The regulation mechanism of ethephon-mediated delaying of postharvest physiological deterioration in cassava storage roots based on quantitative acetylproteomes analysis.

Ethylene plays diverse roles in post-harvest processes of horticultural crops. However, its impact and regulation mechanism on the postharvest physiological deterioration (PPD) of cassava storage roots is unknown. In this study, a notable delay in PPD of cassava storage roots was observed when ethephon was utilized as an ethylene source. Physiological analyses and quantitative acetylproteomes were employed to investigate the regulation mechanism regulating cassava PPD under ethephon treatment. Ethephon was found to enhance the reactive oxygen species (ROS) scavenging system, resulting in a significant decrease in H2O2 and malondialdehyde (MDA) content. The comprehensive acetylome analysis identified 12,095 acetylation sites on 4403 proteins. Subsequent analysis demonstrated that ethephon can regulate the acetylation levels of antioxidant enzymes and members of the energy metabolism pathways. In summary, ethephon could enhance the antioxidant properties and regulate energy metabolism pathways, leading to the delayed PPD of cassava.

Full-length transcriptome revealed the accumulation of polyunsaturated fatty acids in developing seeds of Plukenetia volubilis.

Background: Plukenetia volubilis is cultivated as a valuable oilseed crop, and its mature seeds are rich in polyunsaturated fatty acids (FAs), which are widely used in food and pharmaceutical industries. Recently, next-generation sequencing (NGS) transcriptome studies in P. volubilis indicated that some candidate genes were involved in oil biosynthesis. The NGS were inaccuracies in assembly of some candidate genes, leading to unknown errors in date analyses. However, single molecular real-time (SMRT) sequencing can overcome these assembled errors. Unfortunately, this technique has not been reported in P. volubilis. Methods: The total oil content of P. volubilis seed (PVS) was determined using Soxhlet extraction system. The FA composition were analyzed by gas chromatography. Combining PacBio SMRT and Illumina technologies, the transcriptome analysis of developing PVS was performed. Functional annotation and differential expression were performed by BLAST software (version 2.2.26) and RSEM software (version 1.2.31), respectively. The lncRNA-targeted transcripts were predicted in developing PVS using LncTar tool. Results: By Soxhlet extraction system, the oil content of superior plant-type (SPT) was 13.47% higher than that of inferior plant-type (IPT) at mature PVS. The most abundant FAs were C18:2 and C18:3, among which C18:3 content of SPT was 1.11-fold higher than that of IPT. Combined with PacBio and Illumina platform, 68,971 non-redundant genes were obtained, among which 7,823 long non-coding RNAs (lncRNAs) and 7,798 lncRNA-targeted genes were predicted. In developing seed, the expressions of 57 TFs showed a significantly positive correlation with oil contents, including WRI1-like1, LEC1-like1, and MYB44-like. Comparative analysis of expression profiles between SPT and IPT implied that orthologs of FAD3, PDCT, PDAT, and DAGT2 were possibly important for the accumulation of polyunsaturated FAs. Together, these results provide a reference for oil biosynthesis of P. volubilis and genetic improvement of oil plants.

Integrated metabolome and transcriptome revealed the flavonoid biosynthetic pathway in developing Vernonia amygdalina leaves.

BACKGROUND: Vernonia amygdalina as a tropical horticultural crop has been widely used for medicinal herb, feed, and vegetable. Recently, increasing studies revealed that this species possesses multiple pharmacological properties. Notably, V. amygdalina leaves possess an abundance of flavonoids, but the specific profiles of flavonoids and the mechanisms of fl avonoid bi osynthesis in developing leaves are largely unknown. METHODS: The total flavonoids of V. amygdalina leaves were detected using ultraviolet spectrophotometer. The temporal flavonoid profiles of V. amygdalina leaves were analyzed by LC-MS. The transcriptome analysis of V. amygdalina leaves was performed by Illumina sequencing. Functional annotation and differential expression analysis of V. amygdalina genes were performed by Blast2GO v2.3.5 and RSEM v1.2.31, respectively. qRT-PCR analysis was used to verify the gene expressions in developing V. amygdalina leaves. RESULTS: By LC-MS analysis, three substrates (p-coumaric acid, trans-cinnamic acid, and phenylalanine) for flavonoid biosynthesis were identified in V. amygdalina leaves. Additionally, 42 flavonoids were identified from V. amygdalina leaves, including six dihydroflavones, 14 flavones, eight isoflavones, nine flavonols, two xanthones, one chalcone, one cyanidin, and one dihydroflavonol. Glycosylation and methylation were common at the hydroxy group of C3, C7, and C4' positions. Moreover, dynamic patterns of different flavonoids showed diversity. By Illumina sequencing, the obtained over 200 million valid reads were assembled into 60,422 genes. Blast analysis indicated that 31,872 genes were annotated at least in one of public databases. Greatly increasing molecular resources makes up for the lack of gene information in V. amygdalina. By digital expression profiling and qRT-PCR, we specifically characterized some key enzymes, such as Va-PAL1, Va-PAL4, Va-C4H1, Va-4CL3, Va-ACC1, Va-CHS1, Va-CHI, Va-FNSII, and Va-IFS3, involved in flavonoid biosynthesis. Importantly, integrated metabolome and transcriptome data of V. amygdalina leaves, we systematically constructed a flavonoid biosynthetic pathway with regards to material supplying, flavonoid scaffold biosynthesis, and flavonoid modifications. Our findings contribute significantly to understand the underlying mechanisms of flavonoid biosynthesis in V. amygdalina leaves, and also provide valuable information for potential metabolic engineering.

RNA-seq reveals the salt tolerance of Ipomoea pes-caprae, a wild relative of sweet potato.

Wild relatives of crops are often rich in genetic resources and provide great possibilities for crop improvement. Ipomoea pes-caprae is one of the wild relatives of sweet potato and has high salt tolerance. Transcriptomes in the treatment and control groups at various times were sequenced to identify salt tolerance genes and salt response pathways. A total of 40,525 genes were obtained, of which 2478 and 3334 were differentially expressed in the roots and leaves of I. pes-caprae under salt stress, respectively. Identification of candidate genes revealed that the mitogen-activated protein kinase (MAPK) signaling pathway of plants and plant hormone signal transduction participates in the salt signal of I. pes-caprae under salt stress. Homology to ABI2 (HAB2) and Clade A protein phosphatases type 2C (HAI1), which encode two protein phosphatases 2C (PP2C) in the abscisic acid (ABA) signal pathway, were continuously up-regulated upon salt stress, indicating their key role in the salt signal transduction pathway of I. pes-caprae. The expression of EIN3-binding F-box protein 1 (EBF1) in the ethylene signaling pathway was also up-regulated, revealing that the salt tolerance of I. pes-caprae was related to the scavenging of reactive oxygen species (ROS). This study provides insights into the mechanism of salt-tolerant plants and the mining of salt-tolerant genes in sweet potato for the innovation of germplasm resources.

Effects of exogenous abscisic acid on oil content, fatty acid composition, biodiesel properties and lipid components in developing Siberian apricot (Prunus sibirica) seeds.

Previous studies in Siberian apricot (Prunus sibirica) seed kernel (SASK) have suggested the involvement of abscisic acid (ABA) signaling pathway in oil accumulation. However, there are few reports on the effects of ABA on the metabolism of fatty acids (FA) in seed development. Here, we first evaluated the response of developing SASK to ABA treatment, with a focus on oil content, FA composition, biodiesel properties, lipid compounds and gene expressions. Compared with control samples, the application of exogenous ABA increased the total oil content by 6.55% in mature SASK. The C18:1 content markedly increased in ABA treatment, and conversely C16:0 decreased. Exogenous ABA also improved the biodiesel properties of SASK oil, making it better suited to the specifications of biodiesel standards. Furthermore, the molecular species of phosphatidylcholine (PC), phosphatidic acid (PA), diacylglycerol (DAG) and triacylglycerol (TAG) were detected using lipidomics analysis. The 18:1/18:1 was the main component in PA, PC and DAG, while the main components of 18:1/18:1/18:2, 18:1/18:1/18:3, 18:2/18:2/18:2 and 18:1/18:1/18:1 in TAG. Most lipid species gradually increased with SASK maturity. In addition, the relative contents of TAG-18:1/18:1/18:2 and TAG-18:1/18:1/18:1 in developing SASK increased with the application of exogenous ABA. We also detected elevated gene expression of key genes involved in ABA chemical pathway, which likely affected FA biosynthesis and accumulation. Our results provide insight into the effects of ABA on the oil accumulation in developing SASK, which has direct applications to improving the quality of SASK-derived biodiesel.

Genome-wide characterization of the NUCLEAR FACTOR-Y (NF-Y) family in Citrus grandis identified CgNF-YB9 involved in the fructose and glucose accumulation.

BACKGROUND: Nuclear factor Y (NF-Y) is increasingly known to be involved in many aspects of plant growth and development. To date, the systematic characterization of NF-Y family has never been reported in Citrus grandis. OBJECTIVE: Genome-wide characterization of C. grandis NF-Y (CgNF-Y) family and analysis of their role in sucrose metabolism. METHODS: NF-Y conserved models were employed to identify CgNF-Y genes from genomic data. Phylogenetic tree was generated by the neighbor-joining method using program MEGA 7.0. Based on our previous transcriptomic data, the transcription levels were calculated by RSEM software and were clustered by ShortTime-series Expression Miner. The plant expression vector of CgNF-YB9 was constructed using In-Fusion Cloning and transferred into tobacco by leaf disc transformation method. Soluble sugars and gene expressions were analysis by HPLC and qRT-PCR, respectively. RESULTS: A total of 24 CgNF-Y genes (6 CgNF-YAs, 13 CgNF-YBs and 5 CgNF-YCs) were identified with conserved domains. Phylogenetic analysis of the NF-Y proteins indicated that NF-YA, NF-YB and NF-YC could be categorized into four, five and three clades, respectively. Expression profiling analysis reflected spatio-temporally distinct expression patterns for CgNF-Y genes. Importantly, we observed a positive correlation between the expression level of CgNF-YB9 and the content of soluble sugar. Moreover, CgNF-YB9-corelated genes were enriched in carbohydrate metabolism. In CgNF-YB9 overexpression lines, sucrose content showed a decrease, whereas glucose and fructose contents displayed an increase. As expected, the transcription levels of sucrose-phosphate synthase and vacuolar invertase in transgenic Line 3 were observed with significantly down- and up-regulated, respectively. CONCLUSIONS: The structure, phylogenetic relationship and expression pattern of 24 CgNF-Y genes were identified, and CgNF-YB9 was involved in sucrose metabolism.