Characterization of the Gene Expression Profile Response to Drought Stress in Populus ussuriensis Using PacBio SMRT and Illumina Sequencing

Li, Wenlong; Liu, Zhiwei; He, Feng; Yang, Jingli; Li, Chenghao

doi:10.3390/ijms23073840

Cited by 10 publications

(24 citation statements)

References 82 publications

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“…The amino acid (AA) content was measured using an AA assay kit. The superoxide dismutase (SOD) activity was measured using a total SOD assay kit ( Li et al., 2022 ). The peroxidase (POD) activity was measured using a POD assay kit ( Li et al., 2022 ).…”

Section: Methodsmentioning

confidence: 99%

“…The superoxide dismutase (SOD) activity was measured using a total SOD assay kit ( Li et al., 2022 ). The peroxidase (POD) activity was measured using a POD assay kit ( Li et al., 2022 ). The malondialdehyde (MDA) content was measured using a MDA assay kit ( Li et al., 2022 ).…”

Section: Methodsmentioning

confidence: 99%

“…The peroxidase (POD) activity was measured using a POD assay kit ( Li et al., 2022 ). The malondialdehyde (MDA) content was measured using a MDA assay kit ( Li et al., 2022 ). The endogenous hormones (abscisic acid, auxin and gibberellin) content was determined by high performance liquid chromatography (HPLC) ( Yang et al., 2014 ).…”

Section: Methodsmentioning

confidence: 99%

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Combined analysis of transcriptome and metabolome reveals the molecular mechanism and candidate genes of Haloxylon drought tolerance

Yang

Lv²

2022

Front. Plant Sci.

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Haloxylon ammodendron and Haloxylon persicum, as typical desert plants, show strong drought tolerance and environmental adaptability. They are ideal model plants for studying the molecular mechanisms of drought tolerance. Transcriptomic and metabolomic analyses were performed to reveal the response mechanisms of H. ammodendron and H. persicum to a drought environment at the levels of transcription and physiological metabolism. The results showed that the morphological structures of H. ammodendron and H. persicum showed adaptability to drought stress. Under drought conditions, the peroxidase activity, abscisic acid content, auxin content, and gibberellin content of H. ammodendron increased, while the contents of proline and malondialdehyde decreased. The amino acid content of H. persicum was increased, while the contents of proline, malondialdehyde, auxin, and gibberellin were decreased. Under drought conditions, 12,233 and 17,953 differentially expressed genes (DEGs) were identified in H. ammodendron and H. persicum , respectively, including members of multiple transcription factor families such as FAR1, AP2/ERF, C2H2, bHLH, MYB, C2C2, and WRKY that were significantly up-regulated under drought stress. In the positive ion mode, 296 and 452 differential metabolites (DEMs) were identified in H. ammodendron and H. persicum, respectively; in the negative ion mode, 252 and 354 DEMs were identified, primarily in carbohydrate and lipid metabolism. A combined transcriptome and metabolome analysis showed that drought stress promoted the glycolysis/gluconeogenesis pathways of H. ammodendron and H. persicum and increased the expression of amino acid synthesis pathways, consistent with the physiological results. In addition, transcriptome and metabolome were jointly used to analyze the expression changes of the genes/metabolites of H. ammodendron and H. persicum that were associated with drought tolerance but were regulated differently in the two plants. This study identified drought-tolerance genes and metabolites in H. ammodendron and H. persicum and has provided new ideas for studying the drought stress response of Haloxylon.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Combined analysis of transcriptome and metabolome reveals the molecular mechanism and candidate genes of Haloxylon drought tolerance

Yang

Lv²

2022

Front. Plant Sci.

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“…DE analysis is widely used to analyze the forest plant responses to biotic and abiotic stresses, including drought, heat, salinity, flooding, cold, ultraviolet radiation, diseases, and insects [94,95]. For instance, the gene expression analysis in poplar root under polyethylene glycol-induced drought stress by TGS and NGS transcriptomic sequencing revealed several differentially expressed genes related to plant responses to drought in the biosynthesis and metabolism pathways [96]. In addition, the dual RNA-seq analysis of the interactions between Norway spruce and Heterobasidion revealed that several genes involved in the abscisic acid signaling were differentially expressed in Norway spruce, which might contribute to the Norway spruce response to the pathogen attack [97].…”

Section: Transcriptomicsmentioning

confidence: 99%

Multi-Omics Techniques for Forest Plant Breeding

Wang¹,

Li²,

Zhao³

2023

Preprint

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In recent years, the ecological and economic values of forest plants have been gradually recognized worldwide. However, the growing global demand for new forest plant varieties with higher wood production capacity and better stress tolerance cannot be satisfied by conventional phenotype-based breeding, marker-assisted selection, and genomic selection. In the recent past, diverse omics technologies, including genomics, transcriptomics, epigenomics, proteomics, and metabolomics, have been developed rapidly, providing powerful tools for the precision genetic breeding of forest plants. Genomics lays a solid foundation for understanding complex biological regulatory networks, while other omics technologies provide different perspectives at different levels. Multi-omics integration has combined the different omics technologies, becoming a powerful tool for genome-wide functional element identification in forest plant breeding. This review summarizes the recent progress of omics technologies and their applications in the genetic studies of forest plants. It will provide forest plant breeders with an elementary knowledge of multi-omics techniques for future breeding programs.

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“…Finally, phenylpropanoid metabolism was observed in the pathway enrichment analysis, and this pathway is one of the most important metabolisms in plants, contributing to plant development and plant-environment interactions (Dong and Lin 2021). Studies have revealed that drought, salt stress and biotic stresses induce lignin deposition through regulating phenylpropanoid metabolism to enhance stress tolerance in H. ammodendron(Nakabayashi and Saito 2015;Li et al 2022). The litter of H. ammodendron is degraded by microorganisms in UC soil, and phenylpropanoid metabolism compounds are dissolved in the soil, where they can gradually form a concentration gradient.…”

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confidence: 99%

Mechanism of bare patch formation under Haloxylon ammodendron canopies and patch effects on soil microorganisms in the Gurbantunggut Desert, Northern China

Liu

Li²,

Yuan³

et al. 2022

Preprint

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Background and aims In the Gurbantunggut Desert, Haloxylon ammodendron and Syntrichia caninervis are often found at the base of the dunes. In these areas, bare patches usually form under the H. ammodendron canopy, but not under other shrub canopies. Methods We compared the soil chemical properties under H. ammodendron canopy inside the bare patches (UC) and of soil under moss crust outside of H. ammodendron canopy bare patches (UM), and used UHPLC-MS/MS to analyze soil metabolites and metagenomic sequencing to characterize the structure of soil microflora. Results A total of 951 metabolites were identified in the soil samples, and 518 differential metabolites were observed. The content of amides, such as oleamide, in UC soil was significantly higher than that in UM soil, suggesting that the amides may be the main allelochemicals inhibiting S. caninervis. The differences in soil chemical properties and metabolites impacted soil microorganisms, but the structure and function of microbial communities did not differ significantly. Conclusions The amides secreted by H. ammodendron roots create a concentration gradient under its canopy, with high concentrations inhibiting S. caninervis, causing changes in soil chemical factors inside and outside the bare patch. These changes affect the abundance of microbial species and relevant metabolic pathways. The differences in microbial communities and functions are caused by a combination of soil chemical properties and metabolites, rather than a direct effect of high levels of soil metabolites such as amides.

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Characterization of the Gene Expression Profile Response to Drought Stress in Populus ussuriensis Using PacBio SMRT and Illumina Sequencing

Cited by 10 publications

References 82 publications

Combined analysis of transcriptome and metabolome reveals the molecular mechanism and candidate genes of Haloxylon drought tolerance

Combined analysis of transcriptome and metabolome reveals the molecular mechanism and candidate genes of Haloxylon drought tolerance

Multi-Omics Techniques for Forest Plant Breeding

Mechanism of bare patch formation under Haloxylon ammodendron canopies and patch effects on soil microorganisms in the Gurbantunggut Desert, Northern China

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