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Transcriptome analysis of Lei bamboo (Phyllostachys violascens) shoots during postharvest cold storage

ABSTRACT: Purpose:Bamboo shoots rapidly lose water and accumulate lignin when stored under room temperature, while low temperature conditioning (LTC, 4℃) can alleviate lignification and reduce weightlessness rate. However, few transcriptional response and profiling datasets are available to explore the LTC mechanism of bamboo shoots.The goal of this study is to provides insights into the regulation of Lei bamboo (Phyllostachys violascens) shoots during postharvest cold storage by transcriptome analysis. Methods:Total RNA was extracted using RNAiso Plus (Takara, Japan) according to the protocol, and after quality testing, was used for library construction and transcriptome sequencing by Illumina Novaseq™ 6000. The quality-controlled reads were aligned to the Phyllostachys edulis reference genome (http://gigadb.org/dataset/100498). The edgeR program25 was used for differential expression analyses. Results: After raw data filtering, a high clean data rate from each sample was achieved, and the assessment result for the clean data by FastQC all demonstrated that our sequencing data was of high quality, full representativeness and validity. Compared with CK, a total of 7,452 DEGs were identified during LT storage. The Pearson’s correlation coefficient (r) and principle component analysis (PCA) results all suggested a high correlation among all samples. The above results suggest an effective LT treatment of postharvest bamboo shoots and a high-quality bioinformatics analysis of our RNA-seq results. Conclusions: Our study represents the first detailed analysis of Lei bamboo (Phyllostachys violascens) shoots during postharvest cold storage transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. We conclude that RNA-seq based transcriptome characterization would reveal the essence of ripening and senescence of fruits and vegetables.

ORGANISM(S): Phyllostachys violascens

PROVIDER: GSE149182 | GEO | 2020/10/01

REPOSITORIES: GEO

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Project description:Background: Anthocyanins are the most important compounds for nutritional quality and economic values of blood orange. However, there are few reports on the pre-harvest treatment accelerate the accumulation of anthocyanins in postharvest blood orange fruit. Here, we performed a comparative Transcriptome and metabolomics analysis to elucidate the underlying mechanism involved in seasonal drought (SD) treatment during fruit expansion stage on anthocyanin accumulation in postharvest ‘Tarocco’ blood orange fruit. Results: Our results showed that SD treatment slowed down the fruit enlargement and increased the sugar accumulation during fruit development and matured period. Obviously, under SD treatment, the accumulation of anthocyanin in blood orange fruit during postharvest storage was significantly accelerated and markedly higher than that in CK. Meanwhile, the total flavonoids and phenols contents and antioxidant activity in SD treatment fruit were also sensibly increased during postharvest storage. Based on metabolome, we found that substrates required for anthocyanin biosynthesis, such as amino acids and their derivatives, and phenolic acids, have significantly accumulated and higher in SD treated mature fruit compared with that of CK. Further according to the results of transcriptome data and weighted gene coexpression correlation network analysis (WGCNA) analysis, phenylalanine ammonia-lyase (PAL3) was considered key structural gene. qRT-PCR analysis verified that the PAL3 was highly expressed in SD treated postharvest stored fruit and was significantly positively correlated with the anthocyanin content. Moreover, we found that other structural genes in anthocyanin biosynthesis pathway were also upregulated under SD treatment through transcriptome data and qRT-PCR analysis. Conclusions: The findings suggest that SD treatment promotes the accumulation of substrates necessary for anthocyanin biosynthesis during fruit ripening process, and activates the expression of anthocyanin biosynthesis pathway genes during postharvest storage period, especially PAL3, co-contributed to the rapid accumulation of anthocyanin. The present study provides a theoretical basis for postharvest quality control and water-saving utilization of blood orange fruit.

Project description:Table grapes cv. Cardinal are highly perishable and their quality deteriorates during postharvest storage at low temperature mainly because of sensitivity to fungal decay and senescence of rachis. The application of a 3-day CO2 treatment with 20 kPa CO2 at 0C reduced total decay and retained fruit quality in early and late-harvested table grapes during postharvest storage. In order to study the transcriptional responsiveness of table grapes to low temperature and high CO2 levels in the first stage of storage and how the maturity stage affect these changes, we have performed a comparative large-scale transcriptional analysis. In the first stage of storage, low temperature led to a significantly intense change in grape skin transcriptome irrespective of fruit maturity, although there were different changes within each stage. In the case of CO2 treated samples, in comparison to fruit at time zero, only slight differences were observed. Functional enrichment analysis revealed that major modifications in the transcriptome profile of early- and late-harvested grapes stored at 0C are linked to biotic and abiotic stress-responsive terms. However, in both cases there is a specific reprogramming of the transcriptome during the first stage of storage at 0C in order to withstand the cold stress. Thus, genes involved in gluconeogenesis, photosynthesis, mRNA translation and lipid transport were up-regulated in the case of early-harvested grapes, and genes related to protein folding stability and intracellular membrane trafficking in late-harvested grapes. The beneficial effect of high CO2 treatment maintaining table grape quality seems to be an active process requiring the induction of several transcription factors and kinases in early-harvested grapes, and the activation of processes associated to the maintenance of energy in late-harvested grapes. Table grapes harvested at two maturity stages (early and late). 3 biological replicates. Early-harvested (MI:12.45) : Time zero, 3 days air 0C, 3 days high CO2 levels 0C. Late-harvested (MI: 41.08): Time zero, 3 days air 0C, 3 days high CO2 levels 0C.

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Transcriptome analysis of Lei bamboo (Phyllostachys violascens) shoots during postharvest cold storage

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