Three amphioxus reference genomes reveal gene and chromosome evolution of chordates.

The slow-evolving invertebrate amphioxus has an irreplaceable role in advancing our understanding of the vertebrate origin and innovations. Here we resolve the nearly complete chromosomal genomes of three amphioxus species, one of which best recapitulates the 17 chordate ancestor linkage groups. We reconstruct the fusions, retention, or rearrangements between descendants of whole-genome duplications, which gave rise to the extant microchromosomes likely existed in the vertebrate ancestor. Similar to vertebrates, the amphioxus genome gradually establishes its three-dimensional chromatin architecture at the onset of zygotic activation and forms two topologically associated domains at the Hox gene cluster. We find that all three amphioxus species have ZW sex chromosomes with little sequence differentiation, and their putative sex-determining regions are nonhomologous to each other. Our results illuminate the unappreciated interspecific diversity and developmental dynamics of amphioxus genomes and provide high-quality references for understanding the mechanisms of chordate functional genome evolution.

Integration analysis of ATAC-seq and RNA-seq provides insight into fatty acid biosynthesis in Schizochytrium limacinum under nitrogen limitation stress.

BACKGROUND: Schizochytrium limacinum holds significant value utilized in the industrial-scale synthesis of natural DHA. Nitrogen-limited treatment can effectively increase the content of fatty acids and DHA, but there is currently no research on chromatin accessibility during the process of transcript regulation. The objective of this research was to delve into the workings of fatty acid production in S. limacinum by examining the accessibility of promoters and profiling gene expressions. RESULTS: Results showed that differentially accessible chromatin regions (DARs)-associated genes were enriched in fatty acid metabolism, signal transduction mechanisms, and energy production. By identifying and annotating DARs-associated motifs, the study obtained 54 target transcription factor classes, including BPC, RAMOSA1, SPI1, MYC, and MYB families. Transcriptomics results revealed that several differentially expressed genes (DEGs), including SlFAD2, SlALDH, SlCAS1, SlNSDHL, and SlDGKI, are directly related to the biosynthesis of fatty acids, meanwhile, SlRPS6KA, SlCAMK1, SlMYB3R1, and SlMYB3R5 serve as transcription factors that could potentially influence the regulation of fatty acid production. In the integration analysis of DARs and ATAC-seq, 13 genes were identified, which were shared by both DEGs and DARs-associated genes, including SlCAKM, SlRP2, SlSHOC2, SlTN, SlSGK2, SlHMP, SlOGT, SlclpB, and SlDNAAF3. CONCLUSIONS: SlCAKM may act as a negative regulator of fatty acid and DHA synthesis, while SlSGK2 may act as a positive regulator, which requires further study in the future. These insights enhance our comprehension of the processes underlying fatty acid and DHA production in S. limacinum. They also supply a foundational theoretical framework and practical assistance for the development of strains rich in fatty acids and DHA.

The potential health benefits of aloin from genus Aloe.

The Aloe species is known for its medicinal and cosmetic properties. Aloin is an active ingredient found in the leaves of medicinal plants of the genus Aloe. Aloin has attracted considerable interest for its antiinflammatory, anticancer, antibacterial, and antioxidant activities. However, since its clinical application is restricted by its unclear mechanism of action, a deeper understanding of its pharmacological activity is required. This review provides an overview of current pharmacological and toxicological studies published in English from February 2000 to August 2021. Herein, we summarized the sources and potential health benefits of aloin from a clinical application perspective to guide for further studies on the sources of aloin, aimed at efficiently increasing aloin production. Importantly, the function and mechanism of action of aloin remain unclarified. In future research, it is necessary to develop new approaches for studying the pharmacological molecular mechanisms underlying the activity of this compound against various diseases.

Insights into salvianolic acid B biosynthesis from chromosome-scale assembly of the Salvia bowleyana genome.

Salvia bowleyana is a traditional Chinese medicinal plant that is a source of nutritional supplements rich in salvianolic acid B and a potential experimental system for the exploration of salvianolic acid B biosynthesis in the Labiatae. Here, we report a high-quality chromosome-scale genome assembly of S. bowleyana covering 462.44 Mb, with a scaffold N50 value of 57.96 Mb and 44,044 annotated protein-coding genes. Evolutionary analysis revealed an estimated divergence time between S. bowleyana and its close relative S. miltiorrhiza of ~3.94 million years. We also observed evidence of a whole-genome duplication in the S. bowleyana genome. Transcriptome analysis showed that SbPAL1 (PHENYLALANINE AMMONIA-LYASE1) is highly expressed in roots relative to stem and leaves, paralleling the location of salvianolic acid B accumulation. The laccase gene family in S. bowleyana outnumbered their counterparts in both S. miltiorrhiza and Arabidopsis thaliana, suggesting that the gene family has undergone expansion in S. bowleyana. Several laccase genes were also highly expressed in roots, where their encoded proteins may catalyze the oxidative reaction from rosmarinic acid to salvianolic acid B. These findings provide an invaluable genomic resource for understanding salvianolic acid B biosynthesis and its regulation, and will be useful for exploring the evolution of the Labiatae.

Genomic variation between PRSV resistant transgenic SunUp and its progenitor cultivar Sunset.

BACKGROUND: The safety of genetically transformed plants remains a subject of scrutiny. Genomic variants in PRSV resistant transgenic papaya will provide evidence to rationally address such concerns. RESULTS: In this study, a total of more than 74 million Illumina reads for progenitor 'Sunset' were mapped onto transgenic papaya 'SunUp' reference genome. 310,364 single nucleotide polymorphisms (SNPs) and 34,071 small Inserts/deletions (InDels) were detected between 'Sunset' and 'SunUp'. Those variations have an uneven distribution across nine chromosomes in papaya. Only 0.27% of mutations were predicted to be high-impact mutations. ATP-related categories were highly enriched among these high-impact genes. The SNP mutation rate was about 8.4 × 10- 4 per site, comparable with the rate induced by spontaneous mutation over numerous generations. The transition-to-transversion ratio was 1.439 and the predominant mutations were C/G to T/A transitions. A total of 3430 nuclear plastid DNA (NUPT) and 2764 nuclear mitochondrial DNA (NUMT) junction sites have been found in 'SunUp', which is proportionally higher than the predicted total NUPT and NUMT junction sites in 'Sunset' (3346 and 2745, respectively). Among all nuclear organelle DNA (norgDNA) junction sites, 96% of junction sites were shared by 'SunUp' and 'Sunset'. The average identity between 'SunUp' specific norgDNA and corresponding organelle genomes was higher than that of norgDNA shared by 'SunUp' and 'Sunset'. Six 'SunUp' organelle-like borders of transgenic insertions were nearly identical to corresponding sequences in organelle genomes (98.18 ~ 100%). None of the paired-end spans of mapped 'Sunset' reads were elongated by any 'SunUp' transformation plasmid derived inserts. Significant amounts of DNA were transferred from organelles to the nuclear genome during bombardment, including the six flanking sequences of the three transgenic insertions. CONCLUSIONS: Comparative whole-genome analyses between 'SunUp' and 'Sunset' provide a reliable estimate of genome-wide variations and evidence of organelle-to-nucleus transfer of DNA associated with biolistic transformation.

Overexpression of acetyl-CoA carboxylase increases fatty acid production in the green alga Chlamydomonas reinhardtii.

Chlamydomonas reinhardtii is a photosynthetic unicellular model algae with multiple biotechnological advantages, and its fatty acids can be used to produce biofuels. Numerous studies suggest that acetyl-coA carboxylase (ACCa) catalyzes the first committed and rate-limiting step of fatty acid biosynthesis, thereby playing a central role in oil accumulation. Here, we cloned and overexpressed ACCa in C. reinhardtii to directly evaluate its effect on fatty acid synthesis. GC-MS analysis found that the unsaturated FAs contents of the CW15-24 and CW15-85 strains were 55.45% and 56.15%, which were significantly enriched compared to the wild type CW15 (48.39%). Under the optimized conditions, the content of lipid by overexpressed the ACCa gene in the mutant CW15-85 (0.46 g/l) was 1.16-fold greater than control through optimization of N and P sources. Altogether, our data clearly demonstrate that ACCa overexpression in C. reinhardtii can directly increase the synthesis of fatty acids.

Improved bioethanol production using CRISPR/Cas9 to disrupt the ADH2 gene in Saccharomyces cerevisiae.

Bioethanol, as a form of renewable and clean energy, has become increasingly important to the energy supply. One major obstacle in ethanol production is developing a high-capacity system. Existing approaches for regulating the ethanol production pathway are relatively insufficient, with nonspecific genetic manipulation. Here, we used CRISPR/Cas9 technology to disrupt the alcohol dehydrogenase (ADH) 2 gene via complete deletion of the gene and introduction of a frameshift mutation in the ADH2 locus. Sequencing demonstrated the accurate knockout of the target gene with 91.4% and near 100% targeting efficiency. We also utilized genome resequencing to validate the mutations in the ADH2 mutants targeted by various single-guide RNAs. This extensive analysis indicated the mutations in the CRISPR/Cas9-engineered strains were homozygous. We applied the engineered Saccharomyces cerevisiae strains for bioethanol production. Results showed that the ethanol yield improved by up to 74.7% compared with the yield obtained using the native strain. This work illustrates the applicability of this highly efficient and specific genome engineering approach to promote the improvement of bioethanol production in S. cerevisiae via metabolic engineering. Importantly, this study is the first report of the disruption of a target gene, ADH2, in S. cerevisiae using CRISPR/Cas9 technology to improve bioethanol yield.

Molecular cloning, structure, phylogeny and expression analysis of the invertase gene family in sugarcane.

BACKGROUND: Invertases (INVs) are key enzymes regulating sucrose metabolism and are here revealed to be involved in responses to environmental stress in plants. To date, individual members of the invertase gene family and their expression patterns are unknown in sugarcane due to its complex genome despite their significance in sucrose metabolism. RESULTS: In this study, based on comparative genomics, eleven cDNA and twelve DNA sequences belonging to 14 non-redundant members of the invertase gene family were successfully cloned from sugarcane. A comprehensive analysis of the invertase gene family was carried out, including gene structures, phylogenetic relationships, functional domains, conserved motifs of proteins. The results revealed that the 14 invertase members from sugarcane could be clustered into three subfamilies, including 6 neutral/alkaline invertases (ShN/AINVs), and 8 acid invertases (ShAINVs). Faster divergence occurred in acid INVs than in neutral/alkaline INVs after the split of sugarcane and sorghum. At least a one-time gene duplication event was observed to have occurred in the four groups of acid INVs, whereas ShN/AINV1 and ShN/AINV2 in the ß8 lineage were revealed to be the most recently duplicated genes among their paralogous genes in the ß group of N/AINVs. Furthermore, comprehensive expression analysis of these genes was performed in sugarcane seedlings subjected to five abiotic stresses (drought, low temperature, glucose, fructose, and sucrose) using Quantitative Real-time PCR. The results suggested a functional divergence of INVs and their potential role in response to the five different treatments. Enzymatic activity in sugarcane seedlings was detected under five abiotic stresses treatments, and showed that the activities of all INVs were significantly inhibited in response to five different abiotic stresses, and that the neutral/alkaline INVs played a more prominent role in abiotic stresses than the acid INVs. CONCLUSIONS: In this study, we determined the INV gene family members of sugarcane by PCR cloning using sorghum as a reference, providing the first study of the INV gene family in sugarcane. Combining existing INV gene data from 7 plants with a comparative approach including a series of comprehensive analyses to isolate and identify INV gene family members proved to be highly successful. Moreover, the expression levels of INV genes and the variation of enzymatic activities associated with drought, low temperature, glucose, fructose, and sucrose are reported in sugarcane for the first time. The results offered useful foundation and framework for future research for understanding the physiological roles of INVs for sucrose accumulation in sugarcane.

Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum.

BACKGROUND: Sugarcane is a major sugar and biofuel crop, but genomic research and molecular breeding have lagged behind other major crops due to the complexity of auto-allopolyploid genomes. Sugarcane cultivars are frequently aneuploid with chromosome number ranging from 100 to 130, consisting of 70-80 % S. officinarum, 10-20 % S. spontaneum, and 10 % recombinants between these two species. Analysis of a genomic region in the progenitor autoploid genomes of sugarcane hybrid cultivars will reveal the nature and divergence of homologous chromosomes. RESULTS: To investigate the origin and evolution of haplotypes in the Bru1 genomic regions in sugarcane cultivars, we identified two BAC clones from S. spontaneum and four from S. officinarum and compared to seven haplotype sequences from sugarcane hybrid R570. The results clarified the origin of seven homologous haplotypes in R570, four haplotypes originated from S. officinarum, two from S. spontaneum and one recombinant.. Retrotransposon insertions and sequences variations among the homologous haplotypes sequence divergence ranged from 18.2 % to 60.5 % with an average of 33.7 %. Gene content and gene structure were relatively well conserved among the homologous haplotypes. Exon splitting occurred in haplotypes of the hybrid genome but not in its progenitor genomes. Tajima's D analysis revealed that S. spontaneum hapotypes in the Bru1 genomic regions were under strong directional selection. Numerous inversions, deletions, insertions and translocations were found between haplotypes within each genome. CONCLUSIONS: This is the first comparison among haplotypes of a modern sugarcane hybrid and its two progenitors. Tajima's D results emphasized the crucial role of this fungal disease resistance gene for enhancing the fitness of this species and indicating that the brown rust resistance gene in R570 is from S. spontaneum. Species-specific InDel, sequences similarity and phylogenetic analysis of homologous genes can be used for identifying the origin of S. spontaneum and S. officinarum haplotype in Saccharum hybrids. Comparison of exon splitting among the homologous haplotypes suggested that the genome rearrangements in Saccharum hybrids after hybridization. The combined minimum difference at 19.5 % among homologous chromosomes in S. officinarum would be sufficient for proper genome assembly of this autopolyploid genome. Retrotransposon insertions and sequences variations among the homologous haplotypes sequence divergence may allow sequencing and assembling the autopolyploid Saccharum genomes and the auto-allopolyploid hybrid genomes using whole genome shotgun sequencing.

Silencing the glycerol-3-phosphate dehydrogenase gene in Saccharomyces cerevisiae results in more ethanol being produced and less glycerol.

Transcription of the gene coding for glycerol-3-phosphate dehydrogenase (GPD1) was repressed in an industrial strain of Saccharomyces cerevisiae using a silencing vector. A fusion fragment containing GPD1 and Kan MX genes was generated by overlap extension PCR, then, the vector, pYES2.0 GPD1/Kan MX, was constructed by inserting the fusion fragment into the S. cerevisiae plasmid, pYES2.0. pYES2.0 GPD1/Kan MX, was linearized by KpnI, transformed into S. cerevisiae using the PEG/LiAc/ssDNA method, and integrated into the S. cerevisiae chromosome. GPD1 silencing gave 20 % less glycerol-3-phosphate dehydrogenase activity, 19 % lower glycerol production, and 9.7 % higher ethanol production compared with the original strain. These findings further the development of industrial S. cerevisiae strains with improved ethanol production and reduced glycerol content for the efficient production of bio-ethanol.

Genomics and transcriptomics reveal ß-carotene synthesis mechanism in Dunaliella salina.

Dunaliella salina is by far the most salt-tolerant organism and contains many active substances, including ß-carotene, glycerol, proteins, and vitamins, using in the production of dried biomass or cell extracts for the biofuels, pharmaceutical formulations, food additives, and fine chemicals, especially ß-carotene. We report a high-quality genome sequence of D. Salina FACHB435, which has a 472 Mb genome size, with a contig N50 of 458 Kb. A total of 30,752 protein-coding genes were predicted. The annotation results evaluated by BUSCO was shown that completeness was 91.0% and replication was 53.1%. The fragments were 6.3% and the deletions were 2.6%. Phylogenomic and comparative genomic analyses revealed that A. thaliana diverged from Volvocales about 448 million years ago, then Volvocales C. eustigma, D. salina, and other species diverged about 250 million years ago. High light could promote the accumulation of ß-carotene in D. salina at a 13 d stage of culture. The enrichment of DEGs in KEGG, it notes that the predicted up-regulated genes of carotenoid metabolic pathway include DsCrtB, DsPDS, DsZ-ISO, DsZDS, DsCRTISO, DsLUT5, DsCrtL-B, and DsCCD8, while the predicted down-regulated genes include DsCrtF, and DsLUT1. The four genes that were both up-regulated and down-regulated were DsZEP, DsCrtR-b, DsCruA/P and DsCrtZ 4. The research results can provide scientific basis for the industrialization practice of D. salina.

Rationally designing of Co-WS2 catalysts with optimized electronic structure to enhance hydrogen evolution reaction.

Designing and developing cost-effective, high-performance catalysts for hydrogen evolution reaction (HER) is crucial for advancing hydrogen production technology. Tungsten-based sulfides (WSx) exhibit great potential as efficient HER catalysts, however, the activity is limited by the larger energy required for water dissociation under alkaline conditions. Herein, we adopt a top-down strategy to construct heterostructure Co-WS2 nanofiber catalysts. The experimental results and theoretical simulations unveil that the work functions-induced built-in electric field at the interface of Co-WS2 catalysts facilitates the electron transfer from Co to WS2, significantly reducing water dissociation energy and optimizing the Gibbs free energy of the entire reaction step for HER. Besides, the self-supported catalysts of Co-WS2 nanoparticles confining 1D nanofibers exhibit an increased number of active sites. As expected, the heterostructure Co-WS2 catalysts exhibit remarkable HER activity with an overpotential of 113 mV to reach 10 mA cm-2 and stability with 30 h catalyzing at 23 mA cm-2. This work can provide an avenue for designing highly efficient catalysts applicable to the field of energy storage and conversion.

Haplotype analysis of sucrose synthase gene family in three Saccharum species.

BACKGROUND: Sugarcane is an economically important crop contributing about 80% and 40% to the world sugar and ethanol production, respectively. The complicated genetics consequential to its complex polyploid genome, however, have impeded efforts to improve sugar yield and related important agronomic traits. Modern sugarcane cultivars are complex hybrids derived mainly from crosses among its progenitor species, S. officinarum and S. spontanuem, and to a lesser degree, S. robustom. Atypical of higher plants, sugarcane stores its photoassimilates as sucrose rather than as starch in its parenchymous stalk cells. In the sugar biosynthesis pathway, sucrose synthase (SuSy, UDP-glucose: D-fructose 2-a-D-glucosyltransferase, EC 2.4.1.13) is a key enzyme in the regulation of sucrose accumulation and partitioning by catalyzing the reversible conversion of sucrose and UDP into UDP-glucose and fructose. However, little is known about the sugarcane SuSy gene family members and hence no definitive studies have been reported regarding allelic diversity of SuSy gene families in Saccharum species. RESULTS: We identified and characterized a total of five sucrose synthase genes in the three sugarcane progenitor species through gene annotation and PCR haplotype analysis by analyzing 70 to 119 PCR fragments amplified from intron-containing target regions. We detected all but one (i.e. ScSuSy5) of ScSuSy transcripts in five tissue types of three Saccharum species. The average SNP frequency was one SNP per 108 bp, 81 bp, and 72 bp in S. officinarum, S. robustom, and S. spontanuem respectively. The average shared SNP is 15 between S. officinarum and S. robustom, 7 between S. officinarum and S. spontanuem , and 11 between S. robustom and S. spontanuem. We identified 27, 35, and 32 haplotypes from the five ScSuSy genes in S. officinarum, S. robustom, and S. spontanuem respectively. Also, 12, 11, and 9 protein sequences were translated from the haplotypes in S. officinarum, S. robustom, S. spontanuem, respectively. Phylogenetic analysis showed three separate clusters composed of SbSuSy1 and SbSuSy2, SbSuSy3 and SbSuSy5, and SbSuSy4. CONCLUSIONS: The five members of the SuSy gene family evolved before the divergence of the genera in the tribe Andropogoneae at least 12 MYA. Each ScSuSy gene showed at least one non-synonymous substitution in SNP haplotypes. The SNP frequency is the lowest in S. officinarum, intermediate in S. robustum, and the highest in S. spontaneum, which may reflect the timing of the two rounds of whole genome duplication in these octoploids. The higher rate of shared SNP frequency between S. officinarum and S. robustum than between S. officinarum and in S. spontaneum confirmed that the speciation event separating S. officinarum and S. robustum occurred after their common ancestor diverged from S. spontaneum. The SNP and haplotype frequencies in three Saccharum species provide fundamental information for designing strategies to sequence these autopolyploid genomes.

Integrated Thermofluid Lumped Parameter Model for Analyzing Hemodynamics in Human Fatigue State.

It is well known that driving while fatigued is dangerous and can lead to serious traffic accidents. However, there is a lack of studies on the mechanism of fatigue. This paper sought to infer changes in the cardiovascular system through hand and head skin temperature peripheral factors via an integrated lumped parameter model. A multi-layer inner structure with variable blood perfusion was used to construct a full-body thermal model. The cardiovascular system model provided blood perfusion using lumped parameters. The peripheral resistance and heart rate in the cardiovascular system model were adjusted to match the experimental temperatures of the head and hands obtained from induced fatigue experiments. The simulation results showed that the heart rate and blood pressure decreased, and the peripheral skin resistance of the hands and head increased after fatigue. A decrease in heart rate and an increase in peripheral resistance affect the magnitude of blood flow to the periphery of the body, leading to a decrease in skin temperature during fatigue. The present integrated model elucidates a key effect of human fatigue on the cardiovascular system, which is expected to help improve the accuracy of fatigue monitoring systems.

Vascular response to the microcirculation in the fingertip by local vibration with varied amplitude.

Objectives: We investigated the effect of local vibration intensity on the vascular response to the microcirculation of the finger. Materials and methods: We performed hand-transmitted vibration experiments combined with laser Doppler flowmetry (LDF) to measure the blood perfusion signals of fingertips in the vibrated hand and the contralateral middle finger under the same frequency and different amplitude vibration, and to analyze the changes of microcirculatory blood perfusion levels in the fingers, and to investigate the effects of vibration stimulation on the endothelial, neural and myogenic regulatory frequency ranges of fingertips based on wavelet analysis. Furthermore, the transparent silicone films were fabricated and cultured with vascular endothelial cell (EC), which will undergo the local vibration with varied amplitude. And the expression of inflammatory factors was detected in the ECs. Results: Low-frequency vibration leads to a decreased blood flow in fingertip, and the degree of reduction in fingertip blood flow increases as the amplitude gradually increases, and the period required for blood flow to return to normal level after hand-transmitted vibration gradually increases. The decrease in blood flow is more pronounced in the vibrating hand than in the contralateral hand. In addition, nuclear factor-κB (NF-κB) expression increased significantly with the increase of vibration amplitude. Conclusion: High amplitude vibrations caused the inflammatory reaction of ECs which will lead to the altered endothelial regulatory activity. The endothelial regulatory activity is closely related to the blood perfusion in the microcirculation.

Combined analysis of chromatin accessibility and gene expression profiles provide insight into Fucoxanthin biosynthesis in Isochrysis galbana under green light.

Isochrysis galbana, as a potential accumulator of fucoxanthin, has become a valuable material to develop functional foods for humans. Our previous research revealed that green light effectively promotes the accumulation of fucoxanthin in I. galbana, but there is little research on chromatin accessibility in the process of transcriptional regulation. This study was conducted to reveal the mechanism of fucoxanthin biosynthesis in I. galbana under green light by analyzing promoter accessibility and gene expression profiles. Differentially accessible chromatin regions (DARs)-associated genes were enriched in carotenoid biosynthesis and photosynthesis-antenna protein formation, including IgLHCA1, IgLHCA4, IgPDS, IgZ-ISO, IglcyB, IgZEP, and IgVDE. The motifs for the MYB family were also identified as candidates controlling metabolic regulation responses to green light culture of I. galbana, including IgMYB1, IgMYB2, IgMYB33, IgMYB42, IgMYB98, IgMYB118, and IgMYB119. The results of differential expression analysis and WGCNA showed that several genes or transcription factors (TFs) related to carotenoid metabolism and photosynthesis exhibited a higher expression level and were significantly upregulated in A-G5d compared with A-0d and A-W5d, including IgMYB98, IgLHCA1, IgLHCX2, IgLHCB4, and IgLHCB5. This suggests that upregulation of these genes by green light may be the key factor leading to fucoxanthin accumulation by regulating the photosynthesis-antenna protein pathway. An integrated analysis of ATAC-seq and RNA-seq showed that 3 (IgphoA, IgPKN1, IgOTC) of 34 DARs-associated genes displayed obvious changes in their chromatin regions in ATAC-seq data, suggesting that these genes specific for green light may play a key role in fucoxanthin biosynthesis in I. galbana through a complex regulatory network of multiple metabolic pathways interacting with each other. These findings will facilitate in-depth understanding the molecular regulation mechanisms of fucoxanthin in I. galbana and its role in response to green light regulation, providing technical support for the construction of high fucoxanthin content strains.

Revealing the mechanisms of the bioactive ingredients accumulation in Polygonatum cyrtonema by multiomics analyses.

Polygonatum cyrtonema is a medicinal and edible herb rich in polysaccharides, steroidal saponins, and flavonoids that has been widely used as a food, vegetable, and medicine over the years. Although previous studies have preliminarily explored the metabolic and transcriptional regulatory mechanisms of the main secondary metabolites in P. cyrtonema, the complex mechanism of microRNA (miRNA)-mediated posttranscriptional regulation remains unclear. Metabolome analysis showed that iso-ophiopogonanone B, (25S)-pratioside D1, disporopsin, and isodiosgenin-Glc-Glc, which are associated with intermediates in the flavonoids and saponins pathways, were significantly upregulated in the stem and leaf compared with the rhizome, and most saccharides, including arabinose, cellobiose, maltotetraose, and panose, showed the opposite trend, suggesting that they may contribute to the formation and accumulation of the main active ingredients in P. cyrtonema. We found that 4-hydroxymandelonitrile have a relatively good inhibitory effect on α-glucosidase, indicating that it may play a role in hypoglycemic functions. Transcriptome and weighted gene coexpression network analysis (WGCNA) were combined to reveal several candidate genes involved in the accumulation of polysaccharides, saponins, and flavonoids, including PcSQLE, PcCYP71A1, PcSUS, PcFK, and PcMYB102. Integrated analyses of miRNAs and messengerRNAs (mRNAs) showed that novel_miR14, novel_miR49, novel_miR75, and aof_miR164 were negatively correlated with alpha-linolenic acid metabolism and the mitogen activated protein kinase (MAPK) signaling pathway, including PcAOS, PcSPLA2, PcFRK1, and PcDELLA, indicating that these miRNAs may coordinately regulate the biosynthesis of other secondary metabolites in P. cyrtonema. These findings will facilitate in-depth research on the functions of these miRNAs and mRNAs related to the main active substances for pathological and biological regulation, which will be beneficial to provide theoretical guidance for the molecular breeding of P. cyrtonema.

A comprehensive method to prevent top-coal spontaneous combustion utilizing dry ice as a fire extinguishing medium: test apparatus development and field application.

There is a high potential for coal spontaneous combustion (CSC) above the roof beams of supports during the mining-stopped period. Early detection of temperature abnormal zones and corresponding measures are necessary to prevent CSC. In this work, a top-coal temperature measurement method was proposed, combining the coal surface temperature detection and the drilling temperature observation. Furthermore, an apparatus was developed that dramatically increases the rate of dry ice sublimation, resulting in the rapid release of cryogenic carbon dioxide gas. The device utilizes water from firefighting pipes in underground coal mines as a heat source for dry ice sublimation without electrical energy and has been applied and validated taking Silaogou Coal Mine in China as a field test site. Specifically, we found that during the stoppage period, the coal above the supports near the air inlet tunnel is more likely to appear hot spots; the carbon dioxide gas generated by the dry ice phase change device can quickly reduce the hot spots temperature, and the coal temperature does not rebound after the gas injection is stopped. Based on the above analysis, this work can effectively prevent the early top-coal spontaneous combustion during the stop mining period.

Chromosome-scale assembly and population diversity analyses provide insights into the evolution of Sapindus mukorossi.

Sapindus mukorossi is an environmentally friendly plant and renewable energy source whose fruit has been widely used for biomedicine, biodiesel, and biological chemicals due to its richness in saponin and oil contents. Here, we report the first chromosome-scale genome assembly of S. mukorossi (covering ~391 Mb with a scaffold N50 of 24.66 Mb) and characterize its genetic architecture and evolution by resequencing 104 S. mukorossi accessions. Population genetic analyses showed that genetic diversity in the southwestern distribution area was relatively higher than that in the northeastern distribution area. Gene flow events indicated that southwest species may be the donor population for the distribution areas in China. Genome-wide selective sweep analysis showed that a large number of genes are involved in defense responses, growth and development, including SmRPS2, SmRPS4, SmRPS7, SmNAC2, SmNAC23, SmNAC102, SmWRKY6, SmWRKY26, and SmWRKY33. We also identified several candidate genes controlling six agronomic traits by genome-wide association studies, including SmPCBP2, SmbHLH1, SmCSLD1, SmPP2C, SmLRR-RKs, and SmAHP. Our study not only provides a rich genomic resource for further basic research on Sapindaceae woody trees but also identifies several economically significant genes for genomics-enabled improvements in molecular breeding.

Metabolome and Whole-Transcriptome Analyses Reveal the Molecular Mechanisms Underlying Hypoglycemic Nutrient Metabolites Biosynthesis in Cyclocarya paliurus Leaves During Different Harvest Stages.

Cyclocarya paliurus, a well-known nutrient and beverage plant, is under development for use in functional health care products best and natural and organic foods. We hypothesis that the composition and metabolic accumulation of hypoglycemic nutrient metabolites exhibit significant differences depending on harvest time. Therefore, it is of great significance to establish the best harvest time for C. paliurus leaves for the further development of healthy teas and other products. However, the detail compositions and molecular mechanisms of nutrients biosynthesis in C. paliurus leaves during different harvest stages remain largely unclear. Metabolome analysis showed that a suitable leaf-harvesting strategy for C. paliurus could be in September or October each year due to the high content of hypoglycemic nutrient metabolites. We found that two of the seven differentially accumulated phenolic acid metabolites have a relatively good inhibitory effect on α-amylase, indicating that they may play a role in the hypoglycemic function. Combined analysis of coexpression, ceRNA network, and weighted gene correlation network analysis (WGCNA) showed that several genes or transcription factors (TFs) in three modules correlated highly with hypoglycemic nutrient metabolites, including CpPMM, CpMan, CpFK, CpSUS, CpbglX, Cp4CL, CpHCT, and CpWRKY1. These findings help in the understanding of the molecular mechanisms and regulatory networks of the hypoglycemic nutrient metabolites in C. paliurus leaves which are dependent on harvest time and provide theoretical guidance in the development of functional health care products and foods from C. paliurus.