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Strawberries are mainly propagated by stolons, which can be divided into monopodial and sympodial types. Monopodial stolons consistently produce ramets at each node following the initial single dormant bud, whereas sympodial stolons develop a dormant bud before each ramet. Sympodial stolon encompasses both dormant buds and ramet buds, making it suitable for studying the formation mechanism of different stolon types. In this study, we utilized sympodial stolons from Fragaria nilgerrensis as materials and explored the mechanisms underlying sympodial stolon development through transcriptomic and phytohormonal analyses. The transcriptome results unveiled that auxin, cytokinin, and sugars likely act as main regulators. Endogenous hormone analysis revealed that the inactivation of auxin could influence bud dormancy. Exogenous cytokinin application primarily induced dormant buds to develop into secondary stolons, with the proportion of ramet formation being very low, less than 10%. Furthermore, weighted gene co-expression network analysis identified key genes involved in ramet formation, including auxin transport and response genes, the cytokinin activation gene LOG1, and glucose transport genes SWEET1 and SFP2. Consistently, in vitro cultivation experiments confirmed that glucose enhances the transition of dormant buds into ramets within two days. Collectively, cytokinin and glucose act as dormant breakers, with cytokinin mainly driving secondary stolon formation and glucose promoting ramet generation. This study improved our understanding of stolon patterning and bud development in the sympodial stolon of strawberries.

Hawthorns are important medicinal and edible plants with a long history of health protection in China. Besides cultivated hawthorn, other wild hawthorns may also have excellent medicinal and edible value, such as Crataegus chungtienensis, an endemic species distributed in the Southwest of China. In this study, by integrating the flavor-related metabolome and transcriptome data of the ripening fruit of C. chungtienensis, we have developed an understanding of the formation of hawthorn fruit quality. The results show that a total of 849 metabolites were detected in the young and mature fruit of C. chungtienensis, of which flavonoids were the most detected metabolites. Among the differentially accumulated metabolites, stachyose, maltotetraose and cis-aconitic acid were significantly increased during fruit ripening, and these may be important metabolites affecting fruit flavor change. Moreover, several flavonoids and terpenoids were reduced after fruit ripening compared with young fruit. Therefore, using the unripe fruit of C. chungtienensis may allow us to obtain more medicinal active ingredients such as flavonoids and terpenoids. Furthermore, we screened out some differentially expressed genes (DEGs) related to fruit quality formation, which had important relationships with differentially accumulated sugars, acids, flavonoids and terpenoids. Our study provides new insights into flavor formation in wild hawthorn during fruit development and ripening, and at the same time this study lays the foundation for the improvement of hawthorn fruit flavor.

Abstract Background Fragaria nilgerrensis, which is a diploid wild strawberry with excellent drought-resistance, would provide useful candidate genes for improving drought resistance of cultivated strawberry. So far, its molecular regulatory networks involved in drought stress are unclear. We therefore investigated the drought response regulatory networks of F. nilgerrensis based on the integrated analysis of DNA methylation, transcriptome and physiological traits during four time points under drought stress. Results The most differentially expressed genes and the physiological changes were found at 8 days (T8) compared with 0 day (T0, control). Methylome analysis revealed slight dynamic changes in genome-wide mC levels under drought conditions, while the most hypomethylated and hypermethylated regions were identified at T4 and T8. Association analysis of the methylome and transcriptome revealed that unexpressed genes exhibited expected hypermethylation levels in mCHG and mCHH contexts, and highly expressed genes exhibited corresponding hypomethylation levels in the gene body, but mCG contexts showed the opposite trend. Then, 835 differentially methylated and expressed genes were identified and grouped into four clustering patterns to characterize their functions. The genes with either negative or positive correlation between methylation and gene expression were mainly associated with kinases, Reactive Oxygen Species (ROS) synthesis, scavenging, and the abscisic acid (ABA) signal pathway. Consistently, weighted gene co-expression network analysis (WGCNA) revealed Hub genes including NCED, CYP707A2, PP2Cs and others that play important roles in the ABA signaling pathway. Conclusion F. nilgerrensis drought is dominated by ABA-dependent pathways, possibly accompanied by ABA-independent crosstalk. DNA methylation may affect gene expression, but their correlation was more subtle and multiple types of association exist. Maintaining the balance between ROS regeneration and scavenging is an important factor in drought resistance in F. nilgerrensis. These results deepen our understanding of drought resistance and its application in breeding in strawberry plants.

Abstract Background Understanding how organisms evolve and adapt to extreme habitats is of crucial importance in evolutionary ecology. Altitude gradients are an important determinant of the distribution pattern and range of organisms due to distinct climate conditions at different altitudes. High-altitude regions often provide extreme environments including low temperature and oxygen concentration, poor soil, and strong levels of ultraviolet radiation, leading to very few plant species being able to populate elevation ranges greater than 4000 m. Field pennycress (Thlaspi arvense) is a valuable oilseed crop and emerging model plant distributed across an elevation range of nearly 4500 m. Here, we generate an improved genome assembly to understand how this species adapts to such different environments. Results We sequenced and assembled de novo the chromosome-level pennycress genome of 527.3 Mb encoding 31,596 genes. Phylogenomic analyses based on 2495 single-copy genes revealed that pennycress is closely related to Eutrema salsugineum (estimated divergence 14.32–18.58 Mya), and both species form a sister clade to Schrenkiella parvula and genus Brassica. Field pennycress contains the highest percentage (70.19%) of transposable elements in all reported genomes of Brassicaceae, with the retrotransposon proliferation in the Middle Pleistocene being likely responsible for the expansion of genome size. Moreover, our analysis of 40 field pennycress samples in two high- and two low-elevation populations detected 1,256,971 high-quality single nucleotide polymorphisms. Using three complementary selection tests, we detected 130 candidate naturally selected genes in the Qinghai-Tibet Plateau (QTP) populations, some of which are involved in DNA repair and the ubiquitin system and potential candidates involved in high-altitude adaptation. Notably, we detected a single base mutation causing loss-of-function of the FLOWERING LOCUS C protein, responsible for the transition to early flowering in high-elevation populations. Conclusions Our results provide a genome-wide perspective of how plants adapt to distinct environmental conditions across extreme elevation differences and the potential for further follow-up research with extensive data from additional populations and species.

Transgenerational plasticity (TGP) occurs when maternal environments influence the expression of traits in offspring, and in some cases may increase fitness of offspring and have evolutionary significance. However, little is known about the extent of maternal environment influence on gene expression of offspring, and its relationship with trait variations across generations. In this study, we examined TGP in the traits and gene expression of field pennycress (Thlaspi arvense) in response to cadmium (Cd) stress. In the first generation, along with the increase of soil Cd concentration, the total biomass, individual height, and number of seeds significantly decreased, whereas time to flowering, superoxide dismutase (SOD) activity, and content of reduced glutathione significantly increased. Among these traits, only SOD activity showed a significant effect of TGP; the offspring of Cd-treated individuals maintained high SOD activity in the absence of Cd stress. According to the results of RNA sequencing and bioinformatic analysis, 10,028 transcripts were identified as Cd-responsive genes. Among them, only 401 were identified as transcriptional memory genes (TMGs) that maintained the same expression pattern under normal conditions in the second generation as in Cd-treated parents in the first generation. These genes mainly participated in Cd tolerance-related processes such as response to oxidative stress, cell wall biogenesis, and the abscisic acid signaling pathways. The results of weighted correlation network analysis showed that modules correlated with SOD activity recruited more TMGs than modules correlated with other traits. The SOD-coding gene CSD2 was found in one of the modules correlated with SOD activity. Furthermore, several TMGs co-expressed with CSD2 were hub genes that were highly connected to other nodes and critical to the network’s topology; therefore, recruitment of TMGs in offspring was potentially related to TGP. These findings indicated that, across generations, transcriptional memory of gene expression played an important role in TGP. Moreover, these results provided new insights into the trait evolution processes mediated by phenotypic plasticity.

Research highlights: Ecological policies must balance ecosystem protection by promoting the sustainable livelihoods of farmers living in or near protected areas; however, the intrinsic motivations of farmers to adopt green production behaviors (GPBs) are poorly understood. Background and objectives: We explored how ecological policies affect the GPBs of farmers in agroforestry. Materials and methods: We conducted questionnaires of farmers in 11 counties of Sichuan Province, China, with abundant protected areas and large-scale agroforestry, after which a structural equation model of farmers’ ecological awareness, policy perception, and GPBs was constructed. Results: (1) Ecological policies can stimulate farmers’ GPBs by improving their ecological awareness, creating positive subjective norms, and inducing the “herd effect”. Increases in protection intensity and scope amplify the pressures on farmers to maintain more than long-term policy consistency. (2) Green production is more time-consuming, laborious, expensive, and difficult to learn compared with traditional production methods, which have somewhat limited GPBs adoption. (3) In the rural “acquaintance society”, information and communication from others have a substantial impact on farmers’ perceptions, attitudes, and behaviors; thus, positive subjective norms from formal and informal channels could promote GPB adoption. Conclusions: Future policies should prioritize environmental education over environmental publicity by helping farmers understand the long-term relationship between ecological protection and economic development, teaching individual environmental responsibility, enhancing positive feedback to farmers who adopt GPBs, actively exploring mechanisms for realizing the value of ecological products, and improving farmers’ management skills and learning ability.

Tissue culture is an important tool for asexual propagation and genetic transformation of strawberry plants. In plant tissue culture, variation of DNA methylation is a potential source of phenotypic variation in regenerated plants. However, the genome wide dynamic methylation patterns of strawberry tissue culture remain unclear. In this study, we used whole-genome bisulfite sequencing (WGBS) to study genomic DNA methylation changes of a wild strawberry Fragaria nilgerrensis at six stages: from explants of shoot tips to outplanting and acclimation. Global methylation levels showed that CG sites exhibited the highest methylation level in all stages with an average of 49.5%, followed by CHG (33.2%) and CHH (12.4%). Although CHH accounted for the lowest proportion of total cytosine methylation, it showed the most obvious methylation change and the most of these changes occurred in the transposable element regions. The overall methylation levels alternately decreased and increased during the entire tissue culture process and the distribution of DNA methylation was non-uniform among different genetic regions. Furthermore, much more differentially methylated regions (DMRs) were detected in dedifferentiation and redifferentiation stages and most of them were transposable elements, suggesting these processes involved activating or silencing of amounts of transposons. The functional enrichment of the DMR-related genes indicated that genes involved in hormone metabolic processes, plant development and the stress response changed methylation throughout the tissue culture process. Finally, the quantitative real-time PCR (qRT-PCR) was conducted to examine the association of methylation and gene expression of a set of different methylated genes. Our findings give deeper insight into the epigenetic regulation of gene expression during the plant tissue cultures process, which will be useful in the efficient control of somaclonal variations and in crop improvement.

Abstract Cyanobacterial blooms pose serious threats to aquatic organisms and strongly impact the functioning of aquatic ecosystems. Due to their ability to produce a wide range of potentially bioactive secondary metabolites, so called cyanotoxins, cyanobacteria have been extensively studied in the past decades. Proteomic and metabolomic analyses provide a unique opportunity to evaluate the global response of hundreds of proteins and metabolites at a glance. In this study, we provide the first combined utilization of these methods targeted to identify the response of fish to bloom-forming cyanobacteria. Medaka fish (Oryzias latipes) were exposed for 96 hours either to a MC-producing or to a non-MC-producing strain of Microcystis aeruginosa and cellular, proteome and metabolome changes following exposure to cyanobacteria were characterized in the fish livers. The results suggest that a short-term exposure to cyanobacteria, producing or not MCs, induces sex-dependent molecular changes in medaka fish, without causing any cellular alterations. Globally, molecular entities involved in stress response, lipid metabolism and developmental processes exhibit the most contrasted changes following a cyanobacterial exposure. Moreover, it appears that proteomic and metabolomic analyses are useful tools to verify previous information and to additionally bring new horizons concerning molecular effects of cyanobacteria on fish.

With the development of image processing technology and the improvement of unmanned aerial vehicle (UAV) manufacture, it has been becoming a hot research topic to inspect the transmission line's failure. Here, a method of locating the area of insulator strings in the aerial image captured by UAV system is been introduced. At first, the aerial image is converted to HSV colour space model, and the components of H and S are filtered to segment the insulator strings and background areas. Considering some background areas have the similar colour with the insulator string, the result of segmentation will contain some background areas. Then, the image of result is divided into small pieces with non-overlapping windows. The information of texture on each window is used to remove the remaining background area. The outline of the insulator strings in the image can be obtained. It is easily to detect the edge of the insulator string and locate the area of the insulator string using the outline image. At last, some insulator string images have been used to illustrate the processing of the method. Compared with the method using RGB colour space model, the results of method here is effective and reliable.

Multiple closely related species with genomic sequences provide an ideal system for studies on comparative and evolutionary genomics, as well as the mechanism of speciation. The whole genome sequences of six strawberry species (Fragaria) have been released, which provide one of the richest genomic resources of any plant genus. In this study, we first generated seven transcriptome sequences of Fragaria species de novo, with a total of 48,557–82,537 unigenes per species. Combined with 13 other species genomes in Rosales, we reconstructed a phylogenetic tree at the genomic level. The phylogenic tree shows that Fragaria closed grouped with Rubus and the Fragaria clade is divided into three subclades.East Asian species appeared in every subclade, suggesting that the genus originated in this area at ~7.99 Mya. Four species found in mountains of Southwest China originated at ~3.98 Mya, suggesting that rapid speciation occurred to adapt to changing environments following the uplift of the Qinghai–Tibet Plateau. Moreover, we identified 510 very significantly positively selected genes in the cultivated species F. × ananassa genome. This set of genes was enriched in functions related to specific agronomic traits, such as carbon metabolism and plant hormone signal transduction processes, which are directly related to fruit quality and flavor. These findings illustrate comprehensive evolutionary patterns in Fragaria and the genetic basis of fruit domestication of cultivated strawberry at the genomic/transcriptomic level.

Glutathione S-transferases (GSTs) compose a family of multifunctional enzymes that play important roles in the detoxification of xenobiotics and the oxidative stress response. In the present study, twenty four GST genes from the transcriptome of a metal-tolerant dark septate endophyte (DSE), Exophiala pisciphila, were identified based on sequence homology, and their responses to various heavy metal exposures were also analyzed. Phylogenetic analysis showed that the 24 GST genes from E. pisciphila (EpGSTs) were divided into eight distinct classes, including seven cytosolic classes and one mitochondrial metaxin 1-like class. Moreover, the variable expression patterns of these EpGSTs were observed under different heavy metal stresses at their effective concentrations for inhibiting growth by 50% (EC50). Lead (Pb) exposure caused the up-regulation of all EpGSTs, while cadmium (Cd), copper (Cu) and zinc (Zn) treatments led to the significant up-regulation of most of the EpGSTs (p < 0.05 to p < 0.001). Furthermore, although heavy metal-specific differences in performance were observed under various heavy metals in Escherichia coli BL21 (DE3) transformed with EpGSTN-31, the over-expression of this gene was able to enhance the heavy metal tolerance of the host cells. These results indicate that E. Pisciphila harbored a diverse of GST genes and the up-regulated EpGSTs are closely related to the heavy metal tolerance of E. pisciphila. The study represents the first investigation of the GST family in E. pisciphila and provides a primary interpretation of heavy metal detoxification for E. pisciphila.

The worldwide occurrence of cyanobacterial blooms evokes profound concerns. The presence of microcystins (MCs) in waters and aquatic food increases the risk to human health. Some recent studies have suggested that the gonad is the second most important target organ of MCs, however, the potential toxicity mechanisms are still unclear. For a better understanding of reproductive toxicity of MCs on animals, we conducted the present experimental investigation. Male rats were intraperitoneally injected with MC-LR for 50 d with the doses of 1 and 10 µg/kg body weight per day. After prolonged exposure to MC-LR, the testes index significantly decreased in 10 µg/kg group. Light microscope observation indicated that the space between the seminiferous tubules was increased. Ultrastructural observation showed some histopathological characteristics, including cytoplasmic shrinkage, cell membrane blebbing, swollen mitochondria and deformed nucleus. Using Q-PCR methods, the transcriptional levels of some cytoskeletal and mitochondrial genes were determined. MC-LR exposure affected the homeostasis of the expression of cytoskeletal genes, causing possible dysfunction of cytoskeleton assembly. In MC-LR treatments, all the 8 mitochondrial genes related with oxidative phosphorylation (OXPHOS) significantly increased. The reactive oxygen species (ROS) level significantly increased in 10 µg/kg group. The mitochondria swelling and DNA damage were also determined in 10 µg/kg group. Hormone levels of testis significantly changed. The present study verified that both cytoskeleton disruption possibly due to cytoskeletal reorganization or depolymerization and mitochondria dysfunction interact with each other through inducing of reactive oxygen species and oxidative phosphorylation, and jointly result in testis impairment after exposure to MC-LR.

BACKGROUND: The central function of chloroplasts is to carry out photosynthesis, and its gene content and structure are highly conserved across land plants. Parasitic plants, which have reduced photosynthetic ability, suffer gene losses from the chloroplast (cp) genome accompanied by the relaxation of selective constraints. Compared with the rapid rise in the number of cp genome sequences of photosynthetic organisms, there are limited data sets from parasitic plants. PRINCIPAL FINDINGS/SIGNIFICANCE: Here we report the complete sequence of the cp genome of Cistanche deserticola, a holoparasitic desert species belonging to the family Orobanchaceae. The cp genome of C. deserticola is greatly reduced both in size (102,657 bp) and in gene content, indicating that all genes required for photosynthesis suffer from gene loss and pseudogenization, except for psbM. The striking difference from other holoparasitic plants is that it retains almost a full set of tRNA genes, and it has lower dN/dS for most genes than another close holoparasitic plant, E. virginiana, suggesting that Cistanche deserticola has undergone fewer losses, either due to a reduced level of holoparasitism, or to a recent switch to this life history. We also found that the rpoC2 gene was present in two copies within C. deserticola. Its own copy has much shortened and turned out to be a pseudogene. Another copy, which was not located in its cp genome, was a homolog of the host plant, Haloxylon ammodendron (Chenopodiaceae), suggesting that it was acquired from its host via a horizontal gene transfer.

Phillyrin has good biological activity, but it is insoluble in water, which restricts its use in various industries. In our work, we prepared phillyrin using a green and rapid method from Forsythia suspensa leaves, and its purity is greater than 93%. Then, phillyrin was made to interact with different kinds of cyclodextrins (CDs) as a way to improve the water solubility of phillyrin, and the interaction mechanism between CDs and phillyrin was speculated by various characterization methods. First, phase solubility experiments showed that the phase solubility curves of all three CD inclusion complexes were AL-shaped, indicating that all three inclusion complexes were prepared using phillyrin with CDs in a 1 : 1 stoichiometric ratio. And based on this result, three cyclodextrin inclusion compounds, phillyrin/HP-β-CD (complexation efficiency (CE): 82.58%, the loading efficiency (LE): 22.27%), phillyrin/DM-β-CD IC (CE: 89.31%, LE: 24.83%) and phillyrin/β-CD IC (CE: 68.59%, LE: 23.67%), were prepared. Then, phillyrin was successfully encapsulated as determined by various characterization analyses, after which the conformations of the inclusion complex interactions were analyzed by NMR and molecular docking. The result also indicated that the water solubility of the phillyrin/HP-β-CD, phillyrin/DM-β-CD IC and phillyrin/β-CD IC has significantly improved, which was 30.02, 41.91 and 14.56 times higher than that of pure phillyrin. And the inclusion of CDs also considerably improved the antioxidant capacity of phillyrin, and the DPPH clearance rates of the three inclusion compounds were 4.34, 4.46 and 4.79 times higher than those of pure phillyrin, respectively, and the ABTS clearance rates were 1.35, 1.70 and 1.62 times higher than that of pure phillyrin. The prepared inclusion complexes can be applied in the functional food industry as active ingredients. [ABSTRACT FROM AUTHOR]