Expression profiling of the phenylalanine ammonia-lyase (PAL) gene family in ginkgo biloba L.

The PAL gene family plays an important role in plant growth, development, and response to abiotic stresses and has been identified in a variety of plants. However, a systematic characterization is still lacking in Ginkgo biloba. Using a bioinformatics approach, 11 GbPAL members of the PAL gene family identified in ginkgo were identified in this study. The protein structure and physicochemical properties indicated that the GbPAL genes were highly similar. Based on their exon-intron structures, they can be classified into three groups. A total of 62 cis-elements for hormone, light, and abiotic stress responses were identified in the promoters of GbPAL genes, indicating that PAL is a multifunctional gene family. GbPAL genes were specifically expressed in different tissues and ploidy of ginkgo. These results provide a theoretical basis for further studies on the functional expression of the GbPAL genes.

Morphological Characteristics, Ultrastructure, and Chemical Constituents of the Endotesta in Ginkgo (Ginkgo biloba L.).

Ginkgo biloba L. is a tree species of significant economic and ecological importance. Prior studies of the Ginkgo biloba seed coat have predominantly focused on the sarcotesta and sclerotesta, with less attention paid to the endotesta. In this study, the development and formation of Ginkgo endotesta were examined using light microscopy and transmission electron microscopy. The structural properties of the mature endotesta were analyzed using micro-CT imaging and scanning electron microscopy. The results indicate that the endotesta possess a membranous structure primarily originating from the inner bead peridium, a segment of bead core tissue, and the macrospore membrane. The endotesta from the middle constriction line to the chalazal end comprises a single layer with a greyish-white papery structure. In contrast, the endotesta was divided into two inner and two outer layers, from the middle constriction line to the micropylar end. The outer endosperm adheres closely to the sclerotesta, while the inner endosperm adheres to the seed kernel. The surface of the endotesta was irregularly raised, with thicker wax at the chalazal end, whereas the micropylar end demonstrated similar characteristics with thinner wax and tumor layers. The endotesta contained 17 amino acids, 18 fatty acids, 10 trace elements, and 7 vitamins. Overall, its nutritional value was relatively well balanced.

Genetic diversity, population structure, and genome-wide association analysis of ginkgo cultivars.

Ginkgo biloba is an economically valuable tree worldwide. The species has nearly become extinct during the Quaternary, which has likely resulted in reduction of its genetic variability. The genetic variability is now conserved in few natural populations in China and a number of cultivars that are, however, derived from a few ancient trees, helping the species survive in China through medieval times. Despite the recent interest in ginkgo, however, detailed knowledge of its genetic diversity, conserved in cultivated trees and cultivars, has remained poor. This limits efficient conservation of its diversity as well as efficient use of the existing germplasm resources. Here we performed genotyping-by-sequencing (GBS) on 102 cultivated germplasms of ginkgo collected to explore their genetic structure, kinship, and inbreeding prediction. For the first time in ginkgo, a genome-wide association analysis study (GWAS) was used to attempt gene mapping of seed traits. The results showed that most of the germplasms did not show any obvious genetic relationship. The size of the ginkgo germplasm population expanded significantly around 1500 years ago during the Sui and Tang dynasties. Classification of seed cultivars based on a phylogenetic perspective does not support the current classification criteria based on phenotype. Twenty-four candidate genes were localized after performing GWAS on the seed traits. Overall, this study reveals the genetic basis of ginkgo seed traits and provides insights into its cultivation history. These findings will facilitate the conservation and utilization of the domesticated germplasms of this living fossil plant.

A complete chloroplast genome of bamboo cultivar Phyllostachys edulis f. bicolor (Poaceae: Bambusoideae).

Phyllostachys edulis f. bicolor, a beautiful ornamental bamboo species, is a new variant of P. edulis, with yellow stems and green grooves between nodes. In this study, we assembled and annotated the complete chloroplast (cp) genome of this variety for the first time. The complete cp genome size of P. edulis f. bicolor was 139,678 bp in length and a total of 130 unique genes were annotated, including 85 protein-coding genes, 37 tRNA encoding genes, and eight rRNA encoding genes. Phylogenetic analysis results provided evidence that P. edulis f. bicolor was closely related to P. edulis 'heterocycla'. This study contributes to better understanding of intraspecific type evolution of P. edulis.

Non-thermal plasma modulation of the interaction between whey protein isolate and ginsenoside Rg1 to improve the rheological and oxidative properties of emulsion.

Molecular interaction forces regulate the interfacial properties of oil-in-water emulsion and play a key role in the rheology and stability of the emulsion in the food industry. In this study, the effects of non-thermal plasma (NTP) treatment on the structural and functional properties of whey protein isolate (WPI) and its binding interaction with ginsenoside Rg1 (GR1) were investigated. The results based on surface hydrophobicity, infrared spectroscopy and fluorescence spectroscopy test showed that the NTP treatment induced the unfolding of the structure of WPI and promoted the binding affinity between WPI and GR1. By comparing with untreated WPI (an α-helix content of 19.63 % and a ß-sheet content of 31.66 %), there was a greater decrease in α-helix content and an increase in ß-sheet content of WPI in N20-WPI (α-helix = 9.63 %, ß-sheet = 39.63 %) and N20-WPI-GR1 (α-helix = 4.98 %, ß-sheet = 48.66 %) groups. Importantly, the NTP treatment increased the interfacial adsorption and antioxidant capacity of the WPI-GR1 complexes, which contributed to the improvement of the rheological properties and oxidation stability of the emulsion. As a result, the NTP treatment could markedly improve the rheological and antioxidative properties of the WPI-GR1 complexes and the NTP-treated WPI-GR1 emulsions was more stable than that untreated. The present research indicated that NTP-treated formation of protein-saponin complexes could enhance the functional properties of the proteins, thus expanding their application as functional ingradients in nutritionally fortified food.

Transcriptome and proteome associated analysis of flavonoid metabolism in haploid Ginkgo biloba.

Having different number if genome copies affect transcription and metabolite production of plants. This may be due to different gene transcription and protein expression, but the reasons for this remains poorly known. Here we measured flavonoid content in leaves of three haploid and diploid grafted plants of Ginkgo biloba, a model gymnosperm important economically for its flavonoid content. We reported the first combined transcriptomic and proteomic analysis of the difference in flavonoid content in three haploid ginkgos to investigate the effect of haploidy. Haploids had always smaller leaves and flavonoid content than the diploids. The selected haploid had also generally lower gene dosage than the selected diploid, with 1149 up-regulated (46.8 %) and 1309 down-regulated (53.2 %) among 2452 differentially expressed genes (DEGs). Of 686 differentially expressed proteins (DEPs) detected, 289 proteins (42.1 %) were upregulated, and 397 proteins (57.9 %) were downregulated in haploids. A particular attention deserves the downregulation of PAL, PAM, FLS, OMT1 hub genes involved in flavonoid biosynthesis regulation. Our study confirms the trend of haploids to have lower metabolic contents and points that lower flavonoid content in ginkgo monoploids could be due to reduced dosage of the corresponding regulatory genes and downregulation of genes involved in flavonoid synthesis.

Efficient saccharification of Lycium barbarum leaf biomass by using enzyme cocktails produced by a novel fungus Aspergillus costaricensis LS18.

The utilization of agro-industrial residues is an interesting issue contributing to sustainable development and environmental protection. Lycium barbarum leaves (LBL) are agro-industrial residues of the L. barabrum berry cultivation and seriously underutilized, leading to resource waste and environmental pollution. In this study, we prepared cost-effective enzyme cocktails with high xylanase activity from a novel soil-derived fungal strain Aspergillus costaricensis LS18. The xylanase activity of these on-site produced enzyme cocktails was 3.49 ± 0.55 U/mL. Through the hydrolysis using the enzyme cocktails with 6% substrate loading at 45 °C for 12 h, 86.57 ± 1.81% of total reducing sugars (RS) from LBL was released. The concentration of RS in the hydrolysates reached 8.17 ± 0.33 mg/mL. In this study, LBL were added values by two mutually independent bioprocess ways. On the one hand, LBL were used as the only nutrients in the medium for the on-site production of enzyme cocktails by fermentation. On the other hand, through hydrolysis using this enzyme cocktail, LBL biomass was efficiently hydrolyzed and fermentable monosugars were gained. This study could benefit to the exploitation of LBL resources and provide the references for utilization of other agro-industrial residues.

High-Depth Transcriptome Reveals Differences in Natural Haploid Ginkgo biloba L. Due to the Effect of Reduced Gene Dosage.

As a representative of gymnosperms, the discovery of natural haploids of Ginkgo biloba L. has opened a new door for its research. Haploid germplasm has always been a research material of interest to researchers because of its special characteristics. However, we do not yet know the special features and mechanisms of haploid ginkgo following this significant discovery. In this study, we conducted a homogenous garden experiment on haploid and diploid ginkgo to explore the differences in growth, physiology and biochemistry between the two. Additionally, a high-depth transcriptome database of both was established to reveal their transcriptional differences. The results showed that haploid ginkgo exhibited weaker growth potential, lower photosynthesis and flavonoid accumulation capacity. Although the up-regulated expression of DEGs in haploid ginkgo reached 46.7% of the total DEGs in the whole transcriptome data, the gene sets of photosynthesis metabolic, glycolysis/gluconeogenesis and flavonoid biosynthesis pathways, which were significantly related to these differences, were found to show a significant down-regulated expression trend by gene set enrichment analysis (GSEA). We further found that the major metabolic pathways in the haploid ginkgo transcriptional database were down-regulated in expression compared to the diploid. This study reveals for the first time the phenotypic, growth and physiological differences in haploid ginkgos, and demonstrates their transcriptional patterns based on high-depth transcriptomic data, laying the foundation for subsequent in-depth studies of haploid ginkgos.

Traditional uses, phytochemistry, pharmacology and current uses of underutilized Xanthoceras sorbifolium bunge: A review.

ETHNOPHARMACOLOGICAL RELEVANCE: The Plant Xanthoceras sorbifolium Bunge (X. sorbifolia) has a long history of medicinal use as a traditional Chinese herbal medicine to deal with sterilizing, killing sperm, stabilizing capillary, hemostasis, lowering cholesterol, rheumatism, and pediatric enuresis. Additionally, X. sorbifolia is an oil crop for the production of edible oil due to the health-promotion effect. In recent years, X. sorbifolia has attracted worldwide attention as an important economic crop with low investment and high-income potential. AIM OF THE REVIEW: This review aims to provide a comprehensive appraisal of X. sorbifolia, including the traditional uses, nutrients, phytochemical data, biological activities, and current applications. The natural compounds of X. sorbifolia and potential utilization in pharmacology are highlighted. The aim of this review is to inspire the research enthusiasm to X. sorbifolia and promote the comprehensive utilization of X. sorbifolia. MATERIALS AND METHODS: The research information of X. sorbifolia was collected via Elsevier, American Chemical Society (ACS), PubMed, Web of Science, China National Knowledge Infrastructure (CNKI), Baidu scholar, and Google scholar. Additionally, some information was collected from Ph.D. and Master's dissertations, as well as local books. RESULTS: The identification of approximately 195 major phytochemical compounds from different parts of X. sorbifolia is presented in this review, including triterpenoids, flavonoids, phenolic acids, coumarins, lignans, meroterpenoids, monoterpene, alkaloids, and sterol. Among them, triterpenoids, flavonoids, and phenolic acids are the major compounds. Extracts from X. sorbifolia exhibited a wide range of biological activities, such as antioxidant, antibacterial, anti-tumor, anti-neuroinflammatory, anti-adipogenesis, anti-obesity, anti-HIV, gastroprotective, immunoregulatory, and anti-inflammatory activities. CONCLUSIONS: Modern pharmacological studies have been well supported and clarified the traditional medicinal uses of X. sorbifolia, which brought a promising prospect for the pharmaceutical value of this plant. However, the related mechanisms between the structure and pharmacological effects were seldom reported. Also, at present, effective and in-depth research on X. sorbifolia is still relatively lacking. Moreover, there is little research on toxicological experiments. Further clinical trials should also be performed to accelerate the drug research and development.

Genome-Wide Identification and Expression Analysis of the Plant U-Box Protein Gene Family in Phyllostachys edulis.

The U-box gene encodes a ubiquitin ligase that contains a U-box domain. The plant U-box (PUB) protein plays an important role in the plant stress response; however, very few studies have investigated the role of these proteins in Moso bamboo (Phyllostachys edulis). Thus, more research on PUB proteins is necessary to understand the mechanisms of stress tolerance in P. edulis. In this study, we identified 121 members of the PUB family in P. edulis (PePUB), using bioinformatics based on the P. edulis V2 genome build. The U-box genes of P. edulis showed an uneven distribution among the chromosomes. Phylogenetic analysis of the U-box genes between P. edulis and Arabidopsis thaliana suggested that these genes can be classified into eight subgroups (Groups I-VIII) based on their structural and phylogenetic features. All U-box genes and the structure of their encoded proteins were identified in P. edulis. We further investigated the expression pattern of PePUB genes in different tissues, including the leaves, panicles, rhizomes, roots, and shoots. The qRT-PCR results showed that expression of three genes, PePUB15, PePUB92, and PePUB120, was upregulated at low temperatures compared to that at 25°C. The expression levels of two PePUBs, PePUB60 and PePUB120, were upregulated under drought stress. These results suggest that the PePUB genes play an important role in resistance to low temperatures and drought in P. edulis. This research provides new insight into the function, diversity, and characterization of PUB genes in P. edulis and provides a basis for understanding their biological roles and molecular mechanisms.

Lignans and phenylpropanoids from the liquid juice of phyllostachys edulis.

Seven lignans and eight phenylpropanoids, including one new lignan, 7S,8R,8'R-5,5'-dimethoxyariciresinol-4-O-ß-D-glucopyranoside (1), were isolated from the liquid juice of Phyllostachys edulis. Their structures were established by extensive spectroscopic analyses. The absolute configuration of the new compound was determined by comparing its experimental electronic circular dichroism (ECD) spectra with calculated ECD spectra. All compounds were evaluated for their anti-inflammatory activity and xanthine oxidase inhibitor activity, and the results showed that compound 9 exhibited a moderate activity in these two bioassays. In addition, all the compounds can be detected in health panda faeces by LC-MS.

Identification and quantitation of the actual active components in bamboo juice and its oral liquid by NMR and UPLC-Q-TOF-MS.

Bamboo juice is a traditional Chinese drink and herbal medicine, and bamboo juice oral liquids are widely sold for the treatment of cough and phlegm in China. In this study, 26 main compounds of bamboo juice (Phyllostachys edulis) were separated, precisely identified, and qualitative analysis using NMR (nuclear magnetic resonance) and quantitative analysis using UPLC-Q-TOF-MS (ultra-performance liquid chromatography with high-resolution quadrupole time-of-flight mass spectrometer), respectively. Potentially harmful levels of added excessive preservatives, including benzoic acid, ethylparaben, and sorbic acid, were found in bamboo juice oral liquid. Carbohydrates were determined to be the major components of bamboo juice, with contents as high as 191.13 g L-1, far higher than those of other compounds. The result indicated that the cough relief activity of bamboo juice oral liquid may be related to their high levels of added preservatives.

The genetic diversity and population structure of Sophora alopecuroides (Faboideae) as determined by microsatellite markers developed from transcriptome.

Sophora alopecuroides (Faboideae) is an endemic species, mainly distributed in northwest China. However, the limited molecular markers range for this species hinders breeding and genetic studies. A total of 20,324 simple sequence repeat (SSR) markers were identified from 118,197 assembled transcripts and 18 highly polymorphic SSR markers were used to explore the genetic diversity and population structure of S. alopecuroides from 23 different geographical populations. A relatively low genetic diversity was found in S. alopecuroides based on mean values of the number of effective alleles (Ne = 1.81), expected heterozygosity (He = 0.39) and observed heterozygosity (Ho = 0.55). The results of AMOVA indicated higher levels of variation within populations than between populations. Bayesian-based cluster analysis, principal coordinates analysis and Neighbor-Joining phylogeny analysis roughly divided all genotypes into four major groups with some admixtures. Meanwhile, geographic barriers would have restricted gene flow between the northern and southern regions (separated by Tianshan Mountains), wherein the two relatively ancestral and independent clusters of S. alopecuroides occur. History trade and migration along the Silk Road would together have promoted the spread of S. alopecuroides from the western to the eastern regions of the northwest plateau in China, resulting in the current genetic diversity and population structure. The transcriptomic SSR markers provide a valuable resource for understanding the genetic diversity and population structure of S. alopecuroides, and will assist effective conservation management.

Selection of reference genes for quantitative real-time PCR in bamboo (Phyllostachys edulis).

BACKGROUND: The Moso bamboo (Phyllostachys edulis) is one of the most important forestry resources and plays essential ecological roles in southern China. A draft nuclear genome sequence is expected to be publicly available in the near future; an explosion of gene expression data related to the unique traits of Moso bamboo will undoubtedly follow. Reverse transcription quantitative real-time PCR ((RT-)qPCR) is a widely used method for gene expression analysis. A necessary prerequisite of exact and reliable data is the accurate choice of reference genes. RESULT: In this study, 14 candidate reference genes were chosen, and their expression levels were assessed by (RT-)qPCR in a set of six tissue samples (root, stem, mature stem, leaf, flower, and leaf sheath) and at two developmental stages (before and after flowering) in bamboo specimens obtained in three locations. The stability and suitability of the candidate reference genes were validated using the geNorm, NormFinder and BestKeeper programs. The results showed that TIP41 and NTB were suitable reference genes across all the tissues and at the different developmental stages examined in this study. While the expression of the NTB, TIP41 and UBQ were the mostly stable in different plant tissues samples, the expression of the TIP41, NTB and CAC were ranked the most stable in bamboo plants at various developmental stages. AP2-like gene was further assessed by using the reference genes TIP41 and NTB in comparison to ACT. Significant difference of the expression profile of AP2-like demonstrated the importance of choosing adequate reference genes in bamboo. CONCLUSION: TIP41 and NTB were found to be homogeneously expressed and were adequate for normalization purposes, showing equivalent transcript levels in different samples. They are therefore the recommended reference genes for measuring gene expression in P. edulis.

[Regeneration of Phyllostachys heteroclada and its relations with rhizome carbon- and nitrogen metabolism].

In order to search for the ways to restrain the flowering process and promote the regeneration of bamboo (Phyllostachys heteroclada), five types of regeneration experiments were conducted, including 1) harvesting all the bamboos in the first year and the flowered bamboos in the next year all at the beginning stage of florescence, 2) harvesting the flowered bamboos at the beginning stage of florescence in two consecutive years, 3) harvesting the fully flowered bamboos in the first year and the bamboos at the beginning stage of florescence in the next year, 4) fertilizing the bamboo floor before growing season in consecutive two years, and 5) no any manipulation. In each of the cases, the carbon- and nitrogen metabolism and related enzyme activities in bamboo rhizome were studied. The results showed that treatment 1 had the best effect, which resulted in the greatest number (207) of new shoots produced and with the highest survival rate (69.33%), and had the most obvious effect on restraining bamboo flowering and promoting regeneration. Also, it produced the highest contents of soluble sugar (10.89%) and total sugar (20.39%), the highest total sugar to total nitrogen ratio (34.56), and the highest glutamine synthetase activity (104.52 mg x g(-1) x h(-1)) in bamboo rhizome. These findings demonstrated that the carbon- and nitrogen metabolism in the rhizome had definite relationships with the flowering process and regeneration of bamboo, and the rhizome growth played a critical role in bamboo propagation.