younger Capsella allotetraploid genomes, the presumably autotetraploid Catolobus genome (2n = 32) arose early after the Catolobus/Capsella divergence. Since its origin, the tetraploid Catolobus genome has undergone chromosomal rediploidization, including a reduction in chromosome number from 2n = 32 to 2n = 30. Diploidization occurred through end-to-end chromosome fusion and other chromosomal rearrangements affecting a total of six of 16 ancestral chromosomes. The hypotetraploid Catolobus cytotype expanded toward its present range, accompanied by some longitudinal genetic differentiation. The sister relationship between Catolobus and Capsella allows comparative studies of tetraploid genomes of contrasting ages and different degrees of genome diploidization.

Corrigendum: Evolution of tandem repeats is mirroring post-polyploid cladogenesis in Heliophila (Brassicaceae).

[This corrects the article DOI: 10.3389/fpls.2020.607893.].

Molecular characterization of Heterodera cruciferae Franklin, 1945 from cabbage fields in Nigde province, Turkey.

BACKGROUND: The aim of this study was to identified cyst nematodes in the cabbage production areas in Nigde Province by molecular methods to underpin decision making for field control. The sequences of ribosomal DNA region (rDNA-ITS) and cytochrome oxidase subunit 1 (mtDNA-COI) were used for the first time for identification Heterodera cruciferae (cabbage cyst nematode) in Turkey. METHODS AND RESULTS: Heterodera cruciferae populations extracted from cabbage growing areas of Nigde Province and investigated using sequences of rDNA-ITS and mtDNA-COI. Similarities and differences between 13 geographic populations of H. cruciferae were detected in surveys during 2020-2021. DNA from single cysts was successfully amplified, and genetic variability was revealed within nematode populations. Based on these results, H. cruciferae is reported for the first time from Nigde Province, Turkey. This study showed clear discrimination among the sampled populations of H. cruciferae. CONCLUSION: This finding is important for control and managing cabbage cyst nematode in cabbage fields in Turkey as more than one Heterodera spp. can occur. Future studies should investigate the population dynamics and control of H. cruciferae in fields in the sampled districts.

Idahoa and Subularia: Hidden polyploid origins of two enigmatic genera of crucifers.

PREMISE: The monotypic Idahoa (I. scapigera) and the bispecific Subularia (S. aquatica and S. monticola) belong to Brassicaceae with unclear phylogenetic relationships and no tribal assignment. To fill this knowledge gap, we investigated these species and their closest relatives by combining cytogenomic and phylogenomic methods. METHODS: We used whole plastome sequences in maximum likelihood and Bayesian inference analyses. We tested the phylogenetic informativeness of shared genomic repeats. We combined nuclear gene tree reconciliation and comparative chromosome painting (CCP) to examine the occurrence of past whole-genome duplications (WGDs). RESULTS: The plastid data set corroborated the sister relationship between Idahoa and Subularia within the crucifer Lineage V but failed to resolve consistent topologies using both inference methods. The shared repetitive sequences provided conflicting pwhylogenetic signals. CCP analysis unexpectedly revealed that Idahoa (2n = 16) has a diploidized mesotetraploid genome, whereas two Subularia species (2n = 28 and 30) have diploidized mesoctoploid genomes. Several ancient allopolyploidy events have also been detected in closely related taxa (Chamira circaeoides, Cremolobeae, Eudemeae, and Notothlaspideae). CONCLUSIONS: Our results suggest that the contentious phylogenetic placement of Idahoa and Subularia is best explained by two WGDs involving one or more shared parental genomes. The newly identified mesopolyploid genomes highlight the challenges of studying plant clades with complex polyploidy histories and provide a better framework for understanding genome evolution in the crucifer family.

An expanded role for the transcription factor WRINKLED1 in the biosynthesis of triacylglycerols during seed development.

The transcription factor WRINKLED1 (WRI1) is known as a master regulator of fatty acid synthesis in developing oilseeds of Arabidopsis thaliana and other species. WRI1 is known to directly stimulate the expression of many fatty acid biosynthetic enzymes and a few targets in the lower part of the glycolytic pathway. However, it remains unclear to what extent and how the conversion of sugars into fatty acid biosynthetic precursors is controlled by WRI1. To shortlist possible gene targets for future in-planta experimental validation, here we present a strategy that combines phylogenetic foot printing of cis-regulatory elements with additional layers of evidence. Upstream regions of protein-encoding genes in A. thaliana were searched for the previously described DNA-binding consensus for WRI1, the ASML1/WRI1 (AW)-box. For about 900 genes, AW-box sites were found to be conserved across orthologous upstream regions in 11 related species of the crucifer family. For 145 select potential target genes identified this way, affinity of upstream AW-box sequences to WRI1 was assayed by Microscale Thermophoresis. This allowed definition of a refined WRI1 DNA-binding consensus. We find that known WRI1 gene targets are predictable with good confidence when upstream AW-sites are phylogenetically conserved, specifically binding WRI1 in the in vitro assay, positioned in proximity to the transcriptional start site, and if the gene is co-expressed with WRI1 during seed development. When targets predicted in this way are mapped to central metabolism, a conserved regulatory blueprint emerges that infers concerted control of contiguous pathway sections in glycolysis and fatty acid biosynthesis by WRI1. Several of the newly predicted targets are in the upper glycolysis pathway and the pentose phosphate pathway. Of these, plastidic isoforms of fructokinase (FRK3) and of phosphoglucose isomerase (PGI1) are particularly corroborated by previously reported seed phenotypes of respective null mutations.

Lignans and a neolignan from an aqueous extract of Isatis indigotica roots.

Four new lignans (1-4) and one new neolignan (5), along with two known lignan derivatives (6 and 7), were isolated from an aqueous extract of the Isatis indigotica root (ban lan gen). Their structures were determined by spectroscopic data analysis, chemical method, and theoretical calculation, for which 1 was proved by single-crystal X-ray diffraction. Compound 2 exhibited antiviral activity against influenza virus A/Hanfang/359/95 (H3N2) with an IC50 value of 11.1 µM and a selective index (SI) > 9, while 1 and 5 are the first examples of sulfonated lignan and neolignan from nature.

Interactions of fungi with non-isothiocyanate products of the plant glucosinolate pathway: A review on product formation, antifungal activity, mode of action and biotransformation.

The glucosinolate pathway, which is present in the order Brassicales, is one of the most researched defensive natural product biosynthesis pathways. Its core molecules, the glucosinolates are broken down upon pathogen challenge or tissue damage to yield an array of natural products that may help plants defend against the stressor. Though the most widely known glucosinolate decomposition products are the antimicrobial isothiocyanates, there is a wide range of other volatile and non-volatile natural products that arise from this biosynthetic pathway. This review summarizes our current knowledge on the interaction of these much less examined, non-isothiocyanate products with fungi. It deals with compounds including (1) glucosinolates and their biosynthesis precursors; (2) glucosinolate-derived nitriles (e.g. derivatives of 1H-indole-3-acetonitrile), thiocyanates, epithionitriles and oxazolidine-2-thiones; (3) putative isothiocyanate downstream products such as raphanusamic acid, 1H-indole-3-methanol (= indole-3-carbinol) and its oligomers, 1H-indol-3-ylmethanamine and ascorbigen; (4) 1H-indole-3-acetonitrile downstream products such as 1H-indole-3-carbaldehyde (indole-3-carboxaldehyde), 1H-indole-3-carboxylic acid and their derivatives; and (5) indole phytoalexins including brassinin, cyclobrassinin and brassilexin. Herein, a literature review on the following aspects is provided: their direct antifungal activity and the proposed mechanisms of antifungal action, increased biosynthesis after fungal challenge, as well as data on their biotransformation/detoxification by fungi, including but not limited to fungal myrosinase activity.

Hemilophiacardiocarpa (Brassicaceae), a new species from Yunnan, southwest China.

Hemilophiacardiocarpa (Brassicaceae), the sixth species of the Chinese endemic genus Hemilophia, is described and illustrated. This plant is found in the Jiaozishan Mountains in Dongchuan District, northern Yunnan, southwest China. Morphologically, it shows close relationships with H.rockii and H.pulchella, but differs from it in the leaf shape and size, inflorescence, flower size, shape of fruit and length of its pedicel. An updated key to the taxa of Hemilophia is provided.

Sulfonated alkaloids from an aqueous extract of Isatis indigotica roots.

Eleven new sulfonated alkaloids (1 - 11) having diverse structures were isolated from an aqueous extract of the Isatis indigotica root (ban lan gen). Their structures were determined by spectroscopic data analysis, chemical method, and theoretical calculation, of which (-)-4 was proved by single crystal X-ray diffraction.

Minor bioactive indoles from kimchi mirror the regioselectivity in indole-3-carbinol oligomerization.

Kimchi is a globally consumed food with diverse health-benefits, but the low-abundance bioactive compounds in kimchi remain largely neglected. Here we show that kimchi contains a family of low-abundance (0.5-1.6 µg/g, dried weight) high-order indole oligomers derived from indole-3-carbinol (I3C), a breakdown product released from cruciferous vegetables used for producing the traditional subsidiary food. The structure determination of such complex molecules was accomplished by synthesizing linear indole oligomers as standard materials followed by the LC-HR-MS analysis. One indole tetramer (LTe2) is substantially toxic to tumor MV4-11 (IC50 = 1.94 µM) and THP-1 cells (IC50 = 7.12 µM). Collectively, the work adds valuable information to the knowledge package about kimchi, and may inspire the generation of indole-based molecules, to which many drugs belong.

Beneficial Health Effects of Glucosinolates-Derived Isothiocyanates on Cardiovascular and Neurodegenerative Diseases.

Neurodegenerative diseases (NDDs) and cardiovascular diseases (CVDs) are illnesses that affect the nervous system and heart, all of which are vital to the human body. To maintain health of the human body, vegetable diets serve as a preventive approach and particularly Brassica vegetables have been associated with lower risks of chronic diseases, especially NDDs and CVDs. Interestingly, glucosinolates (GLs) and isothiocyanates (ITCs) are phytochemicals that are mostly found in the Cruciferae family and they have been largely documented as antioxidants contributing to both cardio- and neuroprotective effects. The hydrolytic breakdown of GLs into ITCs such as sulforaphane (SFN), phenylethyl ITC (PEITC), moringin (MG), erucin (ER), and allyl ITC (AITC) has been recognized to exert significant effects with regards to cardio- and neuroprotection. From past in vivo and/or in vitro studies, those phytochemicals have displayed the ability to mitigate the adverse effects of reactive oxidation species (ROS), inflammation, and apoptosis, which are the primary causes of CVDs and NDDs. This review focuses on the protective effects of those GL-derived ITCs, featuring their beneficial effects and the mechanisms behind those effects in CVDs and NDDs.

lepidium-like, a Naturally Occurring Mutant of Capsella bursa-pastoris, and Its Implications on the Evolution of Petal Loss in Cruciferae.

Naturally occurring mutants whose phenotype recapitulates the changes that distinguish closely related species are of special interest from the evolutionary point of view. They can give a key about the genetic control of the changes that led to speciation. In this study, we described lepidium-like (lel), a naturally occurring variety of an allotetraploid species Capsella bursa-pastoris that is characterized by the typical loss of all four petals. In some cases, one or two basal flowers in the raceme had one or two small petals. The number and structure of other floral organs are not affected. Our study of flower development in the mutant showed that once initiated, petals either cease further development and cannot be traced in anthetic flowers or sometimes develop to various degrees. lel plants showed an earlier beginning of floral organ initiation and delayed petal initiation compared to the wild-type plants. lel phenotype has a wide geographical distribution, being found at the northern extremity of the species range as well as in the central part. The genetic analysis of inheritance demonstrated that lel phenotype is controlled by two independent loci. While the flower in the family Cruciferae generally has a very stable structure (i.e., four sepals, four petals, six stamens, and two carpels), several deviations from this ground plan are known, in particular in the genus Lepidium, C. bursa-pastoris is an emerging model for the study of polyploidy (which is also very widespread in Cruciferae); the identification and characterization of the apetalous mutant lays a foundation for further research of morphological evolution in polyploids.

An Improved Technique for Isolation and Characterization of Single-Spore Isolates of Plasmodiophora brassicae.

Clubroot, caused by Plasmodiophora brassicae, is a soilborne disease that occurs in cruciferous crops worldwide. P. brassicae usually exists as a mixture of several pathotypes, which has hampered the research on resistance mechanisms of cruciferous crops against P. brassicae. In this study, clubroot galls were collected from a field in Shenyang, China, as a pathogen source to develop an efficient protocol for a single-spore isolation system of P. brassicae by optimizing the seedling age for inoculation, host inoculation method, and plant culture method. The operational steps of the single-spore isolation method were optimized as follows: the use of 2-day-old seedlings for inoculation, substituting a cryobox (100 × 2.0-ml vials) for culture dishes, the addition of nutrient solution culture, and microscopic observations of single spores. The rate of infection success was substantially improved, and single-spore isolates of four pathotypes (4, 8, 9, and 11) were acquired in this system. Subsequently, the optimized system was used to isolate and characterize the pathotypes of single-spore isolates of P. brassicae collected from five fields in regions in China. Approximately four to nine pathotypes were isolated from each region. Among these, pathotype 4 was the most prevalent. This study provides a source of valuable information that can eventually be used for the genetic analysis of host-P. brassicae interaction.

Effects of Glucosinolate-Derived Isothiocyanates on Fungi: A Comprehensive Review on Direct Effects, Mechanisms, Structure-Activity Relationship Data and Possible Agricultural Applications.

Plants heavily rely on chemical defense systems against a variety of stressors. The glucosinolates in the Brassicaceae and some allies are the core molecules of one of the most researched such pathways. These natural products are enzymatically converted into isothiocyanates (ITCs) and occasionally other defensive volatile organic constituents (VOCs) upon fungal challenge or tissue disruption to protect the host against the stressor. The current review provides a comprehensive insight on the effects of the isothiocyanates on fungi, including, but not limited to mycorrhizal fungi and pathogens of Brassicaceae. In the review, our current knowledge on the following topics are summarized: direct antifungal activity and the proposed mechanisms of antifungal action, QSAR (quantitative structure-activity relationships), synergistic activity of ITCs with other agents, effects of ITCs on soil microbial composition and allelopathic activity. A detailed insight into the possible applications is also provided: the literature of biofumigation studies, inhibition of post-harvest pathogenesis and protection of various products including grains and fruits is also reviewed herein.

Smelowskia sunhangii (Brassicaceae), a new species from China, with a re-evaluation of the S. tibetica complex.

Smelowskia sunhangii, from Qinghai and Tibet (China), is described and illustrated. Morphological and molecular data indicate that S. sunhangii is closely related to Smelowskia tibetica, from which it is easily distinguished by the densely hirsute (vs. glabrous or sparsely pubescent), elliptic to ovate-lanceolate (vs. suborbicular, oblong, or lanceolate) fruits with undulate (vs. straight) margins. A re-evaluation of the widely distributed S. tibetica and related taxa is also provided.