The Euscaphis japonica genome and the evolution of malvids

Malvids is one of the largest clades of rosids, includes 58 families and exhibits remarkable morphological and ecological diversity. Here, we report a high-quality chromosome-level genome assembly for Euscaphis japonica, an early-diverging species within malvids. Genome-based phylogenetic analysis suggests that the unstable phylogenetic position of E. japonica may result from incomplete lineage sorting and hybridization event during the diversification of the ancestral population of malvids. Euscaphis japonica experienced two polyploidization events: the ancient whole genome triplication event shared with most eudicots (commonly known as the c event) and a more recent whole genome duplication event, unique to E. japonica. By resequencing 101 samples from 11 populations, we speculate that the temperature has led to the differentiation of the evergreen and deciduous of E. japonica and the completely different population histories of these two groups. In total, 1012 candidate positively selected genes in the evergreen were detected, some of which are involved in flower and fruit development. We found that reddening and dehiscence of the E. japonica pericarp and long fruit-hanging time promoted the reproduction of E. japonica populations, and revealed the expression patterns of genes related to fruit reddening, dehiscence and abscission. The key genes involved in pentacyclic triterpene synthesis in E. japonica were identified, and different expression patterns of these genes may contribute to pentacyclic triterpene diversification. Our work sheds light on the evolution of E. japonica and malvids, particularly on the diversification of E. japonica and the genetic basis for their fruit dehiscence and abscission.DATA AVAILABILITY STATEMENT : All sequences described in this manuscript have been submitted to the National Genomics Data Center (NGDC). The raw whole-genome data of E. japonica have been deposited in BioProject/GSA (https://bigd.big.ac.cn/gsa.) under the accession codes PRJCA005268/CRA004271, and the assembly and annotation data have been deposited at BioProject/GWH (https://bigd.big.ac.cn/gwh) under the accession codes PRJCA005268/GWHBCHS00000000. The raw transcriptomes data of E. japonica have been deposited in BioProject/GSA (https://bigd.big.ac.cn/gsa.) under the accession codes PRJCA005298/CRA004272.SUPPLEMENTARY MATERIAL 1: Supplementary Note 1. Chromosome number assessment. Supplementary Note 2. Whole-genome duplication identification and dating. Supplementary Note 3. Observation of E. japonica seed dispersal. Supplementary Note 4. Determination of pentacyclic triterpene substances. Figure S1. Cytogenetic analysis of E. japonica. Figure S2. Genome size and heterozygosity of E. japonica estimation using 17 k-mer distribution. Figure S3. Interchromosomal of Hi-C chromosome contact map of E. japonica genome. Figure S4. Gene structure prediction results of E. japonica and other species. Figure S5. Venn diagram shows gene families of malvids. Figure S6. Phylogenetic tree constructed by chloroplast genomes from 17 species. Figure S7. Concatenated- and ASTRAL-based phylogenetic trees. Figure S8. Ks distribution in E. japonica. Figure S9. Distributions of synonymous substitutions per synonymous site (Ks) of one-to-one orthologs identified between E. japonica and P. trichocarpa and V. vinifera. Figure S10. Population structure plot. Figure S11. Fixation index (FST) heat map among E. japonica populations. Figure S12. Phylogenetic analysis of MADS-box genes from O. sativa, A. thaliana, E. japonica, and T. cacao. Figure S13. Observation the fruit development. Figure S14. Animal seed dispersal. Figure S15. Anthocyanin biosynthesis in E. japonica fruits. Figure S16. Carotenoid accumulation and the chlorophyll degradation in E. japonica fruits. Figure S17. Expression profile of fruit dehiscence-related genes. Figure S18. Phylogenetic tree of DELLA genes obtained from six malvids species. Figure S19. Phylogenetic tree of CAD genes obtained from seven malvids species. Figure S20. Expression pattern of fruit abscission-related genes. Figure S21. Structure of pentacyclic triterpene compounds separated from Euscaphis. Figure S22. Phylogenetic tree of HMGR gene in plants. Figure S23. Phylogenetic tree of P450s gene family obtained from A. thaliana and E. japonica.SUPPLEMENTARY MATERIAL 2: Table S1. Assembled statistics of E. japonica genome. Table S2. Evaluation of E. japonica genome assembly. Table S3. Chromosome length of E. japonica. Table S4. Prediction of gene structures of the E. japonica genome. Table S5. Statistics on the function annotation of the E. japonica genome. Table S6. Non-coding RNA annotation results of E. japonica genome. Table S7. BUSCO assessment of the E. japonica annotated genome. Table S8. Statistic of repeat sequence in E. japonica genome. Table S9. Gene-clustering statistics for 17 species. Table S10. KEGG enrichment result of unique genes families of E. japonica. Table S11. Gene Ontology (GO) and KEGG enrichment result of significant shared by malvids species gene families. Table S12. Gene Ontology (GO) and KEGG enrichment result of significant expansion of E. japonica gene families. Table S13. Gene Ontology (GO) enrichment result of significant contraction of E. japonica gene families. Table S14. Statistical sampling population information. Table S15. Statistics population resequencing information. Table S16. Statistical nucleotide polymorphisms in the populations. Table S17. Candidate positive selection genes (PSGs) in the evergreen population. Table S18. Candidate positive selection genes (PSGs) in the deciduous population. Table S19. Gene Ontology (GO) enrichment result of significant PSGs in the evergreen population. Table S20. List of MADS-box genes identified in E. japonica. Table S21. Genes involved in anthocyanin biosynthesis, carotenoid biosynthesis, and chlorophyll degradation. Table S22. Identification fruit dehiscence-related genes in E. japonica. Table S23. Genes related to lignin synthesis that are highly expressed during pericarp dehiscence. Table S24. Gene expression levels (FPKMs) of fruit abscission-related genes in pericarp. Table S25. Triterpene compounds separated from Euscaphis. Table S26. Number of putative pentacyclic triterpene-related genes in the malvids species. Table S27. Identified pentacyclic triterpene synthesis-related genes in E. japonica genome. Table S28. Statistical simple sequence repeat.Fund for Excellent Doctoral Dissertation of Fujian Agriculture and Forestry University, China; Fujian Provincial Department of Science E. japonica Evolution and Selection of Ornamental Medicinal Resources, China; the Project of Forestry Peak Discipline at Fujian Agriculture and Forestry University, China; the Collection, Development and Utilization of Eascaphis konlshli Germplasm Resources; the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program and from Ghent University.https://onlinelibrary.wiley.com/journal/1365313xam2022BiochemistryGeneticsMicrobiology and Plant Patholog

An all-silicon design of a high-efficiency broadband transmissive terahertz polarization convertor

Abstract Polarization, a fundamental behavior of electromagnetic waves, holds immense potential across diverse domains such as environmental monitoring, biomedicine, and ocean exploration. However, achieving efficient modulation of terahertz waves with wide operational bandwidth poses significant challenges. Here, we introduce an all-silicon polarization converter designed specifically to operate in the terahertz range of the electromagnetic spectrum. Simulation results demonstrate that the average conversion efficiency of cross-linear waves exceeds 80% across a wide frequency range spanning from 1.00 to 2.32 THz, with the highest conversion efficiency peaking at an impressive 99.97%. Additionally, our proposed structure facilitates linear-to-circular polarization conversion with an ellipticity of 1 at 0.85 THz. Furthermore, by rotating the cross-shaped microstructure, active control over arbitrary polarization states can be achieved. To summarize, the proposed structure offers remarkable flexibility and ease of integration, providing a reliable and practical solution for achieving broadband and efficient polarization conversion of terahertz waves. Graphical abstrac

Effect of LongZhang Gargle on Dual-Species Biofilm of Candida albicans and Streptococcus mutans

Bioactive natural products have become a hot spot for oral disease treatments. At the present study, LongZhang Gargle was investigated for its effects on single-species biofilms of Candida albicans and dual-species biofilms of Candida albicans and Streptococcus mutans. Two different models of single and dual-species biofilms were grown in YNBB medium under appropriate conditions. Biofilm biomass, biofilm architecture, and cell activity in biofilms were assessed using Crystal Violet Staining, MTT, scanning electron microscopy (SEM), and confocal laser scanning microscopy (CLSM). Significant reductions of biofilm biomass and fungus activity were obtained when treated with LongZhang Gargle at 2% (P<0.05), 4% (P<0.05), and 8% (P<0.05) in single-species biofilms of C. albicans, and at 4% (P<0.05) and 8% (P<0.05) in double-species biofilms. Suppression of density, thickness, and the proportion of hyphae and fungal spores were obtained under SEM and CLSM. In conclusion, LongZhang Gargle affects single and dual-species biofilms by inhibiting biofilm biomass, cell activity, and formation of hyphae, but it does not affect the production of Extracellular polysaccharides (EPS). We speculate that LongZhang Gargle would be a promising natural drug, which can be used in treatment against C. albicans and S. mutans in oral diseases

The complete chloroplast genome sequence of Euscaphis japonica (Staphyleaceae)

Euscaphis japonica is not only an ideal ornamental plant, but also a traditional medicinal plant, which is an extremely valuable species to study. We determined the complete chloroplast genome sequence for E. japonica using Illumina sequencing technology. The complete chloroplast sequence is 160,467 bp in length, including a large single-copy (LSC) region of 88,716 bp, a small single-copy (SSC) region of 18,614 bp, and a pair of invert repeats (IR) regions of 26,568 bp. Plastid genome contains 142 genes, 46 protein-coding genes, 39 tRNA genes, and eight rRNA genes. Phylogenetic analysis base on 14 chloroplast genomes indicates that E. japonica forms an isolated clade and sisters to Glycosmis-Gossypium clade with strong support

Risk factors and incidence of third trimester stillbirths in China

Abstract About 2.6 million third-trimester stillbirths occur annually worldwide, mostly in low- and middle-income countries. However, the causes of stillbirths are rarely investigated. We performed a retrospective, hospital-based study in Zhejiang Province, southern China, of the causes of third-trimester stillbirths. Causes of stillbirths were classified using the Relevant Condition at Death classification system. From January 1, 2013, to December 31, 2018, we enrolled 341 stillbirths (born to 338 women) from 111,275 perinatal fetuses (born to 107,142 women), as well as 293 control cases (born to 291 women). The total incidence of third-trimester stillbirths was 3.06/1000 (341/111,275). There were higher proportions of women with a high body mass index, twins, pregnancy-induced hypertension, assisted reproduction and other risk factors among the antepartum than the control cases. The antepartum stillbirth fetuses were of lower median birth weight and gestational age and had a smaller portion of translucent amniotic fluid than the control cases. The antepartum stillbirth fetuses had a higher frequency of abnormalities detected prenatally and of fetal growth restriction than the control cases. Of 341 cases (born to 338 mothers), the most common causes of stillbirth were fetal conditions [117 (34.3%) cases], umbilical cord [88 (25.8%)], maternal conditions [34 (10.0%)], placental conditions [31 (9.1%)], and intrapartum [28 (8.2%)]. Only eight (2.3%), three (0.9%), and two (0.6%) stillbirths were attributed to amniotic fluid, trauma, and uterus, respectively. In 30 (8.8%) cases, the cause of death was unclassified. In conclusion, targeted investigation can ascertain the causes of most cases of third-trimester stillbirths

Agreement of corneal high-order aberrations measured by three wavefront aberrometers in myopic adults

AIM:To evaluate the agreement of corneal high-order aberrations from Topcon KR-1W, i.Profiler and OPD-Scan Ⅲ wavefront aberrometers in myopic adults.METHODS:A prospective clinical study. A total of 92 adult patients(92 eyes)with myopia in the department of optometry, the People's Hospital of Guangxi Zhuang Autonomous Region from June to August 2022 were enrolled. The third-order and fourth-order corneal aberrations at the pupil diameter of 4 and 6mm were measured by Topcon KR-1W, i.Profiler, and OPD-Scan Ⅲ, respectively. The difference and agreement of the three aberrometers were evaluated.RESULTS: The measurements at 6mm pupil diameter were all greater than those at 4mm pupil diameter. Although there were no statistical differences in the measurements of Z-44、Z-24 by the three aberrometers at 4 pupil diameter(P>0.05), there were statistical differences in other measurements(P<0.05). The aberration results measured by the three aberrometers were statistically different at the 6mm pupil diameter(P<0.05). The 95% limit of agreement(95%LoA)of the measurements of higher-order aberration, including the third-order aberrations at 4mm pupil diameter and the third-order and fourth-order aberrations at 6mm pupil diameter(except for the Z-24)were greater than 0.1μm. The concordance correlation coefficient(Pc)was lower than 0.90, indicating a poor consistency. The correlation coefficients of corneal higher-order aberrations were significantly different among the three aberrometers at 4 and 6mm pupil diameter(r4mm=0.215～0.805, P4mm<0.05; r6mm=0.561～0.916, P6mm<0.001).CONCLUSION:There were significant differences in the measurements of the third- and fourth-order corneal aberrations at 4 and 6mm pupil diameter among Topcon KR-1W, i.Profiler, and OPD-Scan Ⅲ, and the agreements were poor, so they are not interchangeably in clinical applications

A General Synthetic Strategy for the Synthesis of Imine-Linked Covalent Organic Frameworks in Choline Chloride–Hexafluoroisopropanol-Based Deep Eutectic Solvents

The imine-linked covalent organic frameworks (COFs) have garnered significant attention in various fields due to exceptional stability and polyamide structures, etc. However, the conventional synthetic protocols for the high-crystallinity imine-linked COFs often necessitate the use of harmful organic solvent and extra catalyst, rendering their synthesis environmentally detrimental. Therefore, it is imperative to develop facile methods for COF preparation that employ green solvents without the need of extra catalyst. Herein, an environmentally friendly, efficient, general synthetic strategy was developed to synthesize five imine-linked COFs with high yield and high crystallinity by using choline chloride (ChCl)–hexafluoro­isopropanol (HFIP) linked deep eutectic solvents (DESs) as general solvents for the first time. Unlike other reactions that required repeated exploration of the types of solvents to synthesize COFs with high crystallinity, the as-developed method only required changing the molar ratio of ChCl and HFIP in DES; various imine-linked COFs with high crystallinity can be synthesized. To further elucidate the formation of imine-linked COFs in ChCl-HFIP-based DESs, COF-CH-1, which was prepared using 1,3,5-tris(4-amino­phenyl)benzene (TPB) and terephthalaldehyde (TPDD) as precursors, was regarded as an example. The formation process of COF-CH-1 was preliminarily deduced linked on the changes of morphology, functional groups, element compositions, etc., with the change of reaction temperature and reaction time in optimal DES. Finally, according to the results, we also preliminarily speculated on the possible role of DESs in COFs’ formation