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Transcriptome profiling of Fagopyrum tataricum leaves in response to lead stress.

ABSTRACT: BACKGROUND:Lead (Pb) pollution is a widespread environmental problem that is harmful to living organisms. Tartary buckwheat (Fagopyrum tataricum), a member of the family Polygonaceae, exhibits short growth cycles and abundant biomass production, could be an ideal plant for phytoremediation due to its high Pb tolerance. Here, we aimed to explore the molecular basis underlying the responses of this plant to Pb stress. RESULTS:In our study, ultrastructural localization assays revealed that Pb ions primarily accumulate in leaf vacuoles. RNA deep sequencing (RNA-Seq) of tartary buckwheat leaves was performed on two Pb-treated samples, named Pb1 (2000?mg/kg Pb (NO3)2) and Pb2 (10,000?mg/kg Pb (NO3)2), and a control (CK). A total of 88,977 assembled unigenes with 125,203,555 bases were obtained. In total, 2400 up-regulated and 3413 down-regulated differentially expressed genes (DEGs) were identified between CK and Pb1, and 2948 up-regulated DEGs and 3834 down-regulated DEGs were generated between CK and Pb2, respectively. Gene Ontology (GO) and pathway enrichment analyses showed that these DEGs were primarily associated with 'cell wall', 'binding', 'transport', and 'lipid and energy' metabolism. The results of quantitative real-time PCR (qRT-PCR) analyses of 15 randomly selected candidate DEGs and 6 regulated genes were consistent with the results of the transcriptome analysis. Heterologous expression assays in the yeast strain ?ycf1 indicated that overexpressing CCCH-type zinc finger protein 14 (ZFP14) enhanced sensitivity to Pb2+, while 5 other genes, namely, metal transporter protein C2 (MTPC2), phytochelatin synthetase-like family protein (PCSL), vacuolar cation/proton exchanger 1a (VCE1a), natural resistance-associated macrophage protein 3 (Nramp3), and phytochelatin synthetase (PCS), enhanced the Pb tolerance of the mutant strain. CONCLUSION:Combining our findings with those of previous studies, we generated a schematic model that shows the metabolic processes of tartary buckwheat under Pb stress. This study provides important data for further genomic analyses of the biological and molecular mechanisms of Pb tolerance and accumulation in tartary buckwheat.

SUBMITTER: Wang L

PROVIDER: S-EPMC6998078 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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Transcriptome profiling of Fagopyrum tataricum leaves in response to lead stress.

Wang Lei L Zheng Bei B Yuan Yong Y Xu Quanle Q Chen Peng P

BMC plant biology 20200203 1

<h4>Background</h4>Lead (Pb) pollution is a widespread environmental problem that is harmful to living organisms. Tartary buckwheat (Fagopyrum tataricum), a member of the family Polygonaceae, exhibits short growth cycles and abundant biomass production, could be an ideal plant for phytoremediation due to its high Pb tolerance. Here, we aimed to explore the molecular basis underlying the responses of this plant to Pb stress.<h4>Results</h4>In our study, ultrastructural localization assays reveale ...[more]

PMID: 32013882

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Project description:BackgroundTartary buckwheat seed development is an extremely complex process involving many gene regulatory pathways. MicroRNAs (miRNAs) have been identified as the important negative regulators of gene expression and performed crucial regulatory roles in various plant biological processes. However, whether miRNAs participate in Tartary buckwheat seed development remains unexplored.ResultsIn this study, we first identified 26 miRNA biosynthesis genes in the Tartary buckwheat genome and described their phylogeny and expression profiling. Then we performed small RNA (sRNA) sequencing for Tartary buckwheat seeds at three developmental stages to identify the miRNAs associated with seed development. In total, 230 miRNAs, including 101 conserved and 129 novel miRNAs, were first identified in Tartary buckwheat, and 3268 target genes were successfully predicted. Among these miRNAs, 76 exhibited differential expression during seed development, and 1534 target genes which correspond to 74 differentially expressed miRNAs (DEMs) were identified. Based on integrated analysis of DEMs and their targets expression, 65 miRNA-mRNA interaction pairs (25 DEMs corresponding to 65 target genes) were identified that exhibited significantly opposite expression during Tartary buckwheat seed development, and 6 of the miRNA-mRNA pairs were further verified by quantitative real-time polymerase chain reaction (qRT-PCR) and ligase-mediated rapid amplification of 5' cDNA ends (5'-RLM-RACE). Functional annotation of the 65 target mRNAs showed that 56 miRNA-mRNA interaction pairs major involved in cell differentiation and proliferation, cell elongation, hormones response, organogenesis, embryo and endosperm development, seed size, mineral elements transport, and flavonoid biosynthesis, which indicated that they are the key miRNA-mRNA pairs for Tartary buckwheat seed development.ConclusionsOur findings provided insights for the first time into miRNA-mediated regulatory pathways in Tartary buckwheat seed development and suggested that miRNAs play important role in Tartary buckwheat seed development. These findings will be help to study the roles and regulatory mechanism of miRNAs in Tartary buckwheat seed development.

Project description:Hexaploid wheat is the main cereal food crop for most people but it is highly influenced by climatic variations. The influence of these climatic variations was studies in wheat genotype WH -1184 in field conditions under two different environments (normal and late sown) and it was found that the genotype is less yielding under late sown conditions. To study the effects of heat stress at transcript level, it was grown under two different conditions (WH-1184 control and heat treated) in pots and transcriptome analysis based on Illumina Novoseq 6000 was carried out for the identification of the differentially expressed genes (DEGs) and metabolic processes or gene regulations influenced by heat stress which lead to a reduction in both quality and quantity of wheat production. These DEGs were utilized to set up a subsequent unigene assembly and GO analysis was performed using unigenes to analyze functions of DEGs which were classified into three main domains, i.e., biological process, cellular component, and molecular function. KEGG (Kyoto Encyclopedia of Genes and Genomes) ontology was used to visualize the physiological processes or to identify KEGG pathways that provide plants their ability to shield in adverse conditions of heat stress. From KEGG ontology, it was reported that genes which encoded protein detoxification and ABC1 domain-containing protein were upregulated while genes thatencoded glutathione transferase (GST), peroxidase, and chitinase enzymes were downregulated. Downregulation of these enzymes during heat stress causes oxidative damages in plants while upregulated proteins play a main role in detoxification to protect plants from heat stress. It was hypothesized that the yield of WH-1184 decreased 44% under heat stress due to the downregulation of genes that encoded GST, peroxidase, and chitinase enzymes which can protect plants from oxidative damage. Hence, upregulation of these genes might be helpful for the adaptation of this genotype under heat stress condition.

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Transcriptome profiling of Fagopyrum tataricum leaves in response to lead stress.

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Transcriptome profiling of Fagopyrum tataricum leaves in response to lead stress.

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