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The Transcriptome and Metabolome Reveal Stress Responses in Sulfur-Fumigated Cucumber (Cucumis sativus L.).

ABSTRACT: Sulfur (S) fumigation is a commonly used sterilization method in horticultural facilities against fungal diseases. S fumigation damaged cucumber leaves, although the response mechanism is unclear. This study analyzes the growth, transcriptome, and metabolomic profiles of young and mature leaves, ovaries, and commercial cucumber fruits to decipher the mechanism of cucumber stress response under S fumigation. S fumigation significantly changed the photosynthetic efficiency and reactive oxygen species (ROS) in leaves, but not fruit development, fruit mass, and peel color. Transcriptome analysis indicated that S fumigation strongly regulated stress defense genes. The weighted gene co-expression network analysis revealed that S fumigation regulated ASPG1, AMC1 defense genes, LECRK3, and PERK1 protein kinase. The abscisic acid (ABA)-mediated model of regulation under S fumigation was constructed. Metabolome analysis showed that S fumigation significantly upregulated or downregulated the contents of amino acids, organic acids, sugars, glycosides, and lipids (VIP > 1 and P-value < 0.05). The opposite Pearson's correlations of these differential metabolites implied that cucumber had different metabolic patterns in short-term and long-term S fumigation. Besides, the elevated levels of proline and triglyceride indicated that stress-responsive mechanisms existed in S-fumigated cucumber. Moreover, the comprehensive analysis indicated that S fumigation elevated secondary S-containing metabolites but decreased sulfate absorption and transportation in cucumber. Overall, our results provided a comprehensive assessment of S fumigation on cucumber, which laid the theoretical foundation for S fumigation in protected cultivation.

SUBMITTER: Liu J

PROVIDER: S-EPMC8636124 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of gene expression profiles of cucumber under short-term chilling stress. The goals of this study are to transcriptome analysis of cucumber leaves under chilling stress. Methods: mRNA profiles of seedlings exposed to an air temperature of 6°C in the absence of light at 0, 2, 6, and 12 h were generated by deep sequencing, in triplicate, using Illumina Hiseq platform. The reference genome and gene model annotation files were downloaded from the genome website （http://cucurbitgenomics.org/）. An index of the reference genome was built using Bowtie v.2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v.2.0.12. qRT–PCR validation was performed using SYBR Green assays. Results: A total of 55.7 million clean reads was generated. Based on the threshold values of absolute value of log2 ratio ≥ 1 and FDR ≤ 0.05, a total of 2113 DEGs was identified at three time points (2, 6, and 12 h). A total of 30 genes was detected at all time points. The number of DEGs increased with time. In total, 100 TFs from 22 families in three subsets were detected. And 19 kinase families were identified in three subsets. The DEGs identified by RNA sequencing were confirmed by qRT-PCR analysis, indicating that the data were reliable. These findings provide information that can be useful for investigating the molecular mechanisms underlying the response to chilling stress in cucumber and other plants. Conclusions: The results presented here reveal changes in the transcriptome profile of cucumber in response to chilling stress. Exposure to a low temperature induced genes involved in hormone regulation, lipid metabolism, and photosynthesis, including NAC, WRKY, AP2/ERF, ERD, MYB as well as zinc finger TFs and protein kinases such as receptor-like protein kinase, MAPK, and CDK. Most TFs were upregulated whereas CDKs were downregulated. These findings provide information that can be useful for investigating the molecular mechanisms underlying the response to chilling stress in cucumber and other plants.

Project description:BackgroundOvary culture is a useful technique used to generate double haploid (DH) cucumber (Cucumis sativus L.) plants. However, cucumber ovary culture have a low rate of embryo induction and plant regeneration. Moreover, the cucumber embryogenesis mechanism remains unclear. In this study, we explored the molecular basis of cucumber embryogenesis in order to establish a foundation for a more efficient ovary culture method. Using transcriptome sequencing, we also investigated the differential expression of genes during the embryogenesis process.MethodsCytological and morphological observations have divided cucumber ovary culture into three stages: early embryo development (T0), embryo morphogenesis (T1, T2, T3 and T4), and shoot formation (T5). We selected six key time points for transcriptome sequencing and analysis: T0 (the ovules were cultured for 0 d), T1 (the ovules were cultured for 2 d), T2 (the embryos were cultured for 10 d), T3 (the embryos were cultured for 20 d), T4 (the embryos were cultured for 30 d), and T5 (the shoots after 60 d culture).ResultsWe used cytology and morphology to observe the characteristics of the cucumber's developmental transformation during embryogenesis and plant regeneration. The differentially expressed genes(DEGs) at developmental transition points were analyzed using transcriptome sequencing. In the early embryogenesis stage, the cells expanded, which was the signal for gametophytes to switch to the sporophyte development pathway. RNA-seq revealed that when compared to the fresh unpollinated ovaries, there were 3,468 up-regulated genes in the embryos, including hormone signal transduction genes, hormone response genes, and stress-induced genes. The reported embryogenesis-related genes BBM, HSP90 and AGL were also actively expressed during this stage. In the embryo morphogenesis stage (from cell division to cotyledon-embryo formation), 480 genes that functioned in protein complex binding, microtubule binding, tetrapyrrole binding, tubulin binding and other microtubule activities were continuously up-regulated during the T1, T2, T3 and T4 time points. This indicated that the cytoskeleton structure was continuously being built and maintained by the action of microtubule-binding proteins and enzyme modification. In the shoot formation stage, 1,383 genes were up-regulated that were mainly enriched in phenylpropanoid biosynthesis, plant hormone signal transduction, phenylalanine metabolism, and starch and sucrose metabolism. These up-regualted genes included six transcription factors that contained a B3 domain, nine genes in the AP2/ERF family, and two genes encoding WUS homologous domain proteins.ConclusionsEvaluation of molecular gynogenesis events may contribute to a better understanding of the molecular mechanism of cucumber ovarian culture.

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The Transcriptome and Metabolome Reveal Stress Responses in Sulfur-Fumigated Cucumber (Cucumis sativus L.).

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