Diploid and tetraploid genomes of Acorus and the evolution of monocots.

Monocots are a major taxon within flowering plants, have unique morphological traits, and show an extraordinary diversity in lifestyle. To improve our understanding of monocot origin and evolution, we generate chromosome-level reference genomes of the diploid Acorus gramineus and the tetraploid Ac. calamus, the only two accepted species from the family Acoraceae, which form a sister lineage to all other monocots. Comparing the genomes of Ac. gramineus and Ac. calamus, we suggest that Ac. gramineus is not a potential diploid progenitor of Ac. calamus, and Ac. calamus is an allotetraploid with two subgenomes A, and B, presenting asymmetric evolution and B subgenome dominance. Both the diploid genome of Ac. gramineus and the subgenomes A and B of Ac. calamus show clear evidence of whole-genome duplication (WGD), but Acoraceae does not seem to share an older WGD that is shared by most other monocots. We reconstruct an ancestral monocot karyotype and gene toolkit, and discuss scenarios that explain the complex history of the Acorus genome. Our analyses show that the ancestors of monocots exhibit mosaic genomic features, likely important for that appeared in early monocot evolution, providing fundamental insights into the origin, evolution, and diversification of monocots.

Genomes of leafy and leafless Platanthera orchids illuminate the evolution of mycoheterotrophy.

To improve our understanding of the origin and evolution of mycoheterotrophic plants, we here present the chromosome-scale genome assemblies of two sibling orchid species: partially mycoheterotrophic Platanthera zijinensis and holomycoheterotrophic Platanthera guangdongensis. Comparative analysis shows that mycoheterotrophy is associated with increased substitution rates and gene loss, and the deletion of most photoreceptor genes and auxin transporter genes might be linked to the unique phenotypes of fully mycoheterotrophic orchids. Conversely, trehalase genes that catalyse the conversion of trehalose into glucose have expanded in most sequenced orchids, in line with the fact that the germination of orchid non-endosperm seeds needs carbohydrates from fungi during the protocorm stage. We further show that the mature plant of P. guangdongensis, different from photosynthetic orchids, keeps expressing trehalase genes to hijack trehalose from fungi. Therefore, we propose that mycoheterotrophy in mature orchids is a continuation of the protocorm stage by sustaining the expression of trehalase genes. Our results shed light on the molecular mechanism underlying initial, partial and full mycoheterotrophy.

Comparative analysis of Phytophthora genomes data.

The data presented here are related to the article entitled "Comparative analysis of Phytophthora genomes reveals oomycete pathogenesis in crops" [1]. These data contain the description of genomic structure of the two plant pathogens, P. fragariae and P. rubi and characterize several gene families associated with pathogenicity of them: P450, ACX gene families, CAZymes and effector. This data presents the relevant results of two newly sequenced P. fragariae and P. rubi, so as to provide data for further studies by researchers.

Chromosome-scale assembly of the Dendrobium chrysotoxum genome enhances the understanding of orchid evolution.

As one of the largest families of angiosperms, the Orchidaceae family is diverse. Dendrobium represents the second largest genus of the Orchidaceae. However, an assembled high-quality genome of species in this genus is lacking. Here, we report a chromosome-scale reference genome of Dendrobium chrysotoxum, an important ornamental and medicinal orchid species. The assembled genome size of D. chrysotoxum was 1.37 Gb, with a contig N50 value of 1.54 Mb. Of the sequences, 95.75% were anchored to 19 pseudochromosomes. There were 30,044 genes predicted in the D. chrysotoxum genome. Two whole-genome polyploidization events occurred in D. chrysotoxum. In terms of the second event, whole-genome duplication (WGD) was also found to have occurred in other Orchidaceae members, which diverged mainly via gene loss immediately after the WGD event occurred; the first duplication was found to have occurred in most monocots (tau event). We identified sugar transporter (SWEET) gene family expansion, which might be related to the abundant medicinal compounds and fleshy stems of D. chrysotoxum. MADS-box genes were identified in D. chrysotoxum, as well as members of TPS and Hsp90 gene families, which are associated with resistance, which may contribute to the adaptive evolution of orchids. We also investigated the interplay among carotenoid, ABA, and ethylene biosynthesis in D. chrysotoxum to elucidate the regulatory mechanisms of the short flowering period of orchids with yellow flowers. The reference D. chrysotoxum genome will provide important insights for further research on medicinal active ingredients and breeding and enhances the understanding of orchid evolution.

Corrigendum to "Comparative analysis of Phytophthora genomes reveals oomycete pathogenesis in crops" [Heliyon 7 (2) (February 2021) e06317].

[This corrects the article DOI: 10.1016/j.heliyon.2021.e06317.].

Wolfberry genomes and the evolution of Lycium (Solanaceae).

Wolfberry Lycium, an economically important genus of the Solanaceae family, contains approximately 80 species and shows a fragmented distribution pattern among the Northern and Southern Hemispheres. Although several herbaceous species of Solanaceae have been subjected to genome sequencing, thus far, no genome sequences of woody representatives have been available. Here, we sequenced the genomes of 13 perennial woody species of Lycium, with a focus on Lycium barbarum. Integration with other genomes provides clear evidence supporting a whole-genome triplication (WGT) event shared by all hitherto sequenced solanaceous plants, which occurred shortly after the divergence of Solanaceae and Convolvulaceae. We identified new gene families and gene family expansions and contractions that first appeared in Solanaceae. Based on the identification of self-incompatibility related-gene families, we inferred that hybridization hotspots are enriched for genes that might be functioning in gametophytic self-incompatibility pathways in wolfberry. Extremely low expression of LOCULE NUBER (LC) and COLORLESS NON-RIPENING (CNR) orthologous genes during Lycium fruit development and ripening processes suggests functional diversification of these two genes between Lycium and tomato. The existence of additional flowering locus C-like MADS-box genes might correlate with the perennial flowering cycle of Lycium. Differential gene expression involved in the lignin biosynthetic pathway between Lycium and tomato likely illustrates woody and herbaceous differentiation. We also provide evidence that Lycium migrated from Africa into Asia, and subsequently from Asia into North America. Our results provide functional insights into Solanaceae origins, evolution and diversification.

Comparative analysis of Phytophthora genomes reveals oomycete pathogenesis in crops.

The oomycete genus Phytophthora includes devastating plant pathogens that are found in almost all ecosystems. We sequenced the genomes of two quarantined Phytophthora species-P. fragariae and P. rubi. Comparing these Phytophthora species and related genera allowed reconstruction of the phylogenetic relationships within the genus Phytophthora and revealed Phytophthora genomic features associated with infection and pathogenicity. We found that several hundred Phytophthora genes are putatively inherited from red algae, but Phytophthora does not have vestigial plastids originating from phototrophs. The horizontally-transferred Phytophthora genes are abundant transposons that "transmit" exogenous gene to Phytophthora species thus bring about the gene recombination possibility. Several expansion events of Phytophthora gene families associated with cell wall biogenesis can be used as mutational targets to elucidate gene function in pathogenic interactions with host plants. This work enhanced the understanding of Phytophthora evolution and will also be helpful for the design of phytopathological control strategies.

Comprehensive Assessment of the Association between FCGRs polymorphisms and the risk of systemic lupus erythematosus: Evidence from a Meta-Analysis.

We performed a meta analysis to assess the relationship of FCGRs polymorphisms with the risk of SLE. Thirty-five articles (including up to 5741 cases and 6530 controls) were recruited for meta-analysis. The strongest association was observed between FCGR2B rs1050501 and SLE under the recessive genotypic model of C allele in the overall population (CC vs CT/TT, OR = 1.754, 95%CI: 1.422-2.165, P = 1.61 × 10(-7)) and in Asian population (CC vs CT/TT, OR = 1.784, 95%CI; 1.408-2.261, P = 1.67 × 10(-6)). We also found that FCGR3A rs396991 were significant association with the susceptibility to SLE in overall population in recessive model of T allele (TT vs TG/GG, OR = 1.263, 95%CI: 1.123-1.421, P = 9.62 × 10(-5)). The results also showed that significant association between FCGR2A rs1801274 and SLE under the allelic model in the overall population (OR = 0.879 per A allele, 95%CI: 0.819-0.943, P = 3.31 × 10(-4)). The meta-analysis indicated that FCGR3B copy number polymorphism NA1·NA2 was modestly associated with SLE in overall population (OR = 0.851 per NA1, 95%CI: 0.772-0.938, P = 1.2 × 10(-3)). We concluded that FCGR2B rs1050501 C allele and FCGR3A rs396991 T allele might contribute to susceptibility and development of SLE, and were under recessive association model. While, FCGR2A rs1801274 A allele and FCGR3B NA1 were associated with SLE and reduced the risk of SLE.

Ethnicity-stratified analysis of the association between IL-18 polymorphisms and systemic lupus erythematosus in a European population: a meta-analysis.

We performed a meta-analysis to identify the association between polymorphisms in the promoter of interleukin-18 (IL-18) and susceptibility for systemic lupus erythematosus (SLE) . Genotype data for three single-nucleotide polymorphisms (SNPs rs360719, rs1946518, and rs187238) in the IL-18 promoter were extracted from 20 studies of three different ethnicities (European, Asian, and South American). Data from each ethnicity group and their combinations were analyzed. We found distinct evidence of an association between rs360719 and SLE (P = 0.001) in the European/South American group [odds ratio (OR) 1.31 per C allele, 95% confidence interval (CI) 1.11-1.53]. Stratification analysis by ethnicity showed a significant association between rs360719 and SLE in the European population (OR 1.33 per C allele, 95% CI 1.11-1.61, P = 0.003) and a lesser effect in the same direction in the South American population (OR 1.18). A significant association was also identified between rs1946518 and SLE in the European population (OR 1.16 per A allele, 95% CI 1.03-1.30, P = 0.017), although there was no association in the Asian or the combined European/Asian population. We also examined genome-wide association study (GWAS) data from an Asian subpopulation (Chinese) for the association between rs1946518 and SLE, but found no association (P = 0.83). The third SNP, rs187238, was not significantly associated with SLE in any of the populations examined. In summary, this study identified a significant association between SLE and two SNPs within the IL-18 gene promoter region (rs360719 and rs1946518) in a European population, but not in populations of Asian origin.

[The quantification of gemifloxacin by fluorescence quenching method using chitosan-coated CdTe quantum dots].

Chitosan-coated CdTe quantum dots can reduce QDs toxicity and enhance its stability in aqueous solution. Chitosan-coated CdTe QDs were used as fluorescence probes to determine Gemifloxacin on the basis of fluorescence quenching method. The results indicated that the relative fluorescence intensity was linearly proportional to the Gemifloxacin concentration in the range of 3.46 x 10(-9)-3.46 x 10(-7) g x L(-1) with a linear fitting equation of F0/F= 1.0637 + 0.016 7c(g x L(-1)) and the RSD was 2.7%. On the basis of fluorescence quenching method theory, it was concluded that the interaction between QDs and Gemifloxacin was a kind of static quenching through hydrogen bonding and Van der Waals force, and the binding sites value was 0.8. This method with high sensitivity and broad linear range provided a new approach to determining Gemifloxacin.

[Study on the estrogen derivative marked by CdTe quantum dots].

Water-soluble CdTe quantum dots (QDs) stabilized by thioglycolic acid (TGA) with high quantum yield were synthesized. And the small biomolecule 17beta-amino-estradiol was marked successfully by CdTe QDs. The analysis of UV-Vis spectroscopy, fluorescence spectroscopy, infrared spectroscopy and inverted microscope photographs showed that the surface carboxyl of CdTe quantum dots conjugated with the amino of 17beta-amino-estradiol through the activation of N-hydroxysuccinimide. 17beta-amino-estradiol marked by CdTe QDs successfully provided an experimental basis for new drug screening model.

[Quantitative determination of pazufloxacin using water-soluble quantum dots as fluorescent probes].

The quantum dots (QDs) synthesized in aqueous solution have more advantages than those synthesized in organic solution, for drugs always act on the biological systems. In addition, the CdTe QDs surface-bound TGA molecules can not only enhance the fluorescence intensity, but also improve the stability of quantum dots, which makes the integrate of quantum dots and the organism easier. The present paper studied on the interaction of CdTe quantum dots, which were synthesized in aqueous solution with pazufloxacin, the forth generation of quinoloines drugs by fluorescence spectrum and absorption spectrum. The results showed that the fluorescence intensity of CdTe quantum dots decreased regularly with increasing concentration of pazufloxacin. No absorption band was observed in the 400-700 nm wavelength range for pazufloxacin, so the quenching effect of pazufloxacin on the fluorescence of CdTe QDs was not due to an inner filter resulting from the absorption of the emission wavelength by pazufloxacin. No obvious change was observed for the CdTe QDs absorption spectra before and after adding pazufloxacin, and a blue-shift or red-shift of the fluorescence emission spectra was also not seen when the concentration of pazufloxacin was changed from 10.0 to 850 microg x mL(-1), which also meant that CdTe QDs had not aggregated or become smaller after adding pazufloxacin. And the CdTe QDs, which had a good dispersion characteristic, uniform shape and centralized distribution whether in or out of pazufloxacin solution, were observed by the images of transmission electron microscopy. This indicated that the mechanism of the reaction was likely to be that the changes of surface-bound organic molecules of QDs, the --COOH chemical bond, were induced by pazufloxacin, and the Te-oxygen complex was formed at the Cd surface vacancies. Based on the quenching of the fluorescence of CdTe QDs by pazufloxacin, a rapid, novel and specific method for pazufloxacin determination was proposed. In the optimum conditions, pazufloxacin concentration versus quantum dots fluorescence gave a linear response with an excellent 0. 995 4 correlation coefficient, between 10.0 and 850 micorg x mL(-1). The limit of detection (S/N=3) was 3. 254 x 10(-3) microg x mL. And the quenching constant could be obtained, which was 2.188 x 10(4) L x mol(-1). The RSD value about fluorescence quenching of CdTe QDs by 5 groups of 50 microg x mL(-1) concentration of pazufloxacin was 0.3%. The contents of pazufloxacin in freeze-dried powder injection and sodium chloride injection were determined by the proposed method and the results agreed with the claimed values. The proposed method is much more convenient, rapid, sensitive and has a much broader linear range than other methods, such as HPLC, HPCE and UV etc. It is hopeful to contribute to the development of the studies of pharmacal imaging and the reaction mechanisms of medicines in vivo further.

[Interaction between balofloxacin and DNA and the influence of Mg2+ on the interaction].

AIM: To study the binding mode of balofloxacin with DNA and evaluate the influence of Mg2+ on the binding between balofloxacin and DNA. METHODS: Fluorescent spectroscopy was used to study the interaction of balofloxacin with DNA and to calculate the thermodynamic constants. UV-Vis spectra, DNA viscosity titration, competition experiment and the effect of dsDNA and ssDNA on the fluorescense intensity were used to identify the binding mode. RESULTS: Balofloxacin interacted with CT-DNA with a quenching constant of (5.43 +/- 0.07) x 10(3) L x mol(-1). The interaction was exothermic with a Van't Hoff enthalply of - 8.03 kJ x mol(-1) x Mg2+ cation could enhance the quenching constant between balofloxacin and DNA. CONCLUSION: Balofloxacin interacted with CT-DNA in the mode of groove binding and Mg2+ could mediate the binding of balofloxacin to DNA.