Comparative RNA-Seq Analysis of High- and Low-Oil Yellow Horn During Embryonic Development

Toxic effects and safety assessment of Xanthoceras sorbifolium bunge seed kernels

ETHNOPHARMACOLOGICAL RELEVANCE

Xanthoceras sorbifolium Bunge (X. sorbifolia), an oil crop native to northern China, is valued for both its edible and medicinal uses. It has various applications, including the production of edible and bioactive oils, and is used in traditional medicine for its antioxidant and anti-inflammatory properties. However, the toxicity of X. sorbifolia, particularly its widely used seed kernels, remains unclear.

AIM OF THE STUDY

This study aimed to evaluate the acute toxicity and safety risks of X. sorbifolia seed kernels based on human-recommended doses by in vitro or in vivo experiments, and integrating network analysis.

MATERIALS AND METHODS

In this study, rats and mice were employed as model organisms to investigate the acute toxicity of X. sorbifolia seed kernels. The experiments included the Salmonella typhimurium reverse mutation test, red blood cell micronucleus test, spermatocyte chromosome aberration test in mice, and a 90-day exposure study in rats to assess the potential toxicity and safety risks of the seed kernels. Based on this, combined with The Comparative Toxicogenomics Database (CTD), the biological functions of the main active ingredients of X. sorbifolia were further explored through integrated network analysis, and the anti-inflammatory effect of X. sorbifolia was explored through cotton ball granuloma inflammation experiment.

RESULTS

During the experimental period, animals in all treatment groups demonstrated normal growth and development. Although some detection indicators showed significant differences in different treatment groups, the results were still within a reasonable range. In addition, by screening the CTD, 120 target genes with potential interactions of the main active ingredients in the kernel of X. sorbifolia were obtained for analysis, and it was found that these genes were involved in important biological processes such as response to oxidative stress, response to reactive oxygen species, and regulation of inflammatory response. The cotton ball granuloma inflammation experiment in rats also suggested that X. sorbifolia tended to inhibit the proliferation of granulomas, indicating that the kernel of X. sorbifolia has potential anti-inflammatory and antioxidant properties.

CONCLUSION

The findings suggested that X. sorbifolia seed kernels were safe within the recommended dosage range. As a traditional Chinese medicine prescription, it has certain anti-inflammatory and antioxidant effects. This study provides valuable reference guidelines for the clinical application of X. sorbifolia seed kernels and encourages further research into its potential uses and safety.

Agronomic, physiological and transcriptional characteristics provide insights into fatty acid biosynthesis in yellowhorn (Xanthoceras sorbifolium Bunge) during fruit ripening

Yellowhorn (Xanthoceras sorbifolium Bunge) is an oil-bearing tree species in northern China. In this study, we used yellowhorn from Heilongjiang to analyze the morphological and physiological changes of fruit development and conducted transcriptome sequencing. The results showed that the fruit experienced relatively slow growth from fertilization to DAF20 (20 days after flowering). From DAF40 to DAF60, the fruit entered an accelerated development stage, with a rapid increase in both transverse and longitudinal diameters, and the kernel contour developed completely at DAF40. From DAF60 to DAF80, the transverse and vertical diameters of the fruit developed slowly, and the overall measures remained stable until maturity. The soluble sugar, starch, and anthocyanin content gradually accumulated until reaching a peak at DAF80 and then rapidly decreased. RNA-seq analysis revealed differentially expressed genes (DEGs) in the seed coat and kernel, implying that seed components have different metabolite accumulation mechanisms. During the stages of seed kernel development, k-means clustering separated the DEGs into eight sub-classes, indicating gene expression shifts during the fruit ripening process. In subclass 8, the fatty acid biosynthesis pathway was enriched, suggesting that this class was responsible for lipid accumulation in the kernel. WGCNA revealed ten tissue-specific modules for the 12 samples among 20 modules. We identified 54 fatty acid biosynthesis pathway genes across the genome, of which 14 was quantified and confirmed by RT-qPCR. Most genes in the plastid synthesis stage showed high expression during the DAF40-DAF60 period, while genes in the endoplasmic reticulum synthesis stage showed diverse expression patterns. EVM0012847 (KCS) and EVM0002968 (HCD) showed similar high expression in the early stages and low expression in the late stages. EVM0022385 (HCD) exhibited decreased expression from DAF40 to DAF60 and then increased from DAF60 to DAF100. EVM0000575 (KCS) was increasingly expressed from DAF40 to DAF60 and then decreased from DAF60 to DAF100. Finally, we identified transcription factors (TFs) (HB-other, bHLH and ARF) that were predicted to bind to fatty acid biosynthesis pathway genes with significant correlations. These results are conducive to promoting the transcriptional regulation of lipid metabolism and the genetic improvement in terms of high lipid content of yellowhorn.

The lysosome-phagosome pathway mediates immune regulatory mechanisms in Mesocentrotus nudus against Vibrio coralliilyticus infection

Sea urchins are a popular model species for studying invertebrate diseases. The immune regulatory mechanisms of the sea urchin Mesocentrotus nudus during pathogenic infection are currently unknown. This study aimed to reveal the potential molecular mechanisms of M. nudus during resistance to Vibrio coralliilyticus infection by integrative transcriptomic and proteomic analyses. Here, we identified a total of 135,868 unigenes and 4,351 proteins in the four infection periods of 0 h, 20 h, 60 h and 100 h in M. nudus. In the I20, I60 and I100 infection comparison groups, 10,861, 15,201 and 8,809 differentially expressed genes (DEGs) and 2,188, 2,386 and 2,516 differentially expressed proteins (DEPs) were identified, respectively. We performed an integrated comparative analysis of the transcriptome and proteome throughout the infection phase and found very a low correlation between transcriptome and proteome changes. KEGG pathway analysis revealed that most upregulated DEGs and DEPs were involved in immune strategies. Notably, "lysosome" and "phagosome" activated throughout the infection process, could be considered the two most important enrichment pathways at the mRNA and protein levels. The significant increase in phagocytosis of infected M. nudus coelomocytes further demonstrated that the lysosome-phagosome pathway played an important immunological role in M. nudus resistance to pathogenic infection. Key gene expression profiles and protein‒protein interaction analysis revealed that cathepsin family and V-ATPase family genes might be key bridges in the lysosome-phagosome pathway. In addition, the expression patterns of key immune genes were verified using qRT‒PCR, and the different expression trends of candidate genes reflected, to some extent, the regulatory mechanism of immune homeostasis mediated by the lysosome-phagosome pathway in M. nudus against pathogenic infection. This work will provide new insights into the immune regulatory mechanisms of sea urchins under pathogenic stress and help identify key potential genes/proteins for sea urchin immune responses.

Lysophosphatidic acid acyltransferase 2 and 5 commonly, but differently, promote seed oil accumulation in Brassica napus

Background

Increasing seed oil content (SOC) of Brassica napus has become one of the main plant breeding goals over the past decades. Lysophosphatidic acid acyltransferase (LPAT) performs an important molecular function by regulating the production of phosphatidic acid (PA), a key intermediate in the synthesis of membrane and storage lipids. However, the mechanism underlying the effect of LPAT on the SOC of B. napus remains unclear.

Results

In the present study, significant elevation of SOC was achieved by overexpressing BnLPAT2 and BnLPAT5 in B. napus. RNAi and CRISPR–Cas9 were also successfully used to knock down and knock out these two genes in B. napus where SOC significantly decreased. Meanwhile, we found an accumulation of lipid droplets and oil bodies in seeds of BnLPAT2 and BnLPAT5 overexpression lines, whereas an increase of sugar and protein in Bnlpat2 and Bnlpat5 mutant seeds. Sequential transcriptome analysis was further performed on the developing seeds of the BnLPAT2 and BnLPAT5 overexpression, knockdown, and knockout rapeseed lines. Most differentially expressed genes (DEGs) that were expressed in the middle and late stages of seed development were enriched in photosynthesis and lipid metabolism, respectively. The DEGs involved in fatty acid and lipid biosynthesis were active in the overexpression lines but were relatively inactive in the knockdown and knockout lines. Further analysis revealed that the biological pathways related to fatty acid/lipid anabolism and carbohydrate metabolism were specifically enriched in the BnLPAT2 overexpression lines.

Conclusions

BnLPAT2 and BnLPAT5 are essential for seed oil accumulation. BnLPAT2 preferentially promoted diacylglycerol synthesis to increase SOC, whereas BnLPAT5 tended to boost PA synthesis for membrane lipid generation. Taken together, BnLPAT2 and BnLPAT5 can jointly but differently promote seed oil accumulation in B. napus. This study provides new insights into the potential mechanisms governing the promotion of SOC by BnLPAT2 and BnLPAT5 in the seeds of B. napus.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13068-022-02182-2.

Editing of the starch branching enzyme gene SBE2 generates high-amylose storage roots in cassava

The production of high-amylose cassava through CRISPR/Cas9-mediated mutagenesis of the starch branching enzyme gene SBE2 was firstly achieved. High-amylose cassava (Manihot esculenta Crantz) is desirable for starch industrial applications and production of healthier processed food for human consumption. In this study, we report the production of high-amylose cassava through CRISPR/Cas9-mediated mutagenesis of the starch branching enzyme 2 (SBE2). Mutations in two targeted exons of SBE2 were identified in all regenerated plants; these mutations, which included nucleotide insertions, and short or long deletions in the SBE2 gene, were classified into eight mutant lines. Three mutants, M6, M7 and M8, with long fragment deletions in the second exon of SBE2 showed no accumulation of SBE2 protein. After harvest from the field, significantly higher amylose (up to 56% in apparent amylose content) and resistant starch (up to 35%) was observed in these mutants compared with the wild type, leading to darker blue coloration of starch granules after quick iodine staining and altered starch viscosity with a higher pasting temperature and peak time. Further ¹H-NMR analysis revealed a significant reduction in the degree of starch branching, together with fewer short chains (degree of polymerization [DP] 15-25) and more long chains (DP>25 and especially DP>40) of amylopectin, which indicates that cassava SBE2 catalyzes short chain formation during amylopectin biosynthesis. Transition from A- to B-type crystallinity was also detected in the starches. Our study showed that CRISPR/Cas9-mediated mutagenesis of starch biosynthetic genes in cassava is an effective approach for generating novel varieties with valuable starch properties for food and industrial applications.

Small RNA profiling for identification of microRNAs involved in regulation of seed development and lipid biosynthesis in yellowhorn

BACKGROUND

Yellowhorn (Xanthoceras sorbifolium), an endemic woody oil-bearing tree, has become economically important and is widely cultivated in northern China for bioactive oil production. However, the regulatory mechanisms of seed development and lipid biosynthesis affecting oil production in yellowhorn are still elusive. MicroRNAs (miRNAs) play crucial roles in diverse aspects of biological and metabolic processes in seeds, especially in seed development and lipid metabolism. It is still unknown how the miRNAs regulate the seed development and lipid biosynthesis in yellowhorn.

RESULTS

Here, based on investigations of differences in the seed growth tendency and embryo oil content between high-oil-content and low-oil-content lines, we constructed small RNA libraries from yellowhorn embryos at four seed development stages of the two lines and then profiled small RNA expression using high-throughput sequencing. A total of 249 known miRNAs from 46 families and 88 novel miRNAs were identified. Furthermore, by pairwise comparisons among the four seed development stages in each line, we found that 64 miRNAs (53 known and 11 novel miRNAs) were differentially expressed in the two lines. Across the two lines, 15, 11, 10, and 7 differentially expressed miRNAs were detected at 40, 54, 68, and 81 days after anthesis, respectively. Bioinformatic analysis was used to predict a total of 2654 target genes for 141 differentially expressed miRNAs (120 known and 21 novel miRNAs). Most of these genes were involved in the fatty acid biosynthetic process, regulation of transcription, nucleus, and response to auxin. Using quantitative real-time PCR and an integrated analysis of miRNA and mRNA expression, miRNA-target regulatory modules that may be involved in yellowhorn seed size, weight, and lipid biosynthesis were identified, such as miR172b-ARF2 (auxin response factor 2), miR7760-p3_1-AGL61 (AGAMOUS-LIKE 61), miR319p_1-FAD2-2 (omega-6 fatty acid desaturase 2-2), miR5647-p3_1-DGAT1 (diacylglycerol acyltransferase 1), and miR7760-p5_1-MED15A (Mediator subunit 15a).

CONCLUSIONS

This study provides new insights into the important regulatory roles of miRNAs in the seed development and lipid biosynthesis in yellowhorn. Our results will be valuable for dissecting the post-transcriptional and transcriptional regulation of seed development and lipid biosynthesis, as well as improving yellowhorn in northern China.

Growth, Physiological, and Photosynthetic Responses of Xanthoceras sorbifolium Bunge Seedlings Under Various Degrees of Salinity

Xanthoceras sorbifolium Bunge is priced for its medical and energetic values. The species also plays a key role in stabilizing ecologically fragile areas exposed to excess soil salinity. In this study, the effects of salinity on the growth, physiological, and photosynthetic parameters of X. sorbifolium Bunge were investigated. The X. sorbifolium seedlings were subjected to five salt treatments: 0 (control, CK), 70, 140, 210, and 280 mM of sodium chloride (NaCl) solutions. NaCl caused a decrease in plant height, specific leaf area, biomass, and root parameters. Leaf wilting and shedding and changes in root morphology, such as root length, root surface area, and root tips were observed. This study found that X. sorbifolium is tolerant to high salinity. Compared with the CK group, even if the concentration of NaCl was higher than 210 mM, the increase of the relative conductivity was also slow, while intercellular CO₂ concentration had a similar trend. Moreover, NaCl stress caused an increase in the malondialdehyde (MDA), soluble proteins, and proline. Among the enzymes in the plant, the catalase (CAT) activity increases first and decreased with the increase in the intensity of NaCl stress, but the salt treatment had no significant effect on superoxide dismutase (SOD) activity. The peroxidase (POD) showed an increasing trend under salt stress. It was found that the photosynthesis of X. sorbifolium was notably impacted by saline stress. NaCl toxicity induced a noticeable influence on leaf net photosynthetic rate (Pn), stomatal conductance (Gs), intercellular CO₂ concentration (Ci), transpiration rate (E), and water use efficiency (Wue). As salt concentration increased, the content of chlorophyll decreased. It can be found that a low concentration of NaCl induced the increase of photosynthetic capacity but a high-intensity exposure to stress resulted in the reduction of photosynthetic efficiency and SOD activity, which had a positive correlation. In summary, salt-induced ionic stress primarily controlled root morphology, osmotic adjustment, and enzyme activities of salt-treated X. sorbifolium leaves, whereas the low salt load could, in fact, promote the growth of roots.

Role of Xanthoceras sorbifolium MYB44 in tolerance to combined drought and heat stress via modulation of stomatal closure and ROS homeostasis

Yellowhorn (Xanthoceras sorbifolium) is an important edible woody oil tree species that is endemic to China. Drought and heat stresses are factors severely limiting the high-quality development of the yellowhorn industry. Transcription factors (TFs) play critical roles in regulating the response of woody plant species to water deficit or high temperature. However, the MYB TFs that respond to combined drought and heat stress in yellowhorn remain unclear. Here, we first investigated the physiological changes in 5 yellowhorn varieties in response to combined stress treatments. We observed significant changes in antioxidant enzyme activities and photosynthesis. The Maigaiti variety yielded the best results and was selected for subsequent experiments. An R2R3-type MYB TF, designated XsMYB44, was isolated from the leaves of yellowhorn. XsMYB44 expression was strongly induced by combined stress. Suppression of XsMYB44 expression via virus-induced gene silencing weakened yellowhorn tolerance to both individual and combined drought and heat stress, and the increased susceptibility was coupled with decreased plant height, fresh weight and relative water content and inhibited stomatal closure. Moreover, compared with the individual stresses, the combined stress caused increased reactive oxygen species levels and decreased antioxidant enzyme activities and proline content in XsMYB44-silenced plants. Furthermore, the expression levels of several defense-related genes were reduced in the XsMYB44-silenced plants. Overall, we studied the physiological characteristics of 5 yellowhorn varieties, and the results demonstrated that XsMYB44 acts as a positive regulator in the yellowhorn response to combined stress by triggering stomatal closure to maintain water levels and by modulating ROS homeostasis.

The susceptibility of Lymantria dispar larvae to Beauveria bassiana under Cd stress: A multi-omics study

Insect susceptibility to entomopathogenic microorganisms under heavy metal stress, as well as its regulatory mechanism is still poorly understood. This study aims to investigate the susceptibility of gypsy moth larvae to Beauveria bassiana under cadmium (Cd) stress (at 3.248 or 44.473 mg Cd/kg fresh food), and reveal the potential molecular mechanisms underlying the Cd effect on the larval susceptibility to B. bassiana via combined transcriptome and proteome analyses. Our results showed that pre-exposure to Cd increased the susceptibility of gypsy moth larvae to B. bassiana, and there was an additive effect between Cd exposure and B. bassiana infection on the larval mortality. Under the Cd stress at low and high concentrations, 138 and 899 differentially expressed genes (DEGs), as well as 514 and 840 differentially expressed proteins (DEPs) were identified, respectively. Immunotoxic effects induced by Cd exposure at the transcription level increased in a negative dose-response manner, with no immunity-related DEGs obtained at the low Cd concentration and a high number of immunity-related DEGs down-regulated at the high Cd concentration. In contrast, a potentially suppressed or stimulated trend in the Toll and Imd signaling pathway at protein level was revealed under low or high concentration of Cd treatment. Analysis of xenobiotics biodegradation-related pathways at both transcription and translation levels revealed that the gypsy moth larvae possessed an efficient homeostasis regulatory mechanism to the low-level Cd exposure, but exhibited a reduced xenobiotics biodegradation capability to the Cd stress at high levels. Together, these findings demonstrate Cd contamination promote the microbial-based biocontrol efficacy, and unravel the molecular regulatory network of heavy metal exposures that affects susceptibility of insects to pathogenic diseases.

Physiological and transcriptomic analyses of yellow horn (Xanthoceras sorbifolia) provide important insights into salt and saline-alkali stress tolerance

Yellow horn (Xanthoceras sorbifolia) is an oil-rich woody plant cultivated for bio-energy production in China. Soil saline-alkalization is a prominent agricultural-related environmental problem limiting plant growth and productivity. In this study, we performed comparative physiological and transcriptomic analyses to examine the mechanisms of X. sorbifolia seedling responding to salt and alkaline-salt stress. With the exception of chlorophyll content, physiological experiments revealed significant increases in all assessed indices in response to salt and saline-alkali treatments. Notably, compared with salt stress, we observed more pronounced changes in electrolyte leakage (EL) and malondialdehyde (MDA) levels in response to saline-alkali stress, which may contribute to the greater toxicity of saline-alkali soils. In total, 3,087 and 2,715 genes were differentially expressed in response to salt and saline-alkali treatments, respectively, among which carbon metabolism, biosynthesis of amino acids, starch and sucrose metabolism, and reactive oxygen species signaling networks were extensively enriched, and transcription factor families of bHLH, C2H2, bZIP, NAC, and ERF were transcriptionally activated. Moreover, relative to salt stress, saline-alkali stress activated more significant upregulation of genes related to H+ transport, indicating that regulation of intracellular pH may play an important role in coping with saline-alkali stress. These findings provide new insights for investigating the physiological changes and molecular mechanisms underlying the responses of X. sorbifolia to salt and saline-alkali stress.

Yellowhorn drought-induced transcription factor XsWRKY20 acts as a positive regulator in drought stress through ROS homeostasis and ABA signaling pathway

Yellowhorn (Xanthoceras sorbifolium) is a peculiar woody edible oil-bearing tree in China. WRKY transcription factors have specific roles in plant multiple abiotic stress responses. However, it is still not clear that the molecular mechanisms of WRKYs involve in drought tolerance in yellowhorn. In this study, we isolated a drought-induced group I WRKY gene from yellowhorn, designated as XsWRKY20. Expression of XsWRKY20 was strongly induced by PEG6000, NaCl, ABA and SA. Virus-induced gene silencing (VIGS) of XsWRKY20 reduced tolerance to drought stress in yellowhorn, as determined through physiological analyses of POD activity, SOD activity and proline content. This susceptibility was coupled with decreased expression of stress-related genes. In contrast, overexpression of XsWRKY20 in tobacco notably improved drought tolerance. Compared with the WT plants, the XsWRKY20-transgenic lines exhibited lower ROS and MDA content and higher antioxidant enzyme activity and proline content after drought treatment. Moreover, overexpression of XsWRKY20 enhanced the expression of several genes associated with encoding these antioxidant enzymes, proline biosynthesis and ABA signaling pathway. Taken together, XsWRKY20 functions as a positive regulator contributing to drought stress tolerance through either ROS homeostasis by antioxidant systems or ABA-dependent/independent gene expression pathway.

Integrated transcriptomic and metabolomic analyses of yellow horn (Xanthoceras sorbifolia) in response to cold stress

Xanthoceras sorbifolia, a medicinal and oil-rich woody plant, has great potential for biodiesel production. However, little study explores the link between gene expression level and metabolite accumulation of X. sorbifolia in response to cold stress. Herein, we performed both transcriptomic and metabolomic analyses of X. sorbifolia seedlings to investigate the regulatory mechanism of resistance to low temperature (4 °C) based on physiological profile analyses. Cold stress resulted in a significant increase in the malondialdehyde content, electrolyte leakage and activity of antioxidant enzymes. A total of 1,527 common differentially expressed genes (DEGs) were identified, of which 895 were upregulated and 632 were downregulated. Annotation of DEGs revealed that amino acid metabolism, glycolysis/gluconeogenesis, starch and sucrose metabolism, galactose metabolism, fructose and mannose metabolism, and the citrate cycle (TCA) were strongly affected by cold stress. In addition, DEGs within the plant mitogen-activated protein kinase (MAPK) signaling pathway and TF families of ERF, WRKY, NAC, MYB, and bHLH were transcriptionally activated. Through metabolomic analysis, we found 51 significantly changed metabolites, particularly with the analysis of primary metabolites, such as sugars, amino acids, and organic acids. Moreover, there is an overlap between transcript and metabolite profiles. Association analysis between key genes and altered metabolites indicated that amino acid metabolism and sugar metabolism were enhanced. A large number of specific cold-responsive genes and metabolites highlight a comprehensive regulatory mechanism, which will contribute to a deeper understanding of the highly complex regulatory program under cold stress in X. sorbifolia.

Retracted Article: Investigation of yellow horn (Xanthoceras sorbifolia Bunge) transcriptome in response to different abiotic stresses: a comparative RNA-Seq study

Yellow horn (Xanthoceras sorbifolia Bunge) is a well-known oil-rich seed shrub which can grow well in barren and arid environments in the northern part of China. Yellow horn has received worldwide attention because of its excellent economic and environmental value. However, because of its limited genetic data, little information can be found regarding the molecular defense mechanisms of yellow horn exposed to various abiotic stresses. In view of this, the current study aims to investigate the impact of different abiotic stresses (i.e. NaCl, ABA and low temperature) on the transcriptome of yellow horn using RNA-Seq. Based on the transcriptome sequencing data, approximately 27% to 45% of stress-responsive genes were found highly expressed after stress treatment for 24 h. In addition, these genes were found to be still expressed after stress treatment for 48 h. However, many additional genes were stress-regulated after 48 h treatment compared with the 24 h treatment. GO enrichment analysis revealed that the expression patterns of the stress-responsive, type-specific terms were generally down-regulated. Most shared GO terms were primarily involved in protein folding, unfolding protein binding, protein transport and protein modification. Further, transcription factors (TFs), such as ERFs, bHLH, GRAS and NAC, were found to be enriched only in the low temperature treatment group, particularly the ERF TFs families. These combined results suggested that yellow horn may have developed specific molecular defense systems against diverse abiotic stresses.