Integrated full-length transcriptome and metabolome analysis reveals the defence response of melon to gummy stem blight

Gummy stem blight (GSB), a widespread disease causing great loss to cucurbit production, has become a major threat to melon cultivation. However, the melon-GSB interaction remains largely unknown. Here, full-length transcriptome and widely targeted metabolome were used to investigate the defence responses of resistant (PI511089) and susceptible (Payzawat) melon accessions to GSB pathogen infection at 24 h. The biosynthesis of secondary metabolites and MAPK signalling pathway were specifically enriched for differentially expressed genes in PI511890, while carbohydrate metabolism and amino acid metabolism were specifically enriched in Payzawat. More than 1000 novel genes were identified and MAPK signalling pathway was specifically enriched for them in PI511890. There were 11 793 alternative splicing events involving in the defence response to GSB. Totally, 910 metabolites were identified in Payzawat and PI511890, and flavonoids were the dominant metabolites. Integrated full-length transcriptome and metabolome analysis showed eriodictyol and oxalic acid were the potential marker metabolites for GSB resistance in melon. Moreover, posttranscription regulation was widely involved in the defence response of melon to GSB pathogen infection. These results not only improve our understanding on the interaction between melon and GSB, but also facilitate the genetic improvement of melon with GSB resistance.

Integrated Transcriptome and Metabolome Analysis of Salinity Tolerance in Response to Foliar Application of β-Alanine in Cotton Seedlings

Salinity is amongst the serious abiotic stresses cotton plants face, impairing crop productivity. Foliar application of β-alanine is employed to improve salt tolerance in various crops, but the exact mechanism behind it is not yet completely understood. An advanced line SDS-01 of upland cotton Gossypium hirsutum L. was utilized to determine its salt tolerance. Foliar treatment with the β-alanine solution at different concentrations was applied to the seedlings stressed with 0.8% NaCl solution. On the 10th day of treatment, samples were collected for transcriptome and metabolome analyses. β-alanine solution at a concentration of 25 mM was found to be the best treatment with the lowest mortality rate and highest plant height and above-ground biomass under salt stress. Both differentially expressed genes and accumulated metabolites analyses showed improved tolerance of treated seedlings. The photosynthetic efficiency improved in seedlings due to higher expression of photosynthesis-antenna proteins and activation of hormones signal transduction after treatment with β-alanine. Highly expressed transcription factors observed were MYB, HD-ZIP, ARF, MYC, EREB, DELLA, ABF, H2A, H4, WRKY, and HK involved in the positive regulation of salinity tolerance in β-alanine-treated seedlings. Furthermore, compared to the control, the high accumulation of polyamines, coumarins, organic acids, and phenolic compounds in the β-alanine-treated seedlings helped regulate cellular antioxidant (glutathione and L-Cysteine) production. Hence, to improve salt tolerance and productivity in cotton, foliar application of β-alanine at the seedling stage can be a valuable management practice.

Insights into the nutritional properties and molecular basis of biosynthesis of amino acids and vitamins of Gastrodia elata offered by metabolomic and transcriptomic analysis

Gastrodia elata Blume (GE), a traditional and precious Chinese medicinal material, has been approved as a functional food. However, understanding GE's nutritional properties and its molecular basis remains limited. Here, metabolomic and transcriptomic analyses were performed on young and mature tubers of G. elata.f.elata (GEEy and GEEm) and G. elata.f.glauca (GEGy and GEGm). A total of 345 metabolites were detected, including 76 different amino acids and their derivatives containing all human essential amino acids (e.g., l-(+)-lysine, l-leucine), 13 vitamins (e.g., nicotinamide, thiamine), and 34 alkaloids (e.g., spermine, choline). GEGm has higher amino acid accumulation than GEEy, GEEm and GEGy, and vitamin contents were also slightly different in all four samples. Implying that GE, especially GEGm, is a kind of excellent complementary food as amino acid nutrition provider. From assembled 21,513 transcripts (genes) based on the transcriptome, we identified many genes that encode enzymes (e.g., pfkA, bglX, tyrAa, lysA, his B, aroA), which are responsible for the biosynthesis of amino acids and enzymes (e.g., nadA, URH1, NAPRT1, punA, rsgA) that related to vitamins metabolism. A total of 16 pairs of the differentially expressed genes (DEG) and differentially accumulated metabolites (DAM) (e.g., gene-tia006709 coding GAPDH and l-(+)-arginine, and gene-tia010180 coding tyrA and l-(+)-arginine) and three DEG-DAM pairs (e.g., gene-tia015379 coding NadA and nicotinate d-ribonucleoside) show significant similar positive or negative correlation based on three, and two comparisons of GEEy vs. GEGy, GEGy vs. GEGm, GEEy vs. GEGy and GEEm vs. GEGm, which involved into amino acid biosynthesis, and nicotinate nicotinamide metabolism, respectively. These results prove that the enzyme coded by these DEG promotes (positive correlation) or inhibits (negative correlation) the biosynthesis of parallel DAM in GE. Overall, the data and corresponding analysis in this study provide new insights into the nutritional properties of GE and the related molecular basis.

Integrated transcriptome and metabolome analysis unveil the response mechanism in wild rice (Zizania latifolia griseb.) against sheath rot infection

Sheath rot disease (SRD) is one of the most devastating diseases of Manchurian wild rice (MWR) (Zizania latifolia Griseb). Pilot experiments in our laboratory have shown that an MWR cultivar "Zhejiao NO.7"exhibits signs of SRD tolerance. To explore the responses of Zhejiao No. 7 to SRD infection, we used a combined transcriptome and metabolome analysis approach. A total of 136 differentially accumulated metabolites (DAMs, 114 up- and 22 down-accumulated in FA compared to CK) were detected. These up-accumulated metabolites were enriched in tryptophan metabolism, amino acid biosynthesis, flavonoids, and phytohormone signaling. Transcriptome sequencing results showed the differential expression of 11,280 genes (DEGs, 5,933 up-, and 5,347 downregulated in FA compared to CK). The genes expressed in tryptophan metabolism, amino acid biosynthesis, phytohormone biosynthesis and signaling, and reactive oxygen species homeostasis confirmed the metabolite results. In addition, genes related to the cell wall, carbohydrate metabolism, and plant-pathogen interaction (especially hypersensitive response) showed changes in expression in response to SRD infection. These results provide a basis for understanding the response mechanisms in MWR to FA attack that can be used for breeding SRD-tolerant MWR.

The Effects of NAA on the Tuberous Root Yield and Quality of Rehmannia glutinosa and Its Regulatory Mechanism by Transcriptome and Metabolome Profiling

Naphthylacetic acid (NAA) was used to increase the tuberous root yield of Rehmannia glutinosa, but the differences between its NAA-treated and control tuberous roots (NT and CG) and the regulatory mechanism of NAA effect remain unclear. In order to investigate them, NTs and CGs were used as materials, and both yield-related indices were measured; the metabolomics and transcriptomics were used to capture differentially accumulated metabolites (DAM) and to validate them via mining differentially expressed genes (DEGs), respectively. The effects of NAA treatment: increased NT mass per plant by 21.14%, through increasing the number of roots and increasing the mean root diameter; increased catalpol content by 1.2234% (p < 0.05); up-regulated 11DAMs and 596DEGs; and down-regulated 18 DAMs and 517DEGs. In particular, we discovered that NAA regulated its DAMs and biomass via 10 common metabolic pathways, and that the number of NAA-down-regulated DAMs was more than that of NAA-up-regulated DAMs in its tuberous root. Furthermore, HPLC validated the changes of several DAMs and 15 DEGs (4CL, ARF, CCoAOMT, ARGOS, etc.) associated with the yield increase and DAMs were verified by RT-qPCR. This study provided some valuable resources, such as tuberous root indices, key genes, and DAMs of Rehmannia glutinosa in response to NAA for distinguishing the CGs from NTs, and novel insights into the regulatory mechanism of NAA effects on both at the transcriptomic and metabolomic levels, so it will lay a theoretical foundation for NAA-regulated plant yield and quality, and provide references for prohibiting the uses of NAA as a swelling agent in medicinal tuber plants in China.

Comparative metabolomics reveals differences in primary and secondary metabolites between "Shixia" and "Chuliang" longan (Dimocarpus longan Lour.) pulp

Longan was a characteristic fruit for both medicine and food in China, which was rich in primary and secondary metabolites. Comprehensive high-throughput identification and comparison of metabolites in longan pulp among different varieties were still lacked. "Shixia" (SX) and "Chuliang" (CL) were the biggest major cultivars of longan in China. In this study, the content of total soluble solid, total flavonoid, and total phenolics indicated the difference of sweetness and bioactive compound content between the SX and CL pulp. Through a widely targeted metabolome, a total of 514 metabolites were identified and categorized into 23 groups mainly including flavonoids, amino acids & derivatives, lipids, phenolic acids, nucleotides & derivatives, alkaloids, organic acids and sugars & derivatives. A total of 89 metabolites with significantly differential accumulation (variable importance in projection (VIP) value ≧1, p-value <.05) over 1.2 fold were found between SX and CL, which were mainly enriched into pathways including flavone and flavonol biosynthesis, glycolysis/gluconeogenesis, and arginine and proline metabolism. Higher leveled hexose and hexose-phosphate (i.e., β-D-glucose, D(+)-glucose, glucose-1-phosphate and glucose-6-phosphate), dominant organic acids (i.e., citric acid, succinic acid, D-malic acid, and citramalate), and essential amino acids (L-threonine, L-valine, L-isoleucine, L-leucine, L-phenylalanine and L-lysine) in SX pulp might be contributed to the taste and flavor difference between SX and CL. Moreover, the greatly differential accumulated secondary metabolites especially flavonoids and phenolic acids might result in different medicinal and nutritional characteristic between SX and CL. In conclusion, this study provided a systemic metabolic basis for understanding the nutritional differences between SX and CL and would help deepen the molecular biology and pharmacology research on characteristic metabolites in longan pulp.