Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum.

Budding yeasts (subphylum Saccharomycotina) are found in every biome and are as genetically diverse as plants or animals. To understand budding yeast evolution, we analyzed the genomes of 332 yeast species, including 220 newly sequenced ones, which represent nearly one-third of all known budding yeast diversity. Here, we establish a robust genus-level phylogeny comprising 12 major clades, infer the timescale of diversification from the Devonian period to the present, quantify horizontal gene transfer (HGT), and reconstruct the evolution of 45 metabolic traits and the metabolic toolkit of the budding yeast common ancestor (BYCA). We infer that BYCA was metabolically complex and chronicle the tempo and mode of genomic and phenotypic evolution across the subphylum, which is characterized by very low HGT levels and widespread losses of traits and the genes that control them. More generally, our results argue that reductive evolution is a major mode of evolutionary diversification.

Integrated mass spectrometry imaging and single-cell transcriptome atlas strategies provide novel insights into taxoid biosynthesis and transport in Taxus mairei stems.

Taxol, which is a widely used important chemotherapeutic agent, was originally isolated from Taxus stem barks. However, little is known about the precise distribution of taxoids and the transcriptional regulation of taxoid biosynthesis across Taxus stems. Here, we used MALDI-IMS analysis to visualize the taxoid distribution across Taxus mairei stems and single-cell RNA sequencing to generate expression profiles. A single-cell T. mairei stem atlas was created, providing a spatial distribution pattern of Taxus stem cells. Cells were reordered using a main developmental pseudotime trajectory which provided temporal distribution patterns in Taxus stem cells. Most known taxol biosynthesis-related genes were primarily expressed in epidermal, endodermal, and xylem parenchyma cells, which caused an uneven taxoid distribution across T. mairei stems. We developed a single-cell strategy to screen novel transcription factors (TFs) involved in taxol biosynthesis regulation. Several TF genes, such as endodermal cell-specific MYB47 and xylem parenchyma cell-specific NAC2 and bHLH68, were implicated as potential regulators of taxol biosynthesis. Furthermore, an ATP-binding cassette family transporter gene, ABCG2, was proposed as a potential taxoid transporter candidate. In summary, we generated a single-cell Taxus stem metabolic atlas and identified molecular mechanisms underpinning the cell-specific transcriptional regulation of the taxol biosynthesis pathway.

Peptide vaccine from cancer-testis antigen ODF2 can potentiate the cytotoxic T lymphocyte infiltration through IL-15 in non-MSI-H colorectal cancer.

About 85% of patients with colorectal cancer (CRC) have the non-microsatellite instability-high (non-MSI-H) subtype, and many cannot benefit from immune checkpoint blockade. A potential reason for this is that most non-MSI-H colorectal cancers are immunologically "cold" due to poor CD8+ T cell infiltration. In the present study, we screened for potential cancer-testis antigens (CTAs) by comparing the bioinformatics of CD8+ T effector memory (Tem) cell infiltration between MSI-H and non-MSI-H CRC. Two ODF2-derived epitope peptides, P433 and P609, displayed immunogenicity and increased the proportion of CD8+ T effector memory (Tem) cells in vitro and in vivo. The adoptive transfer of peptide pool-induced CTLs inhibited tumor growth and enhanced CD8+ T cell infiltration in tumor-bearing NOD/SCID mice. The mechanistic study showed that knockdown of ODF2 in CRC cells promoted interleukin-15 expression, which facilitated CD8+ T cell proliferation. In conclusion, ODF2, a CTA, was negatively correlated with CD8+ T cell infiltration in "cold" non-MSI-H CRC and was selected based on the results of bioinformatics analyses. The corresponding HLA-A2 restricted epitope peptide induced antigen-specific CTLs. Immunotherapy targeting ODF2 could improve CTA infiltration via upregulating IL-15 in non-MSI-H CRC. This tumor antigen screening strategy could be exploited to develop therapeutic vaccines targeting non-MSI-H CRC.

Lonicera caerulea (Haskap berries): a review of development traceability, functional value, product development status, future opportunities, and challenges.

Lonicera caerulea is a honeysuckle plant with a long development history. It is defined as a "homology of medicine and food" fruit because it is rich in bioactive substances. By-products (such as pomace, leaves, stems, and flowers), which also have beneficial values, will be produced during processing. Nevertheless, the reuse of derivatives and the further development of new products of Lonicera caerulea are still a challenge. Firstly, this paper traced the development history of Lonicera caerulea and summarized its primary nutrients and bioactive substances, subsequently discussed the research progress and underlying molecular mechanisms of its functional properties, and introduced the application and potential of Lonicera caerulea in the fields of food, health products, cosmetics, medicine, and materials. Finally, this paper put forward the future research direction to promote the development of the Lonicera caerulea industry. To sum up, Lonicera caerulea, as a potential raw material, can be used to produce more functional products. Besides, more in-depth clinical trials are needed to clarify the specific molecular mechanism of the practical components of Lonicera caerulea and improve the rate of development and utilization.HighlightsThe original species of Lonicera caerulea subgroup had appeared on the earth as early as the end of the third century.Lonicera caerulea has been introduced into North America since the 18th century, but the introduction process has not ended until now.Lonicera caerulea widely exists in Eurasia and North America and it has excellent cold tolerance, early maturity and ornamental.The fruits, stems, leaves and flowers of Lonicera caerulea all have bioactive value, but the specific molecular mechanism and utilization need to be improved.Lonicera caerulea has been widely used in food, medicine, health products, cosmetics and materials, but there are still great challenges.

3D food printing: Applications of plant-based materials in extrusion-based food printing.

As an emerging digital production technology, 3D food printing intends to meet the demand for customized food design, personalized nutrition, simplification of the food supply chain system, and greater food material diversity. Most 3D food printing studies focus on the development of materials for extrusion-based food printing. Plant-based foods are essential for a healthy diet, and they are growing in popularity as their positive effects on human health gain wider recognition. The number of original studies on plant-based printable materials has increased significantly in the past few years. Currently, there is an absence of a comprehensive systematic review on the applications of plant-based materials in extrusion-based food printing. Thus, this review aims to provide a more intuitive overview and guidance for future research on 3D printing of plant-based materials. The requirements, classifications, and binding mechanisms of extrusion-based food printing materials are first summarized. Additionally, notable recent achievements and emerging trends involving the use of plant-based materials in extrusion-based food printing are reviewed across three categories, namely, hot-melt (e.g., chocolate), hydrogel, and soft (e.g., cereal- and fruit/vegetable-based) materials. Finally, the challenges facing 3D food printing technology as well as its future prospects are discussed.

The completed genome sequence of the pathogenic ascomycete fungus Penicillium digitatum.

P. digitatum, the causative agent of green mold, is one of the most destructive pathogens in the citrus industry. To facilitate basal researches on this important plant pathogen, here we report a finished genome sequence for P. digitatum strain PDW03 using a combination of Illumina, PacBio, and Hi-C sequencing technologies. The assembly comprised 6 chromosomes from telomere to telomere and encodes approximately 9000 proteins. Genomic re-analyses identified 302 Carbohydrate-active enzymes, 420 secreted proteins, and 39 secondary metabolite (SM) gene clusters. Furthermore, we found 10 fragmentary SM clusters in the P. digitatum PDW03 genome. Pangenome analysis based on 5 P. digitatum genomes available showed that conserved orthogroups account for ~68% of the species pangenome. Taken together, this fully completed P. digitatum genome will provide an optimum resource for further researches to investigate the driving forces of fungal host switch and effectors functioning in plant-pathogen interaction.

Chromosome-Scale Genome Sequence of Alternaria alternata Causing Alternaria Brown Spot of Citrus.

Alternaria brown spot (ABS), caused by Alternaria alternata, is an economically important fungal disease of citrus worldwide. The ABS pathogen A. alternata tangerine pathotype can produce a host-specific ACT toxin, which is regulated by ACT toxin gene cluster located in the conditionally dispensable chromosome (CDC). Previously, we have assembled a draft genome of A. alternata tangerine pathotype strain Z7, which comprises 165 contigs. In this study, we report a chromosome-level genome assembly of A. alternata Z7 through the combination of Oxford Nanopore sequencing and Illumina sequencing technologies. The assembly of A. alternata Z7 had a total size of 34.28 Mb, with a GC content of 51.01% and contig N50 of 3.08 Mb. The genome is encompassed 12,067 protein-coding genes, 34 ribosomal RNAs, and 107 transfer RNAs. Interestingly, A. alternata Z7 is composed of 10 essential chromosomes and 2 CDCs, which is consistent with the experimental evidences of pulsed-field gel electrophoresis. To our best knowledge, this is the first chromosome-level genome assembly of A. alternata. In addition, a database for citrus-related Alternaria genomes has been established to provide public resources for the sequences, annotation and comparative genomics data of Alternaria spp. The improved genome sequence and annotation at the chromosome level is a significant step toward a better understanding of the pathogenicity of A. alternata. The database will be updated regularly whenever the genomes of newly isolated Alternaria spp. are available. The citrus-related Alternaria genomes database is open accessible through the Citrus Fungal Disease Database.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Integrating non-targeted metabolomics and toxicology networks to study the mechanism of Esculentoside A-induced hepatotoxicity in rats.

Esculentoside A (EsA) is a kind of triterpenoid saponins from the root tuber of Phytolacca acinosa Roxb. It has extensive medicinal activity, such as antibacterial, anti-inflammatory, immune regulation, and cell proliferation inhibition. However, some researches suggested that EsA can cause hepatotoxicity, whose mechanism is not precise. To ensure the safety and reliability in the clinical use of Phytolacca acinosa Roxb., it is necessary to establish a rapid and accurate method to evaluate the toxicity, analyze and verify the toxicity mechanism of EsA. Therefore, this research explored the mechanism of hepatotoxicity induced by EsA in rats and analyzed endogenous metabolites' changes in rat plasma by combining network toxicology with non-targeted metabolomics. We obtained 58 critical targets of EsA induced hepatotoxicity in rats based on the strategy of network toxicology, including albumin, mitogen-activated protein kinase 1, Caspase-3, etc. Many important pathways were obtained by Kyoto Encyclopedia of Genes and Genomes enrichment analysis, such as HIF-1 signaling pathway, TNF signaling pathway, IL-17 signaling pathway, and other concerning pathways. Sixteen biomarkers, including 5-hydroxykynurenamine, N-acetylserotonin, palmitic acid, etc., were screened from rat plasma using Ultra-performance liquid chromatography coupled with quadrupole time of flight mass spectrometry (UPLC-Q-TOF/MS), mainly involve Glycerophospholipid metabolism, Tryptophan metabolism, and other metabolic pathways. Further analysis showed that EsA may induce liver injury by activating oxidative stress and energy metabolism disorders, triggering inflammation and apoptosis.

Genomic Sequence Resource of Alternaria alternata Strain B3 Causing Leaf Blight on Ophiopogon japonicus.

Black spot of Ophiopogon japonicus is an economically important disease, which can result in significant losses of both yield and quality of this traditional Chinese medicinal plant. The disease is caused by the small-spored fungal pathogen Alternaria alternata, a necrotrophic fungus that is ubiquitously distributed in the environment. Here, we present the draft whole-genome sequence of A. alternata strain B3 that caused black spot on O. japonicus. The assembly consists of 76 contigs with an estimated genome size of 33.8 Mb. Furthermore, we identified genes that may be associated with the pathogenicity, such as carbohydrate-active enzymes, secreted proteins, and secondary metabolite gene clusters. This genome resource will provide a useful source for future research on the evolution of pathogenicity of A. alternata and phylogenomic analysis in delineating phylogenetic lineages within the genus Alternaria.

First Draft Genome Sequence Resource of Colletotrichum liriopes Causing Leaf Anthracnose on Ophiopogon japonicus.

Leaf anthracnose of Ophiopogon japonicus is an important disease that can significantly reduce the quality and economic value of this traditional Chinese medicinal plant. The disease is caused by Colletotrichum liriopes, a necrotrophic fungus that belongs to the Glomerellaceae family of the Sordariomycetes class. Here, we present the draft whole-genome sequence of the C. liriopes strain A2 that caused leaf anthracnose on O. japonicus. The assembly consists of 407 contigs with an estimated genome size of 53.1 Mb. Furthermore, we identified 670 carbohydrate-active enzymes, 1,377 secreted proteins, and 60 secondary metabolite gene clusters, which may be associated with the pathogenicity of this pathogen. This genome resource will provide a valuable resource for future research on the pathogenesis of C. liriopes and comparative genome analyses within genus Colletotrichum.

Genome-wide identification and functional analysis of the horizontally transferred genes in Penicillium.

Horizontal gene transfer (HGT) is the transmission of genetic material between different evolutionary lineages and is believed to be an important source of genomic innovation in fungi. In this study, we searched for prokaryotic-derived HGTs in 23 fully sequenced genomes using a comprehensive phylogenomic pipeline followed by manual curation. We found strong support for 60 HGT events comprising 190 genes putatively acquired from bacteria. HGT affected all Penicillium species to various degrees. Gene duplication events happened to 3 HGT genes after the transmission. Most HGT events include genes encoding a variety of enzymes, which are associated with sugar, amino acid, and lipid metabolism. Transcriptome data from 6 Penicillium species revealed that 33 of 35 HGT genes showed expression under the conditions tested and 16 genes were differentially expressed. Our results suggest an important role for inter-domain gene transfers in shaping the genome of Penicillium fungi.

Involvement of LaeA in the regulation of conidia production and stress responses in Penicillium digitatum.

Involvement of LaeA in various biological processes of filamentous fungi has been demonstrated. However, its role in Penicillium digitatum, the causal agent of citrus postharvest green mold, remains unclear. In this study, a ΔPdLaeA mutant was constructed using homologous recombination. The production of conidia by the ΔPdLaeA mutant was reduced by half compared with that of the wild-type strain. The sensitivity of the ΔPdLaeA mutant increased under alkaline conditions. The virulence assay revealed that PdLaeA was dispensable for the virulence of P. digitatum. Comparative transcriptome analysis revealed that the function loss of PdLaeA resulted in the reduced expression of several secondary metabolite gene clusters. In addition, expression of several key regulators of conidiation (BrlA, FlbA, FlbC, FlbD, and FluG) was also downregulated in the ΔPdLaeA mutant. In summary, the present work demonstrated that PdLaeA was involved in the regulation of SM biosynthesis, as well as the development and environmental adaptation of P. digitatum.

Functional diversification of sterol regulatory element binding proteins following gene duplication in a fungal species.

The sterol regulatory element binding proteins (SREBPs) are functionally well conserved and have been shown to regulate ergosterol synthesis in fungi. However, the distribution and evolution of the SREBPs in fungi, especially in the Pezizomycotina which comprised of a great many of animal and plant pathogens, are unexplored. In this study, we identified 641 SREBPs from 367 out of 530 fungi species. Reconstruction of their evolutionary history showed evidence of gene duplication and gene loss at multiple evolutionary scales. Especially, SREBPs undergo a gene duplication event in the common ancestor of Pezizomycotina, resulting in the formation of two clades of SREBPs. Besides, the conserved motifs in the bHLH domain of both clades within Eurotiomycetes are highly diverged. To better understand the evolutionary diversification of this biologically significant regulator, we performed a series of experiments using Penicillium digitatum, a member of the lineage of Eurotiomycetes, to investigate how the evolutionary process of gene duplication shaped its function. qRT-PCR analysis showed that although PdsreA and PdsreB can be induced by imazalil, they showed different expression pattern; the electrophoretic mobility shift assay showed that PdSreA but not PdSreB can directly bind to the PdMLE1 sequence, an element that leads to the increased resistance to demethylation inhibitors (DMI) fungicides in P. digitatum. These results demonstrated that functions of duplicated SREBPs have largely diverged in P. digitatum, which may be a major feature of the long-term adaptive evolution of a particular group of fungi.

Thioredoxin and Glutaredoxin Systems Required for Oxidative Stress Resistance, Fungicide Sensitivity, and Virulence of Alternaria alternata.

This study determined the function of thioredoxin and glutaredoxin systems in the phytopathogenic fungus Alternaria alternata via analyzing mutants obtained from the targeted deletion of genes encoding thioredoxin peroxidase (Tsa1), thioredoxin reductase (Trr1), and glutathione reductase (Glr1). Trr1 and Glr1, but not Tsa1, are required for growth and conidiation. The reduced growth and conidiation seen in the Trr1 or Glr1 deletion mutant can be restored by glutathione. Deletion mutants showing growth inhibition by oxidants are defective for H2O2 detoxification and induce smaller lesions on citrus leaves. Trr1 and Glr1, but not Tsa1, also contribute to NaCl resistance. Glr1 is required for sorbitol resistance and is responsible for resistance to mancozeb and boscalid but not chlorothalonil fungicides, a novel phenotype that has not been reported in fungi. Trr1 is required for resistance to boscalid and chlorothalonil fungicides but confers susceptibility to mancozeb. The Tsa1 deletion mutant displays wild-type sensitivity to the tested fungicides. The expression of Tsa1 and Trr1 is regulated by the oxidative stress responsive regulators Yap1, Hog1, and Skn7. The expression of Tsa1, but not Trr1, is also regulated indirectly by the NADPH oxidase. The results indicate that the capability to resist oxidative stress is required for virulence of A. alternataIMPORTANCE The thioredoxin and glutaredoxin systems are important thiol antioxidant systems in cells, and knowledge of these two systems in the plant-pathogenic fungus A. alternata is useful for finding new strategies to reduce the virulence of this pathogen. In this study, we demonstrated that thiol antioxidant system-related genes (Tsa1, Trr1, and Glr1) are required for H2O2 detoxification and virulence in A. alternata Moreover, deletion of Trr1 results in hypersensitivity to the fungicides chlorothalonil and boscalid, and Glr1 deletion mutants are highly sensitive to mancozeb, which is the fungicide mostly used in citrus fields. Therefore, our findings demonstrate that the ability to detoxify reactive oxygen species (ROS) plays a critical role in pathogenesis on citrus and provide novel insights into the physiological functions of thiol-containing systems in fungicide sensitivity for A. alternata.

[Effects of tannins in Galla Chinensis on pharmacokinetics of rifampicin in vivo and in vitro].

This study was aimed to explore the effects of tannins in Galla Chinensis on rifampicin in vivo. In the experiment in vitro, UV spectrophotometry and high performance liquid chromatography (HPLC) were used to investigate the solubility of rifampin in pH 1.3, 6.8, artificial gastric juice environment and artificial intestinal fluid environment as well as the effects of tannins on solubility of rifampin in the above conditions. In the experiment in vivo, the process of rifampicin was studied after intragastric administration of rifampicin and rifampicin+ tannins in Galla Chinensis, and then the pharmacokinetic parameters were calculated. The results showed that rifampicin was constantly precipitated in the artificial gastric juice environment over time, and nearly 85% of the rifampicin was precipitated after 6 hours; it showed a good solubility in the artificial intestinal juice environment. After adding the said tannins, the concentration of rifampicin was decreased significantly in both environments, and the concentration of rifampicin in artificial intestinal juice remained relatively stable, while that in artificial gastric juice remained the original downward trend. The pharmacokinetic parameters displayed that as compared with rifampicin alone, AUC0-t and Cmax were decreased significantly, MRT0-t slowed down significantly, Tmax doubled to 7.0 h and the bioavailability was only 31.65% in rifampicin + tannins in Galla Chinensis group. The experiment indicated rifampicin had a poor solubility in acidic environment and the decrease of bioavailability of rifampicin when in combination with tannin was mainly due to the reduction of rifampicin solubility in intestinal tract by complexation of rifampicin with tannin, thus affecting its absorption in intestinal tract. Therefore, rifampicin and the Chinese herbal medicines or Chinese patent medicines rich in tannin should not be taken simultaneously.

In vivo assessment of immunomodulatory activity of hydrolysed peptides from Corylus heterophylla Fisch.

BACKGROUND: Hazelnut dregs are by-products of hazelnut oil expression, which have not been fully exploited. This research aims to assess the immunomodulatory function of hazelnut hydrolysed peptides (HHPs). RESULTS: HHPs with a hydrolysis degree of 38.08% were divided into three fractions by ultra-filtration: the high molecular weight peptide (>10 kDa), medium molecular weight peptide (3 kDa to 10 kDa), and low molecular weight peptide (<3 kDa). Mice were fed daily with HHPs of different molecular weights at doses of 200, 400, and 800 mg kg(-1) body weight. On the 10th, 20th and 30th day of feeding, representative immune indexes were measured. Results showed that HHPs can regulate the immune system of mice, which is affected by the molecular weight of HHP and the feeding time. Generally, short-term feeding (10 d to 20 d) with HHPs of different molecular weights can improve most immune indexes (organ index, spleen lymphocyte proliferation, macrophage activity, secretory immunoglobulin A content, and number of CD4(+) and CD8(+) T cells), whereas during long-term feeding (30 d), low molecular weight HHP can better sustain immune regulation. CONCLUSION: HHPs exhibit potential immunomodulatory properties, which has promising implications for the development of new functional foods. © 2015 Society of Chemical Industry.

Glucosylceramides are required for mycelial growth and full virulence in Penicillium digitatum.

Glucosylceramides (GlcCers) are important lipid components of the membrane systems of eukaryotes. Recent studies have suggested the roles for GlcCers in regulating fungal growth and pathogenesis. In this study, we report the identification and functional characterization of PdGcs1, a gene encoding GlcCer synthase (GCS) essential for the biosynthesis of GlcCers, in Penicilliumdigitatum genome. We demonstrated that the deletion of PdGcs1 in P. digitatum resulted in the complete loss of production of GlcCer (d18:1/18:0 h) and GlcCer (d18:2/18:0 h), a decrease in vegetation growth and sporulation, and a delay in spore germination. The virulence of the PdGcs1 deletion mutant on citrus fruits was also impaired, as evidenced by the delayed occurrence of water soaking lesion and the formation of smaller size of lesion. These results suggest that PdGcs1 is a bona fide GCS that plays an important role in regulating cell growth, differentiation, and virulence of P. digitatum by controlling the biosynthesis of GlcCers.

Pharmacodynamic and targeted amino acid metabolomics researches on the improvement of diabetic retinopathy with Fufang Xueshuantong component compatibility.

The Fufang Xueshuantong capsule (FXT) has significant preventive and therapeutic effects on diabetic retinopathy(DR), but the compatibility of its active components remains to be thoroughly explored. In this study, a zebrafish diabetic retinopathy model was established using high-mixed sugars, and the optimal ratios of notoginseng total saponins, total salvianolic acid, astragaloside, and harpagide were selected through orthogonal experiments. Furthermore, we used UPLC-QqQ/MS to detect the changes in amino acid content of DR zebrafish tissues after administration of FXT and its compatible formula to analyze the effects of FXT and its compatible formula on amino acid metabolites. The results showed that the final compatibility ratios of the components were 8: 5: 1: 6.6 by comprehensive evaluation of the indicators. FXT and its compatibility formula had beneficial effects on retinal vasodilatation, lipid accumulation in the liver, total glucose, and VEGF levels in DR zebrafish, and all of them could call back some amino acid levels in DR zebrafish. In this research, we determined the compatible formulation of the active ingredients in the FXT and investigated their efficacy in DR zebrafish for further clinical applications.

Structural homeostasis and controlled release for anthocyanin in oral film via sulfated polysaccharides complexation.

Oral film is a novel functional carrier, which can provide a new pathway for the efficient absorption of anthocyanin. However, anthocyanin homeostasis in oral film is a prerequisite for achieving efficient absorption and utilization of anthocyanin. Herein, three sulfated polysaccharides, including chondroitin sulfate (CS), fucoidin (FU) and λ-carrageenan (λ-CG), were complexed with blueberry anthocyanin (BA) to prepare oral film formulations using hydroxypropyl methylcellulose (HPMC) as a film-forming matrix. The addition of three sulfated polysaccharides improved the stability of BA in content and color, which were associated with interactions between BA and polysaccharides. The BA retention rate of CS-BA/HPMC system increased 5.5-fold after 8 d of light-accelerated storage compared with the control group, showing the best homeostasis effect. CS and λ-CG enhanced the elongation at break and prolonged disintegration time of oral films. The addition of FU made the oral film denser and smoother, and had the highest BA release (75.72 %) in the simulated oral cavity system. In addition, the oral films of three sulfated polysaccharides complexed with BA showed superior antioxidant capacity. The present study provides new insights into the application of anthocyanin in film formulation carriers.