Synergistic regulation at physiological, transcriptional and metabolic levels in tomato plants subjected to a combination of salt and heat stress.

With global warming and climate change, abiotic stresses often simultaneously occur. Combined salt and heat stress was a common phenomenon that was severe, particularly in arid/semi-arid lands. We aimed to reveal the systematic responsive mechanisms of tomato genotypes with different salt/heat susceptibilities to combined salt and heat stress. Morphological and physiological responses of salt-tolerant/sensitive and heat-tolerant/sensitive tomatoes at control, heat, salt and combined stress were investigated. Based on leaf Fv /Fm and H2 O2 content, samples from tolerant genotype at the four treatments for 36 h were taken for transcriptomics and metabolomics. We found that plant height, dry weight and net photosynthetic rate decreased while leaf Na+ concentration increased in all four genotypes under salt and combined stress than control. Changes in physiological indicators such as photosynthetic parameters and defence enzyme activities in tomato under combined stress were regulated by the expression of relevant genes and the accumulation of key metabolites. We screened five key pathways in tomato responding to a combination of salt and heat stress, such as oxidative phosphorylation (map00190). Synergistic regulation at morphological, physiological, transcriptional and metabolic levels in tomato plants was induced by combined stress. Heat stress was considered as a dominant stressor for tomato plants under the current combined stress. The oxidative phosphorylation pathway played a key role in tomato in response to combined stress, where tapped key genes (e.g. alternative oxidase, Aox1a) need further functional analysis. Our study will provide a valuable resource important for studying stress combination and improving tomato tolerance.

Effects of freeze-thaw cycles on soil greenhouse gas emissions: A systematic review.

In the context of global warming, increasingly widespread and frequent freezing and thawing cycles (FTCs) will have profound effects on the biogeochemical cycling of soil carbon and nitrogen. FTCs can increase soil greenhouse gas (GHG) emissions by reducing the stability of soil aggregates, promoting the release of dissolved organic carbon, decreasing the number of microorganisms, inducing cell rupture, and releasing carbon and nitrogen nutrients for use by surviving microorganisms. However, the similarity and disparity of the mechanisms potentially contributing to changes in GHGs have not been systematically evaluated. The present study consolidates the most recent findings on the dynamics of soil carbon and nitrogen, as well as GHGs, in relation to FTCs. Additionally, it analyzes the impact of FTCs on soil GHGs in a systematic manner. In this study, particular emphasis is given to the following: (i) the reaction mechanism involved; (ii) variations in soil composition in different types of land (e.g., forest, peatland, farmland, and grassland); (iii) changes in soil structure in response to cycles of freezing temperatures; (iv) alterations in microbial biomass and community structure that may provide further insight into the fluctuations in GHGs after FTCs. The challenges identified included the extension of laboratory-scale research to ecosystem scales, the performance of in-depth investigation of the coupled effects of carbon, nitrogen, and water in the freeze-thaw process, and analysis of the effects of FTCs through the use of integrated research tools. The results of this study can provide a valuable point of reference for future experimental designs and scientific investigations and can also assist in the analysis of the attributes of GHG emissions from soil and the ecological consequences of the factors that influence these emissions in the context of global permafrost warming.

Research progress on degradation of biodegradable micro-nano plastics and its toxic effect mechanism on soil ecosystem.

Biodegradable plastics (BPs) are known to decompose into micro-nano plastics (BMNPs) more readily than conventional plastics (CPs). Given the environmental risks posed by BMNPs in soil ecosystems, their impact has garnered increasing attention. However, research focusing on the toxic effects of BMNPs on soils remains relatively limited. The degradation process and duration of BMNPs in soil are influenced by numerous factors, which directly impact the toxic effects of BMNPs. This highlights the urgent need for further research. In this context, this review delineates the classification of BPs, investigates the degradation processes of BPs along with their influencing factors, summarizes the toxic effects on soil ecosystems, and explores the potential mechanisms that underlie these toxic effects. Finally, it provides an outlook on related research concerning BMNPs in soil. The results indicate that specific BMNPs release additives at a faster rate during decomposition, degradation, and aging, with certain compounds exhibiting increased bioavailability. Importantly, a substantial body of research has shown that BMNPs generally manifest more pronounced toxic effects in comparison to conventional micro-nano plastics (CMNPs). The toxic effects associated with BMNPs encompass a decline in soil quality and microbial biomass, disruption of nutrient cycling, inhibition of plant root growth, and negative impacts on invertebrate reproduction, survival, and fertilization rates. The rough and complex surfaces of BMNPs contribute to increased mechanical damage to tested organisms, enhance absorption by microorganisms, and disrupt normal physiological functions. Notably, the toxic effects of BMNPs on soil ecosystems are influenced by factors including concentration, type of BMNPs, exposure conditions, degradation products, and the nature of additives used. Therefore, it is crucial to standardize detection technologies and toxicity testing conditions for BMNPs. In conclusion, this review provides scientific evidence that supports effective prevention and management of BMNP pollution, assessment of its ecological risks, and governance of BMNPs-related products.

Chromosome-level pepino genome provides insights into genome evolution and anthocyanin biosynthesis in Solanaceae.

Pepino (Solanum muricatum, 2n = 2x = 24), a member of the Solanaceae family, is an important globally grown fruit. Herein, we report high-quality, chromosome-level pepino genomes. The 91.67% genome sequence is anchored to 12 chromosomes, with a total length of 1.20 Gb and scaffold N50 of 87.03 Mb. More than half the genome comprises repetitive sequences. In addition to the shared ancient whole-genome triplication (WGT) event in eudicots, an additional new WGT event was present in the pepino. Our findings suggest that pepinos experienced chromosome rearrangements, fusions, and gene loss after a WGT event. The large number of gene removals indicated the instability of Solanaceae genomes, providing opportunities for species divergence and natural selection. The paucity of disease-resistance genes (NBS) in pepino and eggplant has been explained by extensive loss and limited generation of genes after WGT events in Solanaceae. The outbreak of NBS genes was not synchronized in Solanaceae species, which occurred before the Solanaceae WGT event in pepino, tomato, and tobacco, whereas it was almost synchronized with WGT events in the other four Solanaceae species. Transcriptome and comparative genomic analyses revealed several key genes involved in anthocyanin biosynthesis. Although an extra WGT event occurred in Solanaceae, CHS genes related to anthocyanin biosynthesis in grapes were still significantly expanded compared with those in Solanaceae species. Proximal and tandem duplications contributed to the expansion of CHS genes. In conclusion, the pepino genome and annotation facilitate further research into important gene functions and comparative genomic analysis in Solanaceae.

Chromosome-level wild Hevea brasiliensis genome provides new tools for genomic-assisted breeding and valuable loci to elevate rubber yield.

The rubber tree (Hevea brasiliensis) is grown in tropical regions and is the major source of natural rubber. Using traditional breeding approaches, the latex yield has increased by sixfold in the last century. However, the underlying genetic basis of rubber yield improvement is largely unknown. Here, we present a high-quality, chromosome-level genome sequence of the wild rubber tree, the first report on selection signatures and a genome-wide association study (GWAS) of its yield traits. Population genomic analysis revealed a moderate population divergence between the Wickham clones and wild accessions. Interestingly, it is suggestive that H. brasiliensis and six relatives of the Hevea genus might belong to the same species. The selective sweep analysis found 361 obvious signatures in the domesticated clones associated with 245 genes. In a 15-year field trial, GWAS identified 155 marker-trait associations with latex yield, in which 326 candidate genes were found. Notably, six genes related to sugar transport and metabolism, and four genes related to ethylene biosynthesis and signalling are associated with latex yield. The homozygote frequencies of the causal nonsynonymous SNPs have been greatly increased under selection, which may have contributed to the fast latex yield improvement during the short domestication history. Our study provides insights into the genetic basis of the latex yield trait and has implications for genomic-assisted breeding by offering valuable resources in this new domesticated crop.

The Brassicaceae genome resource (TBGR): A comprehensive genome platform for Brassicaceae plants.

The Brassicaceae is an important plant family. We built a user-friendly, web-based, comparative, and functional genomic database, The Brassicaceae Genome Resource (TBGR, http://www.tbgr.org.cn), based on 82 released genomes from 27 Brassicaceae species. The TBGR database contains a large number of important functional genes, including 4,096 glucosinolate genes, 6,625 auxin genes, 13,805 flowering genes, 36,632 resistance genes, 1,939 anthocyanin genes, and 1,231 m6A genes. A total of 1,174,049 specific guide sequences for clustered regularly interspaced short palindromic repeats and 5,856,479 transposable elements were detected in Brassicaceae. TBGR also provides information on synteny, duplication, and orthologs for 27 Brassicaceae species. The TBGR database contains 1,183,851 gene annotations obtained using the TrEMBL, Swiss-Prot, Nr, GO, and Pfam databases. The BLAST, Synteny, Primer Design, Seq_fetch, and JBrowse tools are provided to help users perform comparative genomic analyses. All the genome assemblies, gene models, annotations, and bioinformatics results can be easily downloaded from the TBGR database. We plan to improve and continuously update the database with newly assembled genomes and comparative genomic studies. We expect the TBGR database to become a key resource for the study of the Brassicaceae.

A Novel C Doped MoS2 /CoP/MoO2 Ternary Heterostructure Nanoflower for Hydrogen Evolution Reaction at Wide pH Range and Efficient Overall Water Splitting in Alkaline Media.

The development of low-cost and high-efficiency bifunctional catalysts is still a challenge for hydrogen production through overall water splitting. This paper reports the in-situ synthesis of C-doped MoS2 /CoP/MoO2 using bacterial cellulose (BC) as the reducing agent and the source of C and using BC (MoS2 /Co1.2 MoO4.2 ⋅ 1.2H2 O/BC) as the template. Heterogeneous structure for hydrogen evolution reaction (HER) and alkaline water electrolysis in a wide pH range. Due to the large number of defect sites caused by C doping and the synergy between these three active components (MoS2 , CoP and MoO2 ), the HER and oxygen evolution reaction (OER) activities of the catalyst have been greatly improved. Therefore, during HER, a small initial overpotential (27 mV) was achieved in 1.0 M KOH. In 0.5 M H2 SO4 , 0.1 M PBS and 1.0 M KOH, the current density reached 10 mA cm-2 at overpotentials of 123.4, 150, and 139 mV, respectively. For OER, an overpotential of 268 mV was required to achieve 10 mA cm-2 . The alkaline two-electrode device composed of C doped MoS2 /CoP/MoO2 delivers 10 mA cm-2 at a low potential of 1.51 V and can be easily driven by a single AA battery. This work provides a new design strategy of C doped ternary heterostructures for electrocatalysis and related energy applications.

Large-scale analysis of trihelix transcription factors reveals their expansion and evolutionary footprint in plants.

The trihelix transcription factor (TTF) gene family is an important class of transcription factors that play key roles in regulating developmental processes and responding to various stresses. To date, no comprehensive analysis of the TTF gene family in large-scale species has been performed. A cross-genome exploration of its origin, copy number variation, and expression pattern in plants is also unavailable. Here, we identified and characterized the TTF gene family in 110 species representing typical plant phylogenetic taxa. Interestingly, we found that the number of TTF genes was significantly expanded in Chara braunii compared to other species. Based on the available plant genomic datasets, our comparative analysis suggested that the TTF gene family likely originated from the GT-1-1 group and then expanded to form other groups through duplication or deletion of some domains. We found evidence that whole-genome duplication/triplication contributed most to the expansion of the TTF gene family in dicots, monocots and basal angiosperms. In contrast, dispersed and proximal duplications contributed to the expansion of the TTF gene family in algae and bryophyta. The expression patterns of TTF genes and their upstream and downstream genes in different treatments showed a functional divergence of TTF-related genes. Furthermore, we constructed the interaction network between TTF genes and the corresponding upstream and downstream genes, providing a blueprint for their regulatory pathways. This study provided a cross-genome comparative analysis of TTF genes in 110 species, which contributed to understanding their copy number expansion and evolutionary footprint in plants.

The evolution of N6-methyladenosine regulators in plants.

As a reversible modification, N6-methyladenosine (m6A) plays key roles in series of biological processes. Although it has been found that m6A modification is regulated by writers, erasers and readers, their evolutionary processes are still not clearly and systematically described. In the present work, we identified 1592 m6A modification regulators from 65 representative plant species and performed the phylogenetic relationships, sequence structure, selection pressure, and codon usage analysis across species. The regulators from different species or subfamilies were distinguishable based on the phylogenetic trees. Although the gene structure was structurally and functionally conserved for each kind of regulators, the unique exon/intron structures and motif organizations were observed among different families. The selection pressure analysis demonstrated that the regulators experienced purifying selection. Interestingly, the selection pressure for the regulators in higher plants was more relaxed, indicating that they might have acquired new functions during evolution. In addition, the different codon usage preferences were observed for the different kinds of m6A modification regulators. These results will not only facilitate our understanding of the evolution of m6A regulators, but also shed light on how the evolutionary differences affect their functional divergence.

The high fluorescence sensitivity property and quenching mechanism of one-dimensional Cd-HCIA-1 sensor for nitrobenzene.

The sensing of nitroaromatic compounds in aqueous solution is closely related to environmental sustainability and human health. In this study, a novel Cd(II) coordination polymer (Cd-HCIA-1) was designed and prepared, and its crystal structure, luminescence performance, detection of nitro pollutants in water, and fluorescence quenching mechanisms were studied. Cd-HCIA-1 exhibited a one-dimensional ladder-like chain based on a T-shape ligand of 5-((4-carboxybenzyl) oxy) isophthalic acid (5-H3CIA). The H-bonds and π-π stacking interactions were then used to construct the supramolecular skeleton in common. Luminescence studies revealed that Cd-HCIA-1 can detect nitrobenzene (NB) in aqueous solution with high sensitivity and selectivity, and the limit of detection was 3.03 × 10-9 mol L-1. The fluorescence quenching mechanism of the photo-induced electron transfer for NB by Cd-HCIA-1 was obtained through an investigation of the pore structure, density of states, excitation energy, orbital interactions, hole-electron analysis, charge transfer, and electron transfer spectra by using density functional theory (DFT) and time-dependent DFT methods. NB was absorbed in the pore, π-π stacking increased the orbital overlap, and the LUMO was mainly composed of NB fragments. The charge transfer between ligands was blocked, resulting in fluorescence quenching. This study on fluorescence quenching mechanisms can be used to develop efficient explosive sensors.

Multistable dynamics and attractors self-reproducing in a new hyperchaotic complex Lü system.

Multistable dynamics analysis of complex chaotic systems is an important problem in the field of chaotic communication security. In this paper, a new hyperchaotic complex Lü system is proposed and its basic dynamics are analyzed. Owing to the introduction of complex variables, the new system has some structurally distinctive attractors, such as flower-shaped and airfoil-shaped attractors. In addition, the evolution process of the limit cycle is also investigated. Next, the multistable coexistence behavior of the system is researched by the method of attraction basins, and the coexistence behavior of two types of hyperchaotic attractors and one type of chaotic and periodic attractors of the system are analyzed. The coexisting hyperchaotic attractors also show flower and airfoil shapes, and four types of coexistence flower-shaped attractors with different structures are perfectly explored. Moreover, the variation of coexistence attractors in the plane and space with parameters is discussed. Then, by introducing a specific piecewise function determined by a two-element method into the new high-dimensional system, the self-reproduction of the attractor can be realized to generate the multistability, and the general steps of attractors self-reproducing in the higher dimensional system are given. Finally, the circuit design of the new system is implemented, which lays a foundation for the application of complex chaotic systems.

Metasurface Enabled Photothermoelectric Photoresponse of Semimetal Cd3As2 for Broadband Photodetection.

The artificial engineering of photoresponse is crucial for optoelectronic applications, especially for photodetectors. Here, we designed and fabricated a metasurface on a semimetallic Cd3As2 nanoplate to improve its thermoelectric photoresponse. The metasurface can enhance light absorption, resulting in a temperature gradient. This temperature gradient can contribute to thermoelectric photoresponse through the photothermoelectric effect. Furthermore, power-dependent measurements showed a linearly dependent photoresponse of the Cd3As2 metasurface device, indicating a second-order photocurrent response. Wavelength-dependent measurements showed that the metasurface can efficiently separate photoexcited carriers in the broadband range of 488 nm to 4 µm. The photoresponse near the metasurface boundaries exhibits a responsivity of ∼1 mA/W, which is higher than that near the electrode junctions. Moreover, the designed metasurface device provided an anisotropic polarization-dependent photoresponse rather than the isotropic photoresponse of the original Cd3As2 device. This study demonstrates that metasurfaces have excellent potential for artificial controllable photothermoelectric photoresponse of various semimetallic materials.

Integrated Transcriptome and Proteome Analysis Revealed the Regulatory Mechanism of Hypocotyl Elongation in Pakchoi.

Hypocotyl length is a critical determinant for the efficiency of mechanical harvesting in pakchoi production, but the knowledge on the molecular regulation of hypocotyl growth is very limited. Here, we report a spontaneous mutant of pakchoi, lhy7.1, and identified its characteristics. We found that it has an elongated hypocotyl phenotype compared to the wild type caused by the longitudinal growth of hypocotyl cells. Different light quality treatments, transcriptome, and proteomic analyses were performed to reveal the molecular mechanisms of hypocotyl elongation. The data showed that the hypocotyl length of lhy7.1 was significantly longer than that of WT under red, blue, and white lights but there was no significant difference under dark conditions. Furthermore, we used transcriptome and label-free proteome analyses to investigate differences in gene and protein expression levels between lhy7.1 and WT. At the transcript level, 4568 differentially expressed genes (DEGs) were identified, which were mainly enriched in "plant hormone signal transduction", "photosynthesis", "photosynthesis-antenna proteins", and "carbon fixation in photosynthetic organisms" pathways. At the protein level, 1007 differentially expressed proteins (DEPs) were identified and were mainly enriched in photosynthesis-related pathways. The comprehensive transcriptome and proteome analyses revealed a regulatory network of hypocotyl elongation involving plant hormone signal transduction and photosynthesis-related pathways. The findings of this study help elucidate the regulatory mechanisms of hypocotyl elongation in lhy7.1.

CFVisual: an interactive desktop platform for drawing gene structure and protein architecture.

BACKGROUND: When researchers perform gene family analysis, they often analyze the structural characteristics of the gene, such as the distribution of introns and exons. At the same time, characteristic structural analysis of amino acid sequence is also essential, for example, motif and domain features. Researchers often integrate these analyses into one image to dig out more information, but the tools responsible for this integration are lacking. RESULTS: Here, we developed a tool (CFVisual) for drawing gene structure and protein architecture. CFVisual can draw the phylogenetic tree, gene structure, and protein architecture in one picture, and has rich interactive capabilities, which can meet the work needs of researchers. Furthermore, it also supports arbitrary stitching of the above analysis images. It has become a useful helper in gene family analysis. The CFVisual package was implemented in Python and is freely available from https://github.com/ChenHuilong1223/CFVisual/ . CONCLUSION: CFVisual has been used by some researchers and cited by some articles. In the future, CFVisual will continue to serve as a good helper for researchers in the study of gene structure and protein architecture.

Evolutionary analysis and functional characterization of BZR1 gene family in celery revealed their conserved roles in brassinosteroid signaling.

BACKGROUND: Brassinosteroids (BRs) are a group of essential steroid hormones involved in diverse developmental and physiological processes in plants. The Brassinazole-resistant 1 (BZR1) transcription factors are key components of BR signaling and integrate a wide range of internal and environmental signals to coordinate plant development, growth, and resistance to abiotic and biotic stresses. Although the BZR1 family has been fully studied in Arabidopsis, celery BZR1 family genes remain largely unknown. RESULTS: Nine BZR1 genes were identified in the celery genome, and categorized into four classes based on phylogenetic and gene structure analyses. All the BZR1 proteins shared a typical bHLH (basic helix-loop-helix) domain that is highly conserved across the whole family in Arabidopsis, grape, lettuce, ginseng, and three Apiaceae species. Both duplications and losses of the BZR1 gene family were detected during the shaping of the celery genome. Whole-genome duplication (WGD) or segmental duplication contributed 55.56% of the BZR1 genes expansion, and the γ as well as celery-ω polyploidization events made a considerable contribution to the production of the BZR1 paralogs in celery. Four AgBZR1 members (AgBZR1.1, AgBZR1.3, AgBZR1.5, and AgBZR1.9), which were localized both in the nucleus and cytoplasm, exhibit transcription activation activity in yeast. AgBZR1.5 overexpression transgenic plants in Arabidopsis showed curled leaves with bent, long petioles and constitutive BR-responsive phenotypes. Furthermore, the AgBZR1 genes possessed divergent expression patterns with some overlaps in roots, petioles, and leaves, suggesting an extensive involvement of AgBZR1s in the developmental processes in celery with both functional redundancy and divergence. CONCLUSIONS: Our results not only demonstrated that AgBZR1 played a conserved role in BR signaling but also suggested that AgBZR1 might be extensively involved in plant developmental processes in celery. The findings lay the foundation for further study on the molecular mechanism of the AgBZR1s in regulating the agronomic traits and environmental adaptation of celery, and provide insights for future BR-related genetic breeding of celery and other Apiaceae crops.

Associations of ultrafine and fine particles with childhood emergency room visits for respiratory diseases in a megacity.

BACKGROUND: Ambient fine particulate matter with aerodynamic diameter less than 2.5 µm (PM2.5) has been associated with deteriorated respiratory health, but evidence on particles in smaller sizes and childhood respiratory health has been limited. METHODS: We collected time-series data on daily respiratory emergency room visits (ERVs) among children under 14 years old in Beijing, China, during 2015-2017. Concurrently, size-fractioned number concentrations of particles in size ranges of 5-560 nm (PNC5-560) and mass concentrations of PM2.5, black carbon (BC) and nitrogen dioxide (NO2) were measured from a fixed-location monitoring station in the urban area of Beijing. Confounder-adjusted Poisson regression models were used to estimate excessive risks (ERs) of particle size fractions on childhood respiratory ERVs, and positive matrix factorisation models were applied to apportion the sources of PNC5-560. RESULTS: Among the 136 925 cases of all-respiratory ERVs, increased risks were associated with IQR increases in PNC25-100 (ER=5.4%, 95% CI 2.4% to 8.6%), PNC100-560 (4.9%, 95% CI 2.5% to 7.3%) and PM2.5 (1.3%, 95% CI 0.1% to 2.5%) at current and 1 prior days (lag0-1). Major sources of PNC5-560 were identified, including nucleation (36.5%), gasoline vehicle emissions (27.9%), diesel vehicle emissions (18.9%) and secondary aerosols (10.6%). Emissions from gasoline and diesel vehicles were found of significant associations with all-respiratory ERVs, with increased ERs of 6.0% (95% CI 2.5% to 9.7%) and 4.4% (95% CI 1.7% to 7.1%) at lag0-1 days, respectively. Exposures to other traffic-related pollutants (BC and NO2) were also associated with increased respiratory ERVs. CONCLUSION: Our findings suggest that exposures to higher levels of PNC5-560 from traffic emissions could be attributed to increased childhood respiratory morbidity, which supports traffic emission control priority in urban areas.

High-quality ice plant reference genome analysis provides insights into genome evolution and allows exploration of genes involved in the transition from C3 to CAM pathways.

Ice plant (Mesembryanthemum crystallinum), a member of the Aizoaceae family, is a typical halophyte crop and a model plant for studying the mechanism of transition from C3 photosynthesis to crassulacean acid metabolism (CAM). Here, we report a high-quality chromosome-level ice plant genome sequence. This 98.05% genome sequence is anchored to nine chromosomes, with a total length of 377.97 Mb and an N50 scaffold of 40.45 Mb. Almost half of the genome (48.04%) is composed of repetitive sequences, and 24 234 genes have been annotated. Subsequent to the ancient whole-genome triplication (WGT) that occurred in eudicots, there has been no recent whole-genome duplication (WGD) or WGT in ice plants. However, we detected a novel WGT event that occurred in the same order in Simmondsia chinensis, which was previously overlooked. Our findings revealed that ice plants have undergone chromosome rearrangements and gene removal during evolution. Combined with transcriptome and comparative genomic data and expression verification, we identified several key genes involved in the CAM pathway and constructed a comprehensive network. As the first genome of the Aizoaceae family to be released, this report will provide a rich data resource for comparative and functional genomic studies of Aizoaceae, especially for studies on salt tolerance and C3-to-CAM transitions to improve crop yield and resistance.

Brassica carinata genome characterization clarifies U's triangle model of evolution and polyploidy in Brassica.

Ethiopian mustard (Brassica carinata) in the Brassicaceae family possesses many excellent agronomic traits. Here, the high-quality genome sequence of B. carinata is reported. Characterization revealed a genome anchored to 17 chromosomes with a total length of 1.087 Gb and an N50 scaffold length of 60 Mb. Repetitive sequences account for approximately 634 Mb or 58.34% of the B. carinata genome. Notably, 51.91% of 97,149 genes are confined to the terminal 20% of chromosomes as a result of the expansion of repeats in pericentromeric regions. Brassica carinata shares one whole-genome triplication event with the five other species in U's triangle, a classic model of evolution and polyploidy in Brassica. Brassica carinata was deduced to have formed ∼0.047 Mya, which is slightly earlier than B. napus but later than B. juncea. Our analysis indicated that the relationship between the two subgenomes (BcaB and BcaC) is greater than that between other two tetraploid subgenomes (BjuB and BnaC) and their respective diploid parents. RNA-seq datasets and comparative genomic analysis were used to identify several key genes in pathways regulating disease resistance and glucosinolate metabolism. Further analyses revealed that genome triplication and tandem duplication played important roles in the expansion of those genes in Brassica species. With the genome sequencing of B. carinata completed, the genomes of all six Brassica species in U's triangle are now resolved. The data obtained from genome sequencing, transcriptome analysis, and comparative genomic efforts in this study provide valuable insights into the genome evolution of the six Brassica species in U's triangle.

Salinity, waterlogging, and elevated [CO2] interact to induce complex responses in cultivated and wild tomato.

The effects of individual climatic factors on crops are well documented, whereas the interaction of such factors in combination has received less attention. The frequency of salinity and waterlogging stress is increasing with climate change, accompanied by elevated CO2 concentration (e[CO2]). This study explored how these three variables interacted and affected two tomato genotypes. Cultivated and wild tomato (Solanum lycopersicum and Solanum pimpinellifolium) were grown at ambient [CO2] and e[CO2], and subjected to salinity, waterlogging, and combined stress. Leaf photosynthesis, chlorophyll fluorescence, quenching analysis, pigment, and plant growth were analyzed. The response of tomatoes depended on both genotype and stress type. In cultivated tomato, photosynthesis was inhibited by salinity and combined stress, whereas in wild tomato, both salinity and waterlogging stress, alone and in combination, decreased photosynthesis. e[CO2] increased photosynthesis and biomass of cultivated tomato under salinity and combined stress compared with ambient [CO2]. Differences between tomato genotypes in response to individual and combined stress were observed in key photosynthetic and growth parameters. Hierarchical clustering and principal component analysis revealed genetic variations of tomatoes responding to the three climatic factors. Understanding the interacting effects of salinity and waterlogging with e[CO2] in tomato will facilitate improvement of crop resilience to climate change.

Combustion-Derived Particulate PAHs Associated with Small Airway Dysfunction in Elderly Patients with COPD.

Evidence of the respiratory effects of ambient organic aerosols (e.g., polycyclic aromatic hydrocarbons, PAHs) among patients with chronic diseases is limited. We aimed to assess whether exposure to ambient particle-bound PAHs could worsen small airway functions in patients with chronic obstructive pulmonary disease (COPD) and elucidate the underlying mechanisms involved. Forty-five COPD patients were recruited with four repeated visits in 2014-2015 in Beijing, China. Parameters of pulmonary function and pulmonary/systemic inflammation and oxidative stress were measured at each visit. Linear mixed-effect models were performed to evaluate the associations between PAHs and measurements. In this study, participants experienced an average PAH level of 61.7 ng/m3. Interquartile range increases in exposure to particulate PAHs at prior up to 7 days were associated with reduced small airway functions, namely, decreases of 17.7-35.5% in forced maximal mid-expiratory flow. Higher levels of particulate PAHs were also associated with heightened lung injury and inflammation and oxidative stress. Stronger overall effects were found for PAHs from traffic emissions and coal burning. Exposure to ambient particulate PAHs was capable of impairing small airway functions in elderly patients with COPD, potentially via inflammation and oxidative stress. These findings highlight the importance of control efforts on organic particulate matter from fossil fuel combustion emissions.