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Post-polyploid diploidization associated with descending dysploidy and interspecific introgression drives plant genome evolution by unclear mechanisms. Raphanus is an economically and ecologically important Brassiceae genus and model system for studying post-polyploidization genome evolution and introgression. Here, we report the de novo sequence assemblies for 11 genomes covering most of the typical sub-species and varieties of domesticated, wild and weedy radishes from East Asia, South Asia, Europe, and America. Divergence among the species, sub-species, and South/East Asian types coincided with Quaternary glaciations. A genus-level pan-genome was constructed with family-based, locus-based, and graph-based methods, and whole-genome comparisons revealed genetic variations ranging from single-nucleotide polymorphisms (SNPs) to inversions and translocations of whole ancestral karyotype (AK) blocks. Extensive gene flow occurred between wild, weedy, and domesticated radishes. High frequencies of genome reshuffling, biased retention, and large-fragment translocation have shaped the genomic diversity. Most variety-specific gene-rich blocks showed large structural variations. Extensive translocation and tandem duplication of dispensable genes were revealed in two large rearrangement-rich islands. Disease resistance genes mostly resided on specific and dispensable loci. Variations causing the loss of function of enzymes modulating gibberellin deactivation were identified and could play an important role in phenotype divergence and adaptive evolution. This study provides new insights into the genomic evolution underlying post-polyploid diploidization and lays the foundation for genetic improvement of radish crops, biological control of weeds, and protection of wild species' germplasms.

Simple Summary Raphanus is an important genus of Brassicaceae and has undergone a lengthy evolutionary process. However, the inter- and intraspecific phylogenetic relationships and genetic diversity are not well understood. To elucidate these issues, we SSR-sequenced 939 wild, semi-wild and cultivated accessions, and discovered that Europe was the origin center of radishes with diverse European wild radishes, and Europe, South Asia and East Asia might be three independent domestication centers. There was considerable genetic differentiation within European cultivated radishes. European primitive cultivated radish exhibited gene flow with black radish/oil radish and rat-tail radish. Among Asian cultivated radishes, rat-tail radish was a sister to the clade of Chines big radish (including Japanese wild radish), suggesting that they may share the most recent common ancestry. Japanese wild radish had strong gene exchange with Japanese/Korea big radish, oil radish and rat-tail radish. American wild radish developed from natural hybridization between European wild radish and European small radish. All these demonstrated that European primitive cultivated type, American wild radish and Japanese wild radish might have played indispensable roles in radish evolution. Our study provides new perspectives into the origin, evolution and genetic diversity of Raphanus and facilitates the conservation and exploitation of radish germplasm resources. Abstract Raphanus has undergone a lengthy evolutionary process and has rich diversity. However, the inter- and intraspecific phylogenetic relationships and genetic diversity of this genus are not well understood. Through SSR-sequencing and multi-analysis of 939 wild, semi-wild and cultivated accessions, we discovered that the European wild radish (EWR) population is separated from cultivated radishes and has a higher genetic diversity. Frequent intraspecific genetic exchanges occurred in the whole cultivated radish (WCR) population; there was considerable genetic differentiation within the European cultivated radish (ECR) population, which could drive radish diversity formation. Among the ECR subpopulations, European primitive cultivated radishes (EPCRs) with higher genetic diversity are most closely related to the EWR population and exhibit a gene flow with rat-tail radishes (RTRs) and black radishes (BRs)/oil radishes (ORs). Among Asian cultivated radishes (ACRs), Chinese big radishes (CBRs) with a relatively high diversity are furthest from the EWR population, and most Japanese/Korean big radishes (JKBRs) are close to CBR accessions, except for a few old Japanese landraces that are closer to the EPCR. The CBR and JKBR accessions are independent of RTR accessions; however, phylogenetic analysis indicates that the RTR is sister to the clade of CBR (including JWR), which suggests that the RTR may share the most recent common ancestry with CBRs and JWRs. In addition, Japanese wild radishes (JWRs), (namely, R. sativus forma raphanistroides) are mainly scattered between CBRs and EPCRs in PCoA analysis. Moreover, JWRs have a strong gene exchange with the JKBR, OR and RTR subpopulations. American wild radishes (AWRs) are closely related to European wild and cultivated radishes, and have a gene flow with European small radishes (ESRs), suggesting that the AWR developed from natural hybridization between the EWR and the ESR. Overall, this demonstrates that Europe was the origin center of the radish, and that Europe, South Asia and East Asia appear to have been three independent domestication centers. The EPCR, AWR and JWR, as semi-wild populations, might have played indispensable transitional roles in radish evolution. Our study provides new perspectives into the origin, evolution and genetic diversity of Raphanus and facilitates the conservation and exploitation of radish germplasm resources.

BACKGROUND Garlic is the second largest allium crop after onion and is grown all over the world. The onion maggot (Delia antiqua M.) is a pest that seriously affects the yield and quality of garlic. Cultural controls and insecticides have several potential problems, including pesticide residue and development of resistance. Screening resistant varieties is an ideal alternative method. RESULTS The resistance of 213 accessions of garlic clones against onion maggot was identified. The results showed that the pest index was between 5.56% and 91.11%, with classification into six groups by cluster analysis: HR (highly resistant), R (resistant), MR (moderately resistant), MS (moderately susceptible), S (susceptible) and HS (highly susceptible). Among these accessions, 9 and 30 were HR and R to onion maggot, respectively. Comparing the resistances of seven pairs of accessions between the original accessions and their progenies showed that single bulb clonal selection could be an effective way to improve allicin content, onion maggot resistance and most morphological traits. The relationship between allicin content and resistance was investigated, and a significant positive relationship was found. Accessions with a high content of allicin have great potential as resistant accessions. CONCLUSION This study showed significant differences among garlic germplasm in their response to Delia antiqua M. Some accessions were highly resistant and tolerant. Utilization of these accessions will help minimize environmental pollution, preserve agro‐ecosystems and biodiversity, and make management processes more economical. Furthermore, these accessions could be used in breeding programs to develop new maggot‐resistant onion cultivars. © 2019 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

As the critical driving force for chronic myeloid leukemia (CML), BCR gene fused ABL kinase has been extensively explored as a validated target of drug discovery. Although imatinib has achieved tremendous success as the first-line treatment for CML, the long-term application ultimately leads to resistance, primarily via various acquired mutations occurring in the BCR-ABL kinase. Although dasatinib and nilotinib have been approved as second-line therapies that could overcome some of these mutants, the most prevalent gatekeeper T315I mutant remains unconquered. Here, we report a novel type II kinase inhibitor, CHMFL-48, that potently inhibits the wild-type BCR-ABL (wt) kinase as well as a panel of imatinib-resistant mutants, including T315I, F317L, E255K, Y253F, and M351T. CHMFL-48 displayed great inhibitory activity against ABL wt (IC50: 1 nM, 70-fold better than imatinib) and the ABL T315I mutant (IC50: 0.8 nM, over 10,000-fold better than imatinib) in a biochemical assay and potently blocked the autophosphorylation of BCR-ABL wt and BCR-ABL mutants in a cellular context, which further affected downstream signalling mediators, including signal transducer and activator of transcription 5 (STAT5) and CRK like proto-oncogene (CRKL), and led to the cell cycle progression blockage as well as apoptosis induction. CHMFL-48 also exhibited great anti-leukemic efficacies in vivo in K562 cells and p210-T315I-transformed BaF3 cell-inoculated murine models. This discovery extended the pharmacological diversity of BCR-ABL kinase inhibitors and provided more potential options for anti-CML therapies.

Six new phenolic acid derivatives, salviachinensines A-F (1-6), together with 14 known compounds (7-20) were isolated from the Chinese medicinal plant Salvia chinensis. The structures of salviachinensines A-F (1-6) were elucidated by NMR spectroscopy, bioinspired chemical synthesis, ECD analysis, and quantum chemical calculation methods. Compounds 2 and 3 are a pair of cis- trans isomers, and compounds 5 and 6 a pair of epimers. The solvent-induced isomerization of compounds 5 and 6 and the hypothetical biogenetic pathway of compounds 1-6, as well as the antiproliferative property and the ability of 1 to induce apoptosis and arrest cell cycle progression of MOLM-13 cells, were also investigated.

The cucumber (Cucumis sativus) is characterized by its diversity and seasonal plasticity in sexual type. A long day length condition significantly decreased the cucumber female flower ratio by 17.7–52.9%, and the effect of photoperiod treatment is more significant under low temperature than under high temperature. Transcriptome analysis indicates that the photoperiod treatment preferentially significantly influenced flower development processes, particularly MADS-box genes in shoot apices. The long-day treatment resulted in predominantly transposable element (TE)- and gene-associated CHH-types of DNA methylation changes. Nevertheless, there was significant enrichment of CG- and CHG-types of DNA methylation changes nearing transcription start sites (TSSs)/transcription end sites (TESs) and gene bodies, respectively. Predominantly negative association between differentially methylated regions (DMRs) and differentially expressed genes (DEGs) were observed which implied epiregulation of DEGs. Two MADS-box genes that were significantly downregulated by long photoperiod showed significant hypermethylation in promoter regions that is essentially TE-rich. This study indicates MADS-box genes which are partially regulated by promoter methylation state may mediate photoperiod-dependent regulation of cucumber sex expression.

Metal hard mask TiN was induced as patterning film due to less ULK damage, but TiN tiny particle can make metal line open which is unacceptable. In this paper, the ramp mode of DC power during TiN deposition process was analyzed for tiny particle reduction. TiN as-dep defect scan results showed that DC power with slower ramp rate at ignition and pump down step can reduce tiny particle obviously. According to hard mask AEI defect scan results, metal open defect related with TiN film cannot be found.

Wuchuan Gelao and Miao Autonomous County is located in the northeast of Guizhou Province, and in the border of Guizhou and Chongqing, having a subtropical humid monsoon climate. There is no severe heat in summer, and no severe cold in winter. It has distinct national characteristics, and there are many biological resources with national characteristics. A systematic investigation of biological resources in the county for nearly a month was carried out by organizing a professional investigation team. The investigation covered 5 townships and we visited 12 village committees and 26 villagers' groups, involving three ethnic groups: Gelao, Tujia and Miao. The biological resources closely related to the agricultural production and life of local ethnic groups were investigated, collected and sorted out. A total of 230 samples of all kinds of resources were collected, including 47 food crops, 75 vegetables and annual crops, 37 fruit trees and perennial crops, and 71 medicinal plants. Of these, a total of 73 were unique, superior and special resources. Based on general investigation and professional investigation, this paper analyzes the present situation, growth and decline of local agricultural biological resources, and puts forward some suggestions for the protection, development and utilization of agricultural biological resources.

Background Cucumbers (Cucumis sativus) are known for their plasticity in sex expression. DNA methylation status determines gene activity but is susceptible to environmental condition changes. Thus, DNA methylation-based epigenetic regulation may at least partially account for the instability of cucumber sex expression. Do temperature and photoperiod that are the two most important environmental factors have equal effect on cucumber sex expression by similar epigenetic regulation mechanism? To answer this question, we did a two-factor experiment of temperature and photoperiod and generated methylome and transcriptome data from cucumber shoot apices. Results The seasonal change in the femaleness of a cucumber core germplasm collection was investigated over five consecutive years. As a result, 71.3% of the 359 cucumber accessions significantly decreased their femaleness in early autumn when compared with spring. High temperature and long-day photoperiod treatments, which mimic early autumn conditions, are both unfavorable for female flower formation, and temperature is the predominant factor. High temperatures and long-day treatments both predominantly resulted in hypermethylation compared to demethylation, and temperature effect was decisive. The targeted cytosines shared in high-temperature and long-day photoperiod treatment showed the same change in DNA methylation level. Moreover, differentially expressed TEs (DETs) and the predicted epiregulation sites were clustered across chromosomes, and importantly, these sites were reproducible among different treatments. Essentially, the photoperiod treatment preferentially and significantly influenced flower development processes, while temperature treatment produced stronger responses from phytohormone-pathway-related genes. Cucumber AGAMOUS was likely epicontrolled exclusively by photoperiod while CAULIFLOWER A and CsACO3 were likely epicontrolled by both photoperiod and temperature. Conclusions Seasonal change of sex expression is a germplasm-wide phenomenon in cucumbers. High temperature and long-day photoperiod might have the same effect on the methylome via the same mechanism of gene-TE interaction but resulted in different epicontrol sites that account for different mechanisms between temperature- and photoperiod-dependent sex expression changes. Electronic supplementary material The online version of this article (10.1186/s12870-018-1490-3) contains supplementary material, which is available to authorized users.

Guizhou Province is an important distribution area of wild onion resources, and a large area of wild (Chinese) chives are distributed in Hezhang County. In order to understand and study the distribution of wild chives, the geographical distribution, habitats and climate of wild chives in Hezhang County were investigated, and the main nutrition components of wild chives were analyzed. The results indicated that there were mainly three kinds of wild chives distributed in Hezhang County, including Allium wallichii Kunth., Allium ovalifolium Hand. -Mazz. (tentatively named), and Allium hookeri Thwaites (tentatively named). Among the 17 kinds of amino acids, except for proline, the content of other amino acids in wild chives was higher than that of the cultivated chives (Allaum tuberosum Rottler ex Spreng.). The sugar content of wild chives was significantly lower than the cultivated chives. Among nine trace elements, the manganese, zinc and iron content of A. ovalifolium Hand. -Mazz. were significantly higher than that of the cultivated chives and other wild chives. Among the four kinds of heavy metals, cadmium content in the three kinds of wild chives exceeded the limitation of the national standard, and cadmium content in A. ovalifolium Hand. -Mazz. was significantly higher than that of the others. Arsenic, mercury and lead content in A. ovalifolium Hand. -Mazz. also exceeded the limitation of the national standard. Vitamin C content in leaves and stalk of A. wallichii Kunth. in the original habits was higher than that of the cultivated chives. The biological characteristics and nutrition components of the wild chives from Hezhang County were significantly different from that of the cultivated chives. The collection and preservation of these resources is of great significance to the enriching of diversity of Chinese chive resources and has great development and utilization value to the improvement of nutritional quality of Chinese chives.