Genome-wide analysis of NAC transcription factors and exploration of candidate genes regulating selenium metabolism in Broussonetia papyrifera.

MAIN CONCLUSION: Genome-wide identification revealed 79 BpNAC genes belonging to 16 subfamilies, and their gene structures and evolutionary relationships were characterized. Expression analysis highlighted their importance in plant selenium stress responses. Paper mulberry (Broussonetia papyrifera), a deciduous arboreal plant of the Moraceae family, is distinguished by its leaves, which are abundant in proteins, polysaccharides, and flavonoids, positioning it as a novel feedstock. NAC transcription factors, exclusive to plant species, are crucial in regulating growth, development, and response to biotic and abiotic stress. However, extensive characterization of the NAC family within paper mulberry is lacking. In this study, 79 BpNAC genes were identified from the paper mulberry genome, with an uneven distribution across 13 chromosomes. A comprehensive, genome-wide analysis of BpNACs was performed, including investigating gene structures, promoter regions, and chromosomal locations. Phylogenetic tree analysis, alongside comparisons with Arabidopsis thaliana NACs, allowed for categorizing these genes into 16 subfamilies in alignment with gene structure and motif conservation. Collinearity analysis suggested a significant homologous relationship between the NAC genes of paper mulberry and those in Morus notabilis, Ficus hispida, Antiaris toxicaria, and Cannabis sativa. Integrating transcriptome data and Se content revealed that 12 BpNAC genes were associated with selenium biosynthesis. Subsequent RT-qPCR analysis corroborated the correlation between BpNAC59, BpNAC62 with sodium selenate, and BpNAC55 with sodium selenite. Subcellular localization experiments revealed the nuclear functions of BpNAC59 and BpNAC62. This study highlights the potential BpNAC transcription factors involved in selenium metabolism, providing a foundation for strategically breeding selenium-fortified paper mulberry.

Effect of Different Selenium Species on Indole-3-Acetic Acid Activity of Selenium Nanoparticles Producing Strain Bacillus altitudinis LH18.

Acting as a growth regulator, Indole-3-acetic acid (IAA) is an important phytohormone that can be produced by several Bacillus species. However, few studies have been published on the comprehensive evaluation of the strains for practical applications and the effects of selenium species on their IAA-producing ability. The present study showed the selenite reduction strain Bacillus altitudinis LH18, which is capable of producing selenium nanoparticles (SeNPs) at a high yield in a cost-effective manner. Bio-SeNPs were systematically characterized by using DLS, zeta potential, SEM, and FTIR. The results showed that these bio-SeNPs were small in particle size, homogeneously dispersed, and highly stable. Significantly, the IAA-producing ability of strain was differently affected under different selenium species. The addition of SeNPs and sodium selenite resulted in IAA contents of 221.7 µg/mL and 91.01 µg/mL, respectively, which were 3.23 and 1.33 times higher than that of the control. This study is the first to examine the influence of various selenium species on the IAA-producing capacity of Bacillus spp., providing a theoretical foundation for the enhancement of the IAA-production potential of microorganisms.

A new scheme of PM2.5 and O3 control strategies with the integration of SOM, GA and WRF-CAMx.

Previous air pollution control strategies didn't pay enough attention to regional collaboration and the spatial response sensitivities, resulting in limited control effects in China. This study proposed an effective PM2.5 and O3 control strategy scheme with the integration of Self-Organizing Map (SOM), Genetic Algorithm (GA) and WRF-CAMx, emphasizing regional collaborative control and the strengthening of control in sensitive areas. This scheme embodies the idea of hierarchical management and spatial-temporally differentiated management, with SOM identifying the collaborative subregions, GA providing the optimized subregion-level priority of precursor emission reductions, and WRF-CAMx providing response sensitivities for grid-level priority of precursor emission reductions. With Beijing-Tianjin-Hebei and the surrounding area (BTHSA, "2 + 26" cities) as the case study area, the optimized strategy required that regions along Taihang Mountains strengthen the emission reductions of all precursors in PM2.5-dominant seasons, and strengthen VOCs reductions but moderate NOx reductions in O3-dominant season. The spatiotemporally differentiated control strategy, without additional emission reduction burdens than the 14th Five-Year Plan proposed, reduced the average annual PM2.5 and MDA8 O3 concentrations in 28 cities by 3.2%-8.2% and 3.9%-9.7% respectively in comparison with non-differential control strategies, with the most prominent optimization effects occurring in the heavily polluted seasons (6.9%-18.0% for PM2.5 and 3.3%-14.2% for MDA8 O3, respectively). This study proposed an effective scheme for the collaborative control of PM2.5 and O3 in BTHSA, and shows important methodological implications for other regions suffering from similar air quality problems.

Transcriptome mining of genes in Zanthoxylum armatum revealed ZaMYB86 as a negative regulator of prickly development.

Zanthoxylum armatum DC. is an important economic tree species. Prickle is a type of trichome with special morphology, and there are a lot of prickles on the leaves of Z. armatum, which seriously restricts the development of Z. armatum industry. In this study, the leaves of Z. armatum cv. Zhuye (ZY) and its budding variety 'Rongchangwuci' (WC) (A less prickly mutant variety) at different developmental stages were used as materials, and the transcriptome sequencing data were analyzed. A total of 96,931 differentially expressed genes (DEGs) were identified among the samples, among which 1560 were candidate DEGs that might be involved in hormone metabolism. The contents of JA, auxin and CK phytohormones in ZY leaves were significantly higher than those in WC leaves. Combined with weighted gene co-expression network analysis, eight genes (MYC, IAA, ARF, CRE/AHK, PP2C, ARR-A, AOS and LOX) were identified, including 25 transcripts, which might affect the metabolism of the three hormones and indirectly participate in the formation of prickles. Combining with the proteins successfully reported in other plants to regulate trichome formation, ZaMYB86, a transcription factor of R2R3 MYB family, was identified through local Blast and phylogenetic tree analysis, which might regulate prickle formation of Z. armatum. Overexpression of ZaMYB86 in mutant A. thaliana resulted in the reduction of trichomes in A. thaliana leaves, which further verified that ZaMYB86 was involved in the formation of pickles. Yeast two-hybrid results showed that ZaMYB86 interacted with ZaMYB5. Furthermore, ZaMYB5 was highly homologous to AtMYB5, a transcription factor that regulated trichomes development, in MYB DNA binding domain. Taken together, these results indicated that ZaMYB86 and ZaMYB5 act together to regulate the formation of prickles in Z. armatum. Our findings provided a new perspective for revealing the molecular mechanism of prickly formation.

Effect of Nano-Selenium on Nutritional Quality of Cowpea and Response of ABCC Transporter Family.

It is an important way for healthy Selenium (Se) supplement to transform exogenous Se into organic Se through crops. In the present study, Vigna unguiculata was selected as a test material and sprayed with biological nano selenium (SeNPs) and Na2SeO3, and its nutrient composition, antioxidant capacity, total Se and organic Se content were determined, respectively. Further, the response of ABC transporter family members in cowpea to different exogenous Se treatments was analyzed by transcriptome sequencing combined with different Se forms. The results show that the soluble protein content of cowpea increased after twice Se treatment. SeNPs treatment increased the content of cellulose in cowpea pods. Na2SeO3 treatment increased the content of vitamin C (Vc) in cowpea pods. Se treatments could significantly increase the activities of Peroxidase (POD), polyphenol oxidase (PPO) and catalase (CAT) in cowpea pods and effectively maintain the activity of Superoxide dismutase (SOD). SeNPs can reduce the content of malondialdehyde (MDA) in pods. After Se treatment, cowpea pods showed a dose-effect relationship on the absorption and accumulation of total Se, and Na2SeO3 treatment had a better effect on the increase of total Se content in cowpea pods. After treatment with SeNPs and Na2SeO3, the Se species detected in cowpea pods was mainly SeMet, followed by MeSeCys. Inorganic Se can only be detected in the high concentration treatment group. Analysis of transcriptome data of cowpea treated with Se showed that ABC transporters could play an active role in response to Se stress and Se absorption, among which ABCB, ABCC and ABCG subfamilies played a major role in Se absorption and transportation in cowpea. Further analysis by weighted gene co-expression network analysis (WGCNA) showed that the content of organic Se in cowpea treated with high concentration of SeNPs was significantly and positively correlated with the expression level of three transporters ABCC11, ABCC13 and ABCC10, which means that the ABCC subfamily may be more involved in the transmembrane transport of organic Se in cells.

Exploring drivers of the aggravated surface O3 over North China Plain in summer of 2015-2019: Aerosols, precursors, and meteorology.

Continuous aggravated surface O3 over North China Plain (NCP) has attracted widely public concern. Herein, we evaluated the effects of changes in aerosols, precursor emissions, and meteorology on O3 in summer (June) of 2015-2019 over NCP via 8 scenarios with WRF-Chem model. The simulated mean MDA8 O3 in urban areas of 13 major cities in NCP increased by 17.1%∼34.8%, which matched well with the observations (10.8%∼33.1%). Meanwhile, the model could faithfully reproduce the changes in aerosol loads, precursors, and meteorological conditions. A relatively-even O3 increase (+1.2%∼+3.9% for 24-h O3 and +1.0%∼+3.8% for MDA8 O3) was induced by PM2.5 dropping, which was consistent with the geographic distribution of regional PM2.5 reduction. Meanwhile, the NO2 reduction coupled with a near-constant VOCs led to the elevated VOCs/NOx ratios, and then caused O3 rising in the areas under VOCs-limited regimes. Therein, the pronounced increases occurred in Handan, Xingtai, Shijiazhuang, Tangshan, and Langfang (+10.7%∼+13.6% for 24-h O3 and +10.2%∼+12.2% for MDA8 O3); while the increases in other cities were 5.7%∼10.5% for 24-h O3 and 4.9%∼9.2% for MDA8 O3. Besides, the meteorological fluctuations brought about the more noticeable O3 increases in northern parts (+12.5%∼+13.5% for 24-h O3 and +11.2%∼+12.4% for MDA8 O3) than those in southern and central parts (+3.2%∼+9.3% for 24-h O3 and +3.7%∼+8.8% for MDA8 O3). The sum of the impacts of the three drivers reached 16.7%∼21.9%, which were comparable to the changes of the observed O3. Therefore, exploring reasonable emissions-reduction strategies is essential for the ozone pollution mitigation over this region.

Insights into multidimensional transport flux from vertical observation and numerical simulation in two cities in North China.

This study represents the first quantitative evaluation of pollution transport budget within the boundary layer of typical cities in the Beijing-Tianjin-Hebei (BTH) region from the perspective of horizontal and vertical exchanges and further discusses the impact of the atmospheric boundary layer (ABL)-free troposphere (FT) exchange on concentration of fine particulate matter (PM2.5) within the ABL during heavy pollution. From the perspective of the transport flux balance relationship, differences in pollution transport characteristics between the two cities is mainly reflected in the ABL-FT exchange effect. The FT mainly flowed into the ABL in BJ, while in SJZ, the outflow from the ABL to the FT was more intense. Combined with an analysis of vertical wind profile distribution, BJ was found to be more susceptible to the influence of northwest cold high prevailing in winter, while sinking of strong cold air allowed the FT flowing into the ABL influence the vertical exchange over BJ. In addition, we selected a typical pollution event for targeted analysis to understand mechanistic details of the influence of ABL-FT exchange on the pollution event. These results showed that ABL-FT interaction played an important role in PM2.5 concentration within the ABL during heavy pollution. Especially in the early stage of heavy pollution, FT transport contributed as much as 82.74% of PM2.5 within the ABL. These findings are significant for improving our understanding of pollution transport characteristics within the boundary layer and the effect of ABL-FT exchange on air quality.

A review of the technology and applications of methods for evaluating the transport of air pollutants.

A variety of methods based on air quality models, including tracer methods, the brute-force method (BFM), decoupled direct method (DDM), high-order decoupled direct method (HDDM), response surface models (RSMs) and so on forth, have been widely used to study the transport of air pollutants. These methods have good applicability for the transport of air pollutants with simple formation mechanisms. However, differences in research conclusions on secondary pollutants with obvious nonlinear characteristics have been reported. For example, the tracer method is suitable for the study of simplified scenarios, while HDDM and RSMs are more suitable for the study for nonlinear pollutants. Multiple observation techniques, including conventional air pollutant observation, lidar observation, air sounding balloons, vehicle-mounted and ship-borne technology, aerial surveys, and remote sensing observations, have been utilized to investigate air pollutant transport characteristics with time resolution as high as 1 sec. In addition, based on a multi-regional input-output model combined with emission inventories, the transfer of air pollutant emissions can be evaluated and applied to study the air pollutant transport characteristics. Observational technologies have advantages in temporal resolution and accuracy, while modeling technologies are more flexible in spatial resolution and research plan setting. In order to accurately quantify the transport characteristics of pollutants, it is necessary to develop a research method for interactive verification of observation and simulation. Quantitative evaluation of the transport of air pollutants from different angles can provide a scientific basis for regional joint prevention and control.

Structure and stability analysis of antibacterial substance produced by selenium enriched Bacillus cereus BC1.

Microorganisms can produce many antibiotics against bacteria and fungi, which have been used as a potential choice of new antibiotics. In this paper, we studied the characteristics of antibacterial substances by Bacillus cereus BC1. The results showed that the acid-precipitated substance played the main role in antibacterial activity, and further characterization indicated that the antibacterial substance might be a lipopeptide substance. Then the antibacterial spectrum suggested that the antibacterial substance had an inhibitory effect on Gram-positive bacteria and fungi, while selenium-riched antibacterial substance of Bacillus cereus BC1 could significantly enhance the inhibition. Then the morphological effects of the antibacterial substance to indicator bacteria were determined. The effects of different treatment methods on the stability of antibacterial substances were studied and the results showed that the antibacterial substance was stable to heat, ultrasonic, and ultraviolet treatment, and their antibacterial activity would not be greatly affected. However, they were sensitive to pepsin. The optimum pH range of antibacterial activity was 3-5. This study may contribute to reusing the fermentation supernatant often discarded in the previous fermentation process. At the same time, the lipopeptide antibacterial substance extracted from the fermentation broth of selenium-enriched Bacillus cereus BC1 can be used in the development of antibiotics and biopesticides, and open up a new way for the control of plant diseases.

JAZ1-3 and MYC2-1 Synergistically Regulate the Transformation from Completely Mixed Flower Buds to Female Flower Buds in Castanea mollisima.

Chestnut (Castanea mollisima) is an important woody food crop, but its yield has been low in cultivation, mainly due to the problems of fewer female flowers and more male flowers. Therefore, regulating the transition of chestnut flowers and effectively balancing the proportion of male and female to improve the yield are key factor to be solved in production. In this study, the chestnut floral buds in pre- and post-winter were used as materials. The data of metabolites, hormones, and gene expression during flower bud differentiation of chestnut were analyzed by transcriptomics and metabolomics to preliminarily reveal the possible reason of male and female flower bud transformation in pre- and post-winter. The analysis of Differentially Expressed Genes (DEGs) showed that there were 6323 DEGs in the Complete mixed flower bud (CMF) group in pre- and post-winter, of which 3448 genes were up-regulated and 2875 genes were down-regulated. There were 8037 DEGs in the Incomplete mixed flower bud (IMF) in pre- and post-winter, of which 4546 genes were up-regulated and 3491 genes were down-regulated. A total of 726 genes from the two flower buds were enriched into 251 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in post winter, of which plant hormone signal transduction accounted for 4.13%. The analysis results of differential metabolites showed that the differential metabolites of the two flower buds were mainly concentrated in the secondary metabolic synthesis pathway. The difference of hormone content showed that the content of Gibberellin 9 (GA9) and GA19 in CMF was higher than that in IMF in pre-winter, but the opposite in post-winter. Methyl jasmonate (MeJA) content was only very high in CMF in pre-winter, while Jasmonoyl-(l)-Isoleucine (JA-ILE) showed high content in CMF in post-winter. In post-winter, higher concentration of JA-ILE was positively correlated with the expression of Flowering Locus T (CmFT), and CmFT gene was significantly positively correlated with the expression levels of MYC2-1, MYC2-2 and LFY 3 (LEAFY 3). The higher concentration of JA-ILE was negatively correlated with the transcription level of JAZ1-3. In vitro experiments further verified that Jasmonate-Zim 1-3 (JAZ 1-3) combined with MYC2-1 inhibited the transcription of CmFT gene, while MYC2-1 alone promoted the expression of FT. The results suggested that a higher concentration of GA is conducive to breaking the dormancy of flower buds and promoting the development of male flower buds, while a lower concentration of GA and a higher concentration of JA-ILE are conducive to the differentiation and formation of female flower buds in post-winter, in which JAZ1-3 and MYC2-1 play a key role in the differentiation of female flower buds of chestnut.

Treatment of Ginkgo biloba with Exogenous Sodium Selenite Affects Its Physiological Growth, Changes Its Phytohormones, and Synthesizes Its Terpene Lactones.

Ginkgolide is a unique terpenoid natural compound in Ginkgo biloba, and it has an important medicinal value. Proper selenium has been reported to promote plant growth and development, and improve plant quality, stress resistance, and disease resistance. In order to study the effects of exogenous selenium (Se) on the physiological growth and the content of terpene triolactones (TTLs) in G. biloba seedlings, the seedlings in this work were treated with Na2SeO3. Then, the physiological indexes, the content of the TTLs, and the expression of the related genes were determined. The results showed that a low dose of Na2SeO3 was beneficial to plant photosynthesis as it promoted the growth of ginkgo seedlings and increased the root to shoot ratio. Foliar Se application significantly increased the content of soluble sugar and protein and promoted the content of TTLs in ginkgo leaves; indeed, it reached the maximum value of 7.95 mg/g in the ninth week, whereas the application of Se to the roots inhibited the synthesis of TTLs. Transcriptome analysis showed that foliar Se application promoted the expression levels of GbMECPs, GbMECT, GbHMGR, and GbMVD genes, whereas its application to the roots promoted the expression of GbDXS and GbDXR genes. The combined analysis results of metabolome and transcriptome showed that genes such as GbDXS, GbDXR, GbHMGR, GbMECPs, and GbCYP450 were significantly positively correlated with transcription factors (TFs) GbWRKY and GbAP2/ERF, and they were also positively correlated with the contents of terpene lactones (ginkgolide A, ginkgolide B, ginkgolide M, and bilobalide). Endogenous hormones (MeJA-ILE, ETH, and GA7) were also involved in this process. The results suggested that Na2SeO3 treatment affected the transcription factors related to the regulation of endogenous hormones in G. biloba, and further regulated the expression of genes related to the terpene synthesis structure, thus promoting the synthesis of ginkgo TTLs.

Enhancing the Activity of Carboxymethyl Cellulase Enzyme Using Highly Stable Selenium Nanoparticles Biosynthesized by Bacillus paralicheniformis Y4.

The inorganic selenium is absorbed and utilized inefficiently, and the range between toxicity and demand is narrow, so the application is strictly limited. Selenium nanoparticles have higher bioactivity and biosafety properties, including increased antioxidant and anticancer properties. Thus, producing and applying eco-friendly, non-toxic selenium nanoparticles in feed additives is crucial. Bacillus paralicheniformis Y4 was investigated for its potential ability to produce selenium nanoparticles and the activity of carboxymethyl cellulases. The selenium nanoparticles were characterized using zeta potential analyses, Fourier transform infrared (FTIR) spectroscopy, and scanning electron microscopy (SEM). Additionally, evaluations of the anti-α-glucosidase activity and the antioxidant activity of the selenium nanoparticles and the ethyl acetate extracts of Y4 were conducted. B. paralicheniformis Y4 exhibited high selenite tolerance of 400 mM and the selenium nanoparticles had an average particle size of 80 nm with a zeta potential value of -35.8 mV at a pH of 7.0, suggesting that the particles are relatively stable against aggregation. After 72 h of incubation with 5 mM selenite, B. paralicheniformis Y4 was able to reduce it by 76.4%, yielding red spherical bio-derived selenium nanoparticles and increasing the carboxymethyl cellulase activity by 1.49 times to 8.96 U/mL. For the first time, this study reports that the carboxymethyl cellulase activity of Bacillus paralicheniforis was greatly enhanced by selenite. The results also indicated that B. paralicheniformis Y4 could be capable of ecologically removing selenite from contaminated sites and has great potential for producing selenium nanoparticles as feed additives to enhance the added value of agricultural products.

Comparative study of the effects of selenium yeast and sodium selenite on selenium content and nutrient quality in broccoli florets (Brassica oleracea L. var. italica).

BACKGROUND: Approximately 0.5-1 billion people worldwide face the risk of selenium (Se) deficiency because of the low Se concentration in their diets. Broccoli can accumulate Se and comprises a source of daily Se supplement for humans. Se biofortification is an effective strategy for enhancing Se content in crops. In the present study, the effects of Se yeast and selenite application on the Se content and nutrient quality of broccoli were investigated. RESULTS: Broccoli growth was promoted by Se yeast but inhibited by selenite. The total Se content of broccoli florets remarkably increased with increasing exogenous Se fertilizer concentrations. The main Se species in broccoli florets were methyl-selenocysteine and selenomethionine, and their contents were significantly higher under Se yeast treatments than under selenite treatments. Se(VI) was detected only under selenite treatments. Se yeast and selenite had different influences on soluble sugar, soluble protein, vitamin C and free amino acid contents in broccoli florets. The total phenolic acid and glucosinolate contents were substantially increased by Se yeast and selenite, although the total flavonoid content was reduced by Se yeast. Tests on antioxidant enzyme activities revealed that several antioxidant enzymes (catalase, peroxidase, superoxide dismutase and glutathione peroxidase) responded to Se yeast and selenite treatments. CONCLUSION: Se yeast is preferred over selenite for maximizing Se uptake and nutrient accumulation in Se-rich broccoli cultivation. However, an extremely high Se content in broccoli florets cannot be directly consumed by humans, although they can be processed into Se supplements. © 2021 Society of Chemical Industry.

Exploring the causes for co-pollution of O3 and PM2.5 in summer over North China.

Co-pollution of surface O3 and PM2.5 has become the most predominant type of air pollutions in Beijing-Tianjin-Hebei region in the hot season since 2017, particularly in May-July. Analysis based on observational data showed that co-pollution was always accompanied by high temperature, moderate relative humidity, extremely high SO2, and higher NO2. We also found that the meteorology and precursor dependence of O3 was similar between co-pollution and O3- single pollution. While PM2.5 in co-pollution was more related to temperature, relative humidity, and precursors, that in PM2.5-singe pollution were more related to small winds. These results indicate that co-pollution seemed to be more affected by atmospheric chemistry. According to the PM2.5 components, secondary inorganic aerosols (SIA) composed 44.3-48.7% of PM2.5 in co-pollution, while those accounting for 42.1-46.5% and 41.2-44.3%, respectively, in O3- and PM2.5-single pollution, which further confirmed the relatively stronger atmospheric chemistry processes in co-pollution. And the high proportion of SIA in co-pollution was mainly attributed to SO42-, which was observed to rapidly boom in non-refractory submicron aerosol (NR-PM1) on the condition of high level of O3 at daytime. Additionally, we further explored the interactions of O3 and PM2.5 in co-pollution. It was found that most (~61.9%) co-pollution episodes were initiated by high O3 at daytime; while for other episodes, high PM2.5 firstly occurred under the more stable meteorological conditions, and then accumulation of precursors further induced high O3. A higher SIA concentration was observed in O3-initiated co-pollution, indicating that the atmospheric oxidation in co-pollution caused by chemical processes was stronger than that by physical processes, which was further approved by the higher values of SOR and NOR in O3-initiated co-pollution. This observational study revealed that controlling O3 and precursor SO2 is the key to abating co-pollution in the hot season.

Temporal and spatial characteristics of PM2.5 transport fluxes of typical inland and coastal cities in China.

Local pollution and the cross-boundary transmission of pollutants between cities have an inevitable impact on the atmosphere. Quantitative assessments of the contribution of transport to pollution in inland and coastal cities are necessary for the implementation of practical, regional, and joint emission control strategies. In this study, the Comprehensive Air Quality Model (CAMx), together with the Weather Research and Forecasting model (WRF), was used to simulate the contributions to pollution of different cities in 2016. The monthly inflow, outflow, and net flux from the ground to the extended layers served as the three main indicators for the analysis of the interactions of PM2.5 transport between adjacent cities. Between inland and coastal cities, the magnitude of inflow and outflow are larger in the former than in the latter. The inflow flux in the inland cities (Beijing and Shijiazhuang) was 10.6 and 10.7 kt/day, respectively, while that in the coastal cities (Tianjin, Shanghai, Hefei, Nanjing, and Hangzhou) was 9.1, 3.3, 5.8, 4.4, and 3.7 kt/day, respectively. In terms of variation over the year, the strongest inflow in the BTH region occurred in April, followed by October, July, and January, while that in the coastal cities in YRD occurred in January, followed by October, April, and July. Therefore, based on the flux intensity calculations and the transport flux pathways, effective joint control measures can be provided with scientific support, and a better understanding of the evolutionary mechanism among inland and coastal cities can be acquired.

Integration analysis of PacBio SMRT- and Illumina RNA-seq reveals candidate genes and pathway involved in selenium metabolism in hyperaccumulator Cardamine violifolia.

BACKGROUND: Cardamine violifolia, native to China, is one of the selenium (Se) hyperaccumulators. The mechanism of Se metabolism and tolerance remains unclear, and only limited genetic information is currently available. Therefore, we combined a PacBio single-molecule real-time (SMRT) transcriptome library and the Illumina RNA-seq data of sodium selenate (Na2SeO4)-treated C. violifolia to further reveal the molecular mechanism of Se metabolism. RESULTS: The concentrations of the total, inorganic, and organic Se in C. violifolia seedlings significantly increased as the Na2SeO4 treatment concentration increased. From SMRT full-length transcriptome of C. violifolia, we obtained 26,745 annotated nonredundant transcripts, 14,269 simple sequence repeats, 283 alternative splices, and 3407 transcription factors. Fifty-one genes from 134 transcripts were identified to be involved in Se metabolism, including transporter, assimilatory enzyme, and several specific genes. Analysis of Illumina RNA-Seq data showed that a total of 948 differentially expressed genes (DEGs) were filtered from the four groups with Na2SeO4 treatment, among which 11 DEGs were related to Se metabolism. The enrichment analysis of KEGG pathways of all the DEGs showed that they were significantly enriched in five pathways, such as hormone signal transduction and plant-pathogen interaction pathways. Four genes related to Se metabolism, adenosine triphosphate sulfurase 1, adenosine 5'-phosphosulfate reductase 3, cysteine (Cys) desulfurase 1, and serine acetyltransferase 2, were regulated by lncRNAs. Twenty potential hub genes (e.g., sulfate transporter 1;1, Cys synthase, methionine gamma-lyase, and Se-binding protein 1) were screened and identified to play important roles in Se accumulation and tolerance in C. violifolia as concluded by weighted gene correlation network analysis. Based on combinative analysis of expression profiling and annotation of genes as well as Se speciation and concentration in C. violifolia under the treatments with different Na2SeO4 concentrations, a putative Se metabolism and assimilation pathway in C. violifolia was proposed. CONCLUSION: Our data provide abundant information on putative gene transcriptions and pathway involved in Se metabolism of C. violifolia. The findings present a genetic resource and provide novel insights into the mechanism of Se hyperaccumulation in C. violifolia.

Screening and identification of miRNAs related to sexual differentiation of strobili in Ginkgo biloba by integration analysis of small RNA, RNA, and degradome sequencing.

BACKGROUND: Ginkgo biloba, a typical dioecious plant, is a traditional medicinal plant widely planted. However, it has a long juvenile period, which severely affected the breeding and cultivation of superior ginkgo varieties. RESULTS: In order to clarify the complex mechanism of sexual differentiation in G. biloba strobili. Here, a total of 3293 miRNAs were identified in buds and strobili of G. biloba, including 1085 known miRNAs and 2208 novel miRNAs using the three sequencing approaches of transcriptome, small RNA, and degradome. Comparative transcriptome analysis screened 4346 and 7087 differentially expressed genes (DEGs) in male buds (MB) _vs_ female buds (FB) and microstrobilus (MS) _vs_ ovulate strobilus (OS), respectively. A total of 6032 target genes were predicted for differentially expressed miRNA. The combined analysis of both small RNA and transcriptome datasets identified 51 miRNA-mRNA interaction pairs that may be involved in the process of G. biloba strobili sexual differentiation, of which 15 pairs were verified in the analysis of degradome sequencing. CONCLUSIONS: The comprehensive analysis of the small RNA, RNA and degradome sequencing data in this study provided candidate genes and clarified the regulatory mechanism of sexual differentiation of G. biloba strobili from multiple perspectives.

Effects of different exogenous selenium on Se accumulation, nutrition quality, elements uptake, and antioxidant response in the hyperaccumulation plant Cardamine violifolia.

Cardamine violifolia (Brassicaceae) is a novel selenium(Se) hyperaccumulation plant with rich nutrients, and serves as a good source of special vegetables in Enshi, China. The present study aimed to investigate the effects of the application of selenate, selenite, and Se yeast (50-800 mg/L) on the growth, Se accumulation, nutrient uptake, and antioxidant response of C. violifolia. The results showed that the Se accumulation efficiency was selenate > selenite > Se yeast, the maximum Se concentration could achieve over 7000 mg/kg, and about 90% was organic Se. The major Se speciation found was mainly SeCys2 and the proportion of various Se species were affected by the Se forms and concentrations. Besides, the plant growth, nutrition quality indexes, element uptakes, and antioxidant responses indicated that 200 mg/L selenate was optimum for C. violifolia to accumulate Se without much impacts, while to obtain more proportion of organic Se, 200 mg/L selenite might be a better choice.

Adsorption performance of CMK-3 and C-FDU-15 in NO removal at low temperature.

CMK-3 and C-FDU-15 samples were synthesized using hard-templating and evaporation-induced self-assembly (EISA) methods, respectively. The pore structures of CMK-3 and C-FDU-15 as well as commercial activated carbon were characterized by means of X-ray diffraction, field emission scanning electron microscopy, transmission electron microscopy, and N2 adsorption-desorption. Adsorption of NO was investigated by means of thermogravimetric analysis, temperature-programmed desorption of NO + O2, and in situ diffuse reflectance Fourier transform infrared spectroscopy. The results show that the CMK-3 and C-FDU-15 materials possessed ordered and uniform structures. The co-adsorption capacity of NO and O2 decreased in the sequence CMK-3 (88.6 mg/g) > C-FDU-15 (71.7 mg/g) > AC (25.3 mg/g). There were two main adsorption species on CMK-3 and C-FDU-15: nitrite and nitrate. Nitrite is converted to nitrate easily. However, the adsorption species were more complex on AC, with nitrite being the main species. Moreover, CMK-3 and C-FDU-15 exhibit excellent regeneration efficiency compared with AC. The excellent NO adsorption performance of CMK-3 and C-FDU-15 was associated with their ordered mesoporous structures and high surface areas. The research provides more options for NO adsorption in the future.

Comparative transcriptome analysis revealing the potential mechanism of seed germination stimulated by exogenous gibberellin in Fraxinus hupehensis.

BACKGROUND: Fraxinus hupehensis is an endangered tree species that is endemic to in China; the species has very high commercial value because of its intricate shape and potential to improve and protect the environment. Its seeds show very low germination rates in natural conditions. Preliminary experiments indicated that gibberellin (GA3) effectively stimulated the seed germination of F. hupehensis. However, little is known about the physiological and molecular mechanisms underlying the effect of GA3 on F. hupehensis seed germination. RESULTS: We compared dormant seeds (CK group) and germinated seeds after treatment with water (W group) and GA3 (G group) in terms of seed vigor and several other physiological indicators related to germination, hormone content, and transcriptomics. Results showed that GA3 treatment increases seed vigor, energy requirements, and trans-Zetain (ZT) and GA3 contents but decreases sugar and abscisic acid (ABA) contents. A total of 116,932 unigenes were obtained from F. hupehensis transcriptome. RNA-seq analysis identified 31,856, 33,188 and 2056 differentially expressed genes (DEGs) between the W and CK groups, the G and CK groups, and the G and W groups, respectively. Up-regulation of eight selected DEGs of the glycolytic pathway accelerated the oxidative decomposition of sugar to release energy for germination. Up-regulated genes involved in ZT (two genes) and GA3 (one gene) biosynthesis, ABA degradation pathway (one gene), and ABA signal transduction (two genes) may contribute to seed germination. Two down-regulated genes associated with GA3 signal transduction were also observed in the G group. GA3-regulated genes may alter hormone levels to facilitate germination. Candidate transcription factors played important roles in GA3-promoted F. hupehensis seed germination, and Quantitative Real-time PCR (qRT-PCR) analysis verified the expression patterns of these genes. CONCLUSION: Exogenous GA3 increased the germination rate, vigor, and water absorption rate of F. hupehensis seeds. Our results provide novel insights into the transcriptional regulation mechanism of effect of exogenous GA3 on F. hupehensis seed germination. The transcriptome data generated in this study may be used for further molecular research on this unique species.