JA/ethylene and NaWRKY6/3 regulated Alternaria resistance depends on ethylene response factor 1B-like in wild tobacco.

Biosynthesis of the phytoalexins scopoletin and scopolin in Nicotiana species is regulated by upstream signals including jasmonate (JA), ethylene (ET) and NaWRKY3 in response to the necrotrophic fungus Alternaria alternata, which causes brown spot disease. However, how these signals are coordinated to regulate these phytoalexins remains unknown. By analyzing RNA sequencing data and RNA interference, we identified NaERF1B-like (NaERF1B-L) as a key player in Nicotiana attenuata during A. alternata infection by regulating the transcripts of Feruloyl-CoA 6'-hydroxylase 1 (NaF6'H1), encoding a key enzyme for scopoletin biosynthesis, and NaVS1-like (NaVS1-L), a putative biosynthetic gene of the phytoalexin solavetivone. We further demonstrated that the synergistic induction of these two genes by JA and ET signaling is mediated by NaERF1B-L. Additionally, we found that the two closely related proteins NaWRKY6 and NaWRKY3 physically interact to enhance NaERF1B-L expression by directly binding and activating the NaERF1B-L promoter. Collectively, our current results demonstrate that NaERF1B-L plays a positive role in resistance to A. alternata by modulating phytoalexins biosynthesis through the integration of JA/ET and NaWRKY6/3 signaling. Our findings reveal a fine-tuned transcriptional regulatory hierarchy mediated by NaERF1B-L for brown spot disease resistance in wild tobacco.

Evolution and Genetic Differentiation of Pleurotus tuoliensis in Xinjiang, China, Based on Population Genomics.

Pleurotus tuoliensis is a unique species discovered in Xinjiang, China, which is recognized for its significant edible, medicinal, and economic value. It has been successfully incorporated into industrial production. Controversy has emerged concerning the evolution and environmental adaptability of this species due to inadequate interspecific ecology and molecular data. This study examines the germplasm resources of P. tuoliensis in the Xinjiang region. A total of 225 wild and cultivated strains of P. tuoliensis were gathered from seven representative regions. Phylogenetic analysis revealed that seven populations were notably segregated into three distinct groups, primarily attributed to environmental factors as the underlying cause for this differentiation. Population historical size data indicate that P. tuoliensis underwent two expansion events, one between 2 and 0.9 Mya (Miocene) and the other between 15 and 4 Mya (Early Pleistocene). The ancient climate fluctuations in the Xinjiang region might have contributed to the comparatively modest population size during the Pliocene epoch. Moreover, through the integration of biogeography and ancestral state reconstruction, it was determined that group C of P. tuoliensis emerged initially and subsequently dispersed to groups D and B, in that order. Subsequently, group D underwent independent evolution, whereas group B continued to diversify into groups A and EFG. The primary factor influencing this mode of transmission route is related to the geographical conditions and prevailing wind direction of each group. Subsequent research endeavors focused on assessing the domestication adaptability of P. tuoliensis to different substrates. It was found that the metabolic processes adapted during the domestication process were mainly related to energy metabolism, DNA repair, and environmental adaptability. Processes adapted to the host adaptability include responses to the host (meiosis, cell cycle, etc.) and stress in the growth environment (cysteine and methionine metabolism, sulfur metabolism, etc.). This study analyzed the systematic evolution and genetic differentiation of P. tuoliensis in Xinjiang. The identified loci and genes provide a theoretical basis for the subsequent improvement of germplasm resources and conducting molecular breeding.

Disruption of the Contents of Endogenous Hormones Cause Pollen Development Obstruction and Abortion in Male-Sterile Hybrid Lily Populations.

Lilies are well-known flowers with large anthers and a high quantity of pollen that easily contaminates clothing and tepals. The anthers need to be artificially removed, leading to production problems. Cultivating male-sterile or pollen-free lilies could solve these problems. The key period of male sterility in a specific male-sterile hybrid lily population was determined through cytological observation. The contents of hormones, soluble sugar, soluble protein, and proline were determined by high-performance liquid chromatography, tandem mass spectrometry and colorimetry. Transcriptome sequencing was used to identify the genes with altered expression. The key period of male sterility was determined to be the microspore mother and tetrad stages. The hormone contents were abnormal in the sterile line compared with the fertile line. The indole-3-acetic acid (IAA) content was higher in the sterile line than in the fertile line at all stages, while the gibberellic acid 4 (GA4) content showed the opposite result. Abscisic acid (ABA) accumulated in the sterile line in both the microspore mother and tetrad stages, and the zeatin riboside (ZR) content in the sterile line increased at the microspore mother stage but decreased at the tetrad stage. The contents of soluble sugar, soluble protein and proline were higher in the fertile line than in the sterile line. Genes involved in auxin and ABA synthesis and signalling pathways were highly expressed in the male-sterile line. Our data suggested that abnormal contents of hormones in the microspore mother and tetrad stages resulted in pollen abortion in a male-sterile hybrid lily population, which indicated that the hormone balance in specific stages plays critical functions in pollen development in lilies.

Heterologous Expression of Platycodon grandiflorus PgF3'5'H Modifies Flower Color Pigmentation in Tobacco.

Flavonoid-3',5'-hydroxylase (F3'5'H) is the key enzyme for the biosynthesis of delphinidin-based anthocyanins, which are generally required for purple or blue flowers. Previously, we isolated a full-length cDNA of PgF3'5'H from Platycodon grandiflorus, which shared the highest homology with Campanula medium F3'5'H. In this study, PgF3'5'H was subcloned into a plant over-expression vector and transformed into tobacco via Agrobacterium tumefaciens to investigate its catalytic function. Positive transgenic tobacco T0 plants were obtained by hygromycin resistance screening and PCR detection. PgF3'5'H showed a higher expression level in all PgF3'5'H transgenic tobacco plants than in control plants. Under the drive of the cauliflower mosaic virus (CaMV) 35S promoter, the over-expressed PgF3'5'H produced dihydromyricetin (DHM) and some new anthocyanin pigments (including delphinidin, petunidin, peonidin, and malvidin derivatives), and increased dihydrokaempferol (DHK), taxifolin, tridactyl, cyanidin derivatives, and pelargonidin derivatives in PgF3'5'H transgenic tobacco plants by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) analysis, resulting in a dramatic color alteration from light pink to magenta. These results indicate that PgF3'5'H products have F3'5'H enzyme activity. In addition, PgF3'5'H transfer alters flavonoid pigment synthesis and accumulation in tobacco. Thus, PgF3'5'H may be considered a candidate gene for gene engineering to enhance anthocyanin accumulation and the molecular breeding project for blue flowers.

Transcriptomic analysis reveals candidate genes associated with anther development in Lilium Oriental Hybrid 'Siberia'.

Lily (Lilium spp. and hybrids) is an important cut flower crop worldwide. Lily flowers have large anthers, which release a large amount of pollen that stains the tepals or clothing and thus can affect the commercial value of cut flowers. In this study, lily Oriental 'Siberia' was used to investigate the regulatory mechanism of lily anther development, which may provide information to prevent pollen pollution in the future. Based on the flower bud length, anther length and color, and anatomical observations, lily anther development was categorized into five stages: green (G), green-to-yellow 1 (GY1), green-to-yellow 2 (GY2), yellow (Y), and purple (P). Total RNA was extracted from the anthers at each stage for transcriptomic analysis. A total of 268.92-Gb clean reads were generated, and 81,287 unigenes were assembled and annotated. The number of differentially expressed genes (DEGs) and unique genes were largest for the pairwise comparison between the G and GY1 stages. The G and P samples were clustered separately, whereas the GY1, GY2, and Y samples were clustered together in scatter plots from a principal component analysis. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses of DEGs detected in the GY1, GY2, and Y stages revealed that the pectin catabolic process, hormone levels, and phenylpropanoid biosynthesis were enriched. The DEGs associated with jasmonic acid biosynthesis and signaling were highly expressed at the early stages (G and GY1), whereas the DEGs associated with phenylpropanoid biosynthesis were mainly expressed in the intermediate stages (GY1, GY2, and Y). The DEGs involved in the pectin catabolic process were expressed at advanced stages (Y and P). Cucumber mosaic virus-induced gene silencing of LoMYB21 and LoAMS caused a strongly inhibited anther dehiscence phenotype, but without affecting the development of other floral organs. These results provide novel insights for understanding the regulatory mechanism of anther development in lily and other plants.

Transcriptome Analysis of Key Genes Involved in Color Variation between Blue and White Flowers of Iris bulleyana.

Iris bulleyana Dykes (Southwest iris) is an extensively distributed Iridaceae species with blue or white flowers. Hereby, we performed a systematic study, employing metabolomics and transcriptomics to uncover the subtle color differentiation from blue to white in Southwest iris. Fresh flower buds from both cultivars were subjected to flavonoid/anthocyanin and carotenoid-targeted metabolomics along with transcriptomic sequencing. Among 297 flavonoids, 24 anthocyanins were identified, and 13 showed a strong down-accumulation pattern in the white flowers compared to the blue flowers. Significant downregulation of 3GT and 5GT genes involved in the glycosylation of anthocyanins was predicted to hinder the accumulation of anthocyanins, resulting in white coloration. Besides, no significant altered accumulation of carotenoids and expression of their biosynthetic genes was observed between the two cultivars. Our study systematically addressed the color differentiation in I. bulleyana flowers, which can aid future breeding programs.

Toward Detecting Previously Undiscovered Interaction Types in Networked Systems.

Studying networked systems in a variety of domains, including biology, social science, and Internet of Things, has recently received a surge of attention. For a networked system, there are usually multiple types of interactions between its components, and such interaction-type information is crucial since it always associated with important features. However, some interaction types that actually exist in the network may not be observed in the metadata collected in practice. This article proposes an approach aiming to detect previously undiscovered interaction types (PUITs) in networked systems. The first step in our proposed PUIT detection approach is to answer the following fundamental question: is it possible to effectively detect PUITs without utilizing metadata other than the existing incomplete interaction-type information and the connection information of the system? Here, we first propose a temporal network model which can be used to mimic any real network and then discover that some special networks which fit the model shall a common topological property. Supported by this discovery, we finally develop a PUIT detection method for networks which fit the proposed model. Both analytical and numerical results show this detection method is more effective than the baseline method, demonstrating that effectively detecting PUITs in networks is achievable. More studies on PUIT detection are of significance and in great need since this approach should be as essential as the previously undiscovered node-type detection which has gained great success in the field of biology.

Phylogenetic Analysis of Wild Species and the Maternal Origin of Cultivars in the Genus Lilium Using 114 Plastid Genomes.

Lilies are one of the most important ornamental flowers worldwide with approximately 100 wild species and numerous cultivars, but the phylogenetic relationships among wild species and their contributions to these cultivars are poorly resolved. We collected the major Lilium species and cultivars and assembled their plastome sequences. Our phylogenetic reconstruction using 114 plastid genomes, including 70 wild species representing all sections and 42 cultivars representing six hybrid divisions and two outgroups, uncovered well-supported genetic relationships within Lilium. The wild species were separated into two distinct groups (groups A and B) associated with geographical distribution, which further diversified into eight different clades that were phylogenetically well supported. Additional support was provided by the distributions of indels and single-nucleotide variants, which were consistent with the topology. The species of sections Archelirion, Sinomartagon III, and Leucolirion 6a and 6b were the maternal donors for Oriental hybrids, Asiatic hybrids, Trumpet hybrids, and Longiflorum hybrids, respectively. The maternal donors of the OT hybrids originated from the two sections Archelirion and Leucolirion 6a, and LA hybrids were derived from the two sections Leucolirion 6b and Sinomartagon. Our study provides an important basis for clarifying the infrageneric classification and the maternal origin of cultivars in Lilium.

Transcriptomics-Based Identification of Genes Related to Tapetum Degradation and Microspore Development in Lily.

Lily is a popular and economically ornamental crop around the world. However, its high production of pollen grains causes serious problems to consumers, including allergies and staining of clothes. During anther development, the tapetum is a crucial step for pollen formation and microspore release. Therefore, it is important to understand the mechanism of tapetum degradation and microspore development in lily where free pollen contamination occurs. Here, we used the cut lily cultivar 'Siberia' to characterize the process of tapetum degradation through the use of cytology and transcriptomic methods. The cytological observation indicated that, as the lily buds developed from 4 cm (Lo 4 cm) to 8 cm (Lo 8 cm), the tapetum completed the degradation process and the microspores matured. Furthermore, by comparing the transcriptome profiling among three developmental stages (Lo 4 cm, Lo 6 cm and Lo 8 cm), we identified 27 differentially expressed genes. These 27 genes were classed into 4 groups by function, namely, cell division and expansion, cell-wall morphogenesis, transcription factors, LRR-RLK (leucine-rich repeat receptor-like kinases), plant hormone biosynthesis and transduction. Quantitative real-time PCR was performed as validation of the transcriptome data. These selected genes are candidate genes for the tapetum degradation and microspore development of lily and our work provides a theoretical basis for breeding new lily cultivars without pollen.

Method of optical manipulation of gold nanoparticles for surface-enhanced Raman scattering in a microcavity.

In this study, an optical manipulation and micro-surface-enhanced Raman scattering (microSERS) setup based on a microcavity was developed for efficient capture of gold nanoparticles using the photothermal effect. In addition, optical manipulation of gold nanoparticles and SERS signal detection were performed using only one laser. The results show that the SERS enhancement effect based on the microcavity was more than 20 times that based on a gold colloid solution. The laser power and velocity of nanoparticles exhibited a good linear relationship, and the velocity of nanoparticles decreased with decreasing radius r, which verifies the detriment of the radial thermophoresis in this study. This method can be used to quickly and efficiently drive metal nanoparticles and provides a promising approach for analysis of substances in the fields of chemistry and biology.

Preparation of reduced graphene oxide nanosheet/FexOy/nitrogen-doped carbon layer aerogel as photo-Fenton catalyst with enhanced degradation activity and reusability.

In this manuscript, a novel reduced graphene oxide nanosheet/FexOy/nitrogen-doped carbon layer (rGS/FexOy/NCL) aerogel with FexOy NPs sandwiched between rGS and NCL was prepared via a two-step method. Their catalytic performance was evaluated in a photo-Fenton degradation of rhodamine B. It was found that rGS/FexOy/NCL aerogel represented higher degradation activity than the sum of rGS/NCL support and FexOy NPs, suggesting synergistic effect was established between support and reactive species. The degradation activity was investigated on the basis of aerogel usage, FexOy loading, H2O2 dosage, pH value and RhB concentration. To test stability and reusability, leaching experiments, cyclic experiments and structural analysis were carried out. Based on inhibitor experiment and intermediate detection, a possible catalytic mechanism and degradation pathway of RhB were proposed.

Sustainability evaluation and implication of a large scale membrane bioreactor plant.

Membrane bioreactor (MBR) technology is receiving increasing attention in wastewater treatment and reuse. This study presents an integral sustainability evaluation of a full scale MBR plant. The plant is capable of achieving prominent technical performance in terms of high compliance rate, low variation in effluent quality and high removal efficiency during long term operation. It is also more responsive to the new local standard with rigorous limits. However, electricity consumption is found to be the dominant process resulting in elevated life cycle environmental impacts and costs, accounting for 51.6% of the costs. As such, it is suggested to optimize energy use in MBR unit and implement sludge treatment and management. The prolonged membrane life span could also contribute largely to reduced life cycle environmental concerns and expenses. This study is of great theoretical significance and applicable value in guaranteeing the performance and sustainability of large scale MBR schemes.

One-step preparation of nanobeads-based polypyrrole hydrogel by a reactive-template method and their applications in adsorption and catalysis.

In this manuscript, nanobeads-based polypyrrole (PPy) hydrogel was prepared by a reactive-template method in one-step. Fe3O4 nanoparticles were selected as reactive-templates, which not only acted as the oxidants to initiate polymerization of pyrrole monomer, but also guided the growth of polymer chains. No surfactants were involved in whole preparation procedure, leading to a superior purity of products. Because PPy hydrogels were obtained by cross-linking individual nanobeads, they have bridged nano-dimension and macro-dimension together; thus displayed a three-dimensional hierarchical porous structure. By taking advantage of structural merits, PPy hydrogels exhibited large surface area and plenty of interconnected channels, which made them act as good candidates for adsorbents of rhodamine B (RhB). During the adsorption experiment, their adsorption kinetics were carefully investigated. In comparison tests, their equilibrium adsorption capacities were higher than that of referenced PPy (R-PPy) hydrogels prepared by a classical oxidation polymerization. In addition to be used as adsorbent, PPy hydrogels could serve as support to load Pd nanoclusters. During the catalytic reduction of RhB with NaBH4 as reducing agent under the same Pd loadings, PPy/Pd hydrogels displayed better catalytic activity than that of R-PPy/Pd hydrogels, and their rate constant and turnover frequency was 12 and 4.8 times higher than that of the latter.