Genome-wide expression analysis of LACS gene family implies GhLACS25 functional responding to salt stress in cotton.

BACKGROUND: Long-chain acyl-coenzyme A synthetase (LACS) is a type of acylating enzyme with AMP-binding, playing an important role in the growth, development, and stress response processes of plants. RESULTS: The research team identified different numbers of LACS in four cotton species (Gossypium hirsutum, Gossypium barbadense, Gossypium raimondii, and Gossypium arboreum). By analyzing the structure and evolutionary characteristics of the LACS, the GhLACS were divided into six subgroups, and a chromosome distribution map of the family members was drawn, providing a basis for further research classification and positioning. Promoter cis-acting element analysis showed that most GhLACS contain plant hormones (GA, MeJA) or non-biological stress-related cis-elements. The expression patterns of GhLACS under salt stress treatment were analyzed, and the results showed that GhLACS may significantly participate in salt stress response through different mechanisms. The research team selected 12 GhLACSs responsive to salt stress for tissue expression analysis and found that these genes are expressed in different tissues. CONCLUSIONS: There is a certain diversity of LACS among different cotton species. Analysis of promoter cis-acting elements suggests that GhLACS may be involved in regulating plant growth, development and stress response processes. GhLACS25 was selected for in-depth study, which confirmed its significant role in salt stress response through virus-induced gene silencing (VIGS) and induced expression in yeast cells.

Combined metabolome and transcriptome analyses reveal that growing under Red shade affects secondary metabolite content in Huangjinya green tea.

Shading treatments impact the tea (Camellia sinensis L.) quality. The sunlight sensitive varieties can be grown under shading nets for better growth and secondary metabolite content. Here, we studied the responses of a sunlight sensitive green tea variety "Huangjinya" by growing under colored shading nets (red, yellow, blue, and black (75% and 95%) shading rates) to find out the most suitable color of the shading net. Red shading was the most promising treatment as it positively affected the weight and length of 100 one-bud-three leaves and reduced the degree and rate of new shoots burn compared to control (natural sunlight). We then explored the comparative metabolomic changes in response to red shading by using UPLC-ESI-MS/MS system. The amino acids and derivatives, flavonoids, and alkaloids were downaccumulated whereas lipids, organic acids, and lignans were upaccumulated in Red shade grown tea samples. The red shading nets caused a decreased catechin, epicatechin, dopamine, and L-tyramine contents but increased caffeine content. We then employed transcriptome sequencing to find key changes in expressions of related genes and pathways. Notably, key genes associated with the phenylpropanoid and flavonoid biosynthesis pathways exhibited complex regulation. These expression changes suggested a potential trend of polymerization or condensation of simple molecules like catechin or pelargonidin into larger molecules like glucoside or proanthocyanidins. Here, Red shading net triggered higher expression of genes enriched in lipid biosynthesis and jasmonic acid biosynthesis, suggesting an interplay of fatty acids and JA in improving tea performance. These findings contribute to the metabolic responses of Huangjinya tea to red shading nets which might have implications for flavor and health benefits. Our data provide a foundation for further exploration and optimization of cultivation practices for this unique tea variety.

Integrated transcriptome and metabolome analysis unveil the response mechanism in wild rice (Zizania latifolia griseb.) against sheath rot infection.

Sheath rot disease (SRD) is one of the most devastating diseases of Manchurian wild rice (MWR) (Zizania latifolia Griseb). Pilot experiments in our laboratory have shown that an MWR cultivar "Zhejiao NO.7"exhibits signs of SRD tolerance. To explore the responses of Zhejiao No. 7 to SRD infection, we used a combined transcriptome and metabolome analysis approach. A total of 136 differentially accumulated metabolites (DAMs, 114 up- and 22 down-accumulated in FA compared to CK) were detected. These up-accumulated metabolites were enriched in tryptophan metabolism, amino acid biosynthesis, flavonoids, and phytohormone signaling. Transcriptome sequencing results showed the differential expression of 11,280 genes (DEGs, 5,933 up-, and 5,347 downregulated in FA compared to CK). The genes expressed in tryptophan metabolism, amino acid biosynthesis, phytohormone biosynthesis and signaling, and reactive oxygen species homeostasis confirmed the metabolite results. In addition, genes related to the cell wall, carbohydrate metabolism, and plant-pathogen interaction (especially hypersensitive response) showed changes in expression in response to SRD infection. These results provide a basis for understanding the response mechanisms in MWR to FA attack that can be used for breeding SRD-tolerant MWR.

Characterization of the chloroplast genome of Zingiber mioga (Thunb.) Rosc.

Zingiber mioga (Thunb.) Rosc. is an important plant species in tropical Asia widely used for decoration, and in traditional food and medicine. In this study, we reported for the first time the complete chloroplast genome sequence of Z. mioga. The assembled chloroplast genome was 159,868 bp long with a typical quadripartite structure consisting of two reverse repeated regions of 26,652 bp in length, separated by a large single-copy (89,431 bp) and a small single-copy (17,133 bp) region. We annotated 113 genes including 78 protein-coding, 31 tRNA and 4 rRNA genes. Phylogenetic analysis with 27 other species showed that Z. mioga clustered with Z. officinale and Z. spectabile, all belonging to the Zingiberaceae family of the Zingiberales order. The results of this study will facilitate the breeding process and conservation of the species.

Genomic divergence in cotton germplasm related to maturity and heterosis.

Commercial varieties of upland cotton (Gossypium hirsutum) have undergone extensive breeding for agronomic traits, such as fiber quality, disease resistance, and yield. Cotton breeding programs have widely used Chinese upland cotton source germplasm (CUCSG) with excellent agronomic traits. A better understanding of the genetic diversity and genomic characteristics of these accessions could accelerate the identification of desirable alleles. Here, we analyzed 10,522 high-quality single-nucleotide polymorphisms (SNP) with the CottonSNP63K microarray in 137 cotton accessions (including 12 hybrids of upland cotton). These data were used to investigate the genetic diversity, population structure, and genomic characteristics of each population and the contribution of these loci to heterosis. Three subgroups were identified, in agreement with their known pedigrees, geographical distributions, and times since introduction. For each group, we identified lineage-specific genomic divergence regions, which potentially harbor key alleles that determine the characteristics of each group, such as early maturity-related loci. Investigation of the distribution of heterozygous loci, among 12 commercial cotton hybrids, revealed a potential role for these regions in heterosis. Our study provides insight into the population structure of upland cotton germplasm. Furthermore, the overlap between lineage-specific regions and heterozygous loci, in the high-yield hybrids, suggests a role for these regions in cotton heterosis.

Physicochemical and functional properties of protein isolate obtained from cottonseed meal.

To investigate the effect of preparation methods of cottonseed meals on protein properties, the physicochemical and functional properties of proteins isolated from hot-pressed solvent extraction cottonseed meal (HCM), cold-pressed solvent extraction cottonseed meal (CCM) and subcritical fluid extraction cottonseed meal (SCM) were investigated. Cottonseed proteins had two major bands (at about 45 and 50kD), two X-ray diffraction peaks (8.5° and 19.5°) and one endothermic peak (94.31°C-97.72°C). Proteins of HCM showed relatively more ß-sheet (38.3%-40.5%), and less ß-turn (22.2%-25.8%) and α-helix (15.8%-19.5%), indicating the presence of highly denatured protein molecules. Proteins of CCM and SCM exhibited high water/oil absorption capacity, emulsifying abilities, surface hydrophobicity and fluorescence intensity, suggesting that the proteins have potential as functional ingredients in the food industry.

A novel chemiluminescence sensor for sensitive detection of cholesterol based on the peroxidase-like activity of copper nanoclusters.

A sensitive and selective chemiluminescence (CL) sensor based on the peroxidase-like activity of copper nanoclusters was established for the detection of cholesterol. Copper nanoclusters catalyse the CL reaction between luminol and H2O2. Because H2O2 is the oxidative product of cholesterol in the presence of cholesterol oxidase, the oxidation of cholesterol can be quantitatively converted to a CL response by combining the two reactions. The proposed method is simple and can be completed in a few minutes with high sensitivity. Under the optimal conditions, the CL intensity was proportional to the concentration of cholesterol over a wide range of 0.05-10 mM, with a detection limit of 1.5 µM. Furthermore, the method was successfully applied to determine cholesterol in milk powder and human serum with satisfactory accuracy and precision. This method expands the applications of nano-mimic enzymes in the field of CL-based sensors.

Simultaneous determination of six synthetic phenolic antioxidants in edible oils using dispersive liquid-liquid microextraction followed by high-performance liquid chromatography with diode array detection.

A simple, rapid, organic-solvent- and sample-saving pretreatment technique, called dispersive liquid-liquid microextraction, was developed for the determination of six synthetic phenolic antioxidants from edible oils before high-performance liquid chromatography with diode array detection. The entire procedure was composed of a two-step microextraction and a centrifugal process and could be finished in about 5 min, only consuming only 25 mg of sample and 1 mL of the organic solvent for each extraction. The influences of several important parameters on the microextraction efficiency were thoroughly investigated. Recovery assays for oil samples were spiked at three concentration levels, 50, 100 and 200 mg/kg, and provided recoveries in the 86.3-102.5% range with a relative standard deviation below 3.5%. The intra-day and inter-day precisions for the analysis were less than 3.8%. The proposed method was successfully applied for the determination of synthetic phenolic antioxidants in different oil samples, and satisfactory results were obtained. Thus, the developed method represents a viable alternative for the quality control of synthetic phenolic antioxidant concentrations in edible oils.

Enzymatic saccharification of high pressure assist-alkali pretreated cotton stalk and structural characterization.

Cotton stalk is a potential biomass for bioethanol production, while the conversion of direct saccharification or biotransformation of cotton stalk is extremely low due to the recalcitrant nature of lignocellulose. To enhance the enzymatic conversion of cotton stalks, the enzymatic saccharification parameters of high pressure assist-alkali pretreatment (HPAP) cotton stalk were optimized in the present study. Results indicated that a maximum reducing sugar yield of 54.7g/100g dry biomass cellulose was achieved at a substrate concentration of 2%, 100rpm agitation, 0.6g/g enzyme loading, 40°C hydrolysis temperature, 50h saccharification time, and pH 5.0. Scanning electron microscopy, X-ray diffraction, and Fourier transform infrared spectroscopy were used to identify structural changes in native, pretreated biomass and hydrolyzed residues. Structural analysis revealed large part of amorphous cellulose and partial crystalline cellulose in the HPAP cotton stalk were hydrolyzed during enzymatic treatment. HPAP cotton stalk can be used as a potential feed stock for bioethanol production.

Global analysis of the developmental dynamics of Gossypium hirsutum based on strand-specific transcriptome.

Cotton is an economically important crop that provides both natural fiber and by-products such as oil and protein. Its global gene expression could provide insight into the biological processes underlying growth and development, which involve suites of genes expressed with temporal and spatial control by regulatory networks. Generally, the goal for cotton breeding is improvement of the fiber; thus, most previous research has focused on identifying genes specific to the fiber. However, seeds may also play an important role in fiber development. In this study, we constructed and systematically analyzed 21 strand-specific RNA-Seq libraries for Gossypium hirsutum, covering different tissues, organs and development stages, from which approximately 970 million reads were generated to provide a global view of gene expression during cotton development. The organ (tissue)-specific gene expression patterns were investigated, providing further insight into the dynamic programming associated with developmental processes and a way to study the coordination of development between fiber cells and ovules. Series of transcription factors and seed-specific genes have been identified as candidate genes that could elucidate key mechanisms and regulatory networks in nutrient accumulation during ovule development and in fiber development. This study reports comprehensive transcriptome dynamics at various stages of cotton development and will serve as a valuable genome-wide transcriptome resource for initial gene discovery and functional characterization of genes in cotton.

Enhancing anaerobic digestion of cotton stalk by pretreatment with a microbial consortium (MC1).

Microbial pretreatment is beneficial in some anaerobic digestion systems, but the consortia used to date have not been able to effectively increase methane production from cotton stalk. In this study, a thermophilic microbial consortium (MC1) was used for pretreatment in order to enhance biogas and methane production yields. The results indicated that the concentrations of soluble chemical oxygen demand and volatile organic products increased significantly in the early stages of pretreatment. Ethanol, acetic acid, propionic acid, and butyric acid were the predominant volatile organic products in the MC1 hydrolysate. Biogas and methane production yields from cotton stalk were significantly increased following MC1 pretreatment. In addition, the methane production rate from the treated cotton stalk was greater than that from the untreated sample.

High pressure assist-alkali pretreatment of cotton stalk and physiochemical characterization of biomass.

Ground cotton stalks were pretreated with sodium hydroxide (NaOH) at concentrations of 1-4% (w/v), pressures of 30-130 kPa, durations of 15-75 min, and liquid/solid ratios of 10:1-30:1. Modeling of the high pressure assist-alkali pretreatment (HPAP) of cotton stalk was attempted. The levels of NaOH concentration, pressure, and duration were optimized using a Box-Behnken design to enhance the cellulose content of treated solid residue. The optimum pretreatment conditions were as follows: liquid/solid ratio, 20:1; pressure, 130 kPa; NaOH concentration, 3.0%; duration, 40 min. During the conditions, cellulose content of pretreated cotton stalk residue was 64.07%. The maximum cellulose conversion of 45.82% and reducing sugar yield of 0.293 g/g upon hydrolysis were obtained. Significant differences were observed in biomass composition and physiochemical characteristics between native and alkali-treated biomass. High NaOH concentration and pressure were conducive to lignin dissolution and resulted in increased cellulose content and conversion.