Identification of key gene networks controlling vernalization development characteristics of Isatis indigotica by full-length transcriptomes and gene expression profiles

AbstractIsatis indigotica Fort., as a common Chinese medicinal raw material, will lose its medicinal value if it blooms early, so it is highly valuable to clarify the induction mechanism of the vernalization of I. indigotica at low temperature. In this study, the concentrations of soluble sugar, proline, glutathione and zeatin in two germplasms of I. indigotica with different degrees of low temperature tolerance (Y1 and Y2) were determined at 10 days, 20 days and 30 days of low-temperature treatment, and the full-length transcriptome of 24 samples was sequenced by Nanopore sequencing with Oxford Nanopore Technologies (ONT). After that, the data of transcripts involved in the vernalization of I. indigotica at low temperature were obtained, and these transcripts were identified using weighted gene co-expression network analysis (WGCNA). The results revealed the massive accumulation of soluble sugar and proline in Y1 and Y2 after low temperature induction. A total of 18,385 new transcripts, 6168 transcription factors and 470 lncRNAs were obtained. Differential expression analysis showed that gibberellin, flavonoids, fatty acids and some processes related to low temperature response were significantly enriched. Eight key transcripts were identified by WGCNA, among which ONT.14640.1, ONT.9119.1, ONT.13080.2 and ONT.16007.1 encodes a flavonoid transporter, 9-cis-epoxycarotenoid dioxygenase 3 (NCED3), growth factor gene and L-aspartate oxidase in plants, respectively. It indicated that secondary metabolites such as hormones and flavonoids play an important role in the vernalization of I. indigotica. qRT-PCR proved the reliability of transcriptome results. These results provide important insights on the low-temperature vernalization of I. indigotica, and provide a research basis for analyzing the vernalization mechanism of I. indigotica.

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Full-length transcriptome sequencing reveals the low-temperature-tolerance mechanism of Medicago falcata roots

BMC Plant Biology ◽

10.1186/s12870-019-2192-1 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 3

Author(s):

Guowen Cui ◽

Hua Chai ◽

Hang Yin ◽

Mei Yang ◽

Guofu Hu ◽

...

Keyword(s):

Low Temperature ◽

Temperature Stress ◽

Electrolyte Leakage ◽

Temperature Tolerance ◽

Low Temperature Stress ◽

Full Length ◽

Rna Seq ◽

Smrt Sequencing ◽

Tolerance Mechanism ◽

Low Temperature Tolerance

Abstract Background Low temperature is one of the main environmental factors that limits crop growth, development, and production. Medicago falcata is an important leguminous herb that is widely distributed worldwide. M. falcata is related to alfalfa but is more tolerant to low temperature than alfalfa. Understanding the low temperature tolerance mechanism of M. falcata is important for the genetic improvement of alfalfa. Results In this study, we explored the transcriptomic changes in the roots of low-temperature-treated M. falcata plants by combining SMRT sequencing and NGS technologies. A total of 115,153 nonredundant sequences were obtained, and 8849 AS events, 73,149 SSRs, and 4189 lncRNAs were predicted. A total of 111,587 genes from SMRT sequencing were annotated, and 11,369 DEGs involved in plant hormone signal transduction, protein processing in endoplasmic reticulum, carbon metabolism, glycolysis/gluconeogenesis, starch and sucrose metabolism, and endocytosis pathways were identified. We characterized 1538 TF genes into 45 TF gene families, and the most abundant TF family was the WRKY family, followed by the ERF, MYB, bHLH and NAC families. A total of 134 genes, including 101 whose expression was upregulated and 33 whose expression was downregulated, were differentially coexpressed at all five temperature points. PB40804, PB75011, PB110405 and PB108808 were found to play crucial roles in the tolerance of M. falcata to low temperature. WGCNA revealed that the MEbrown module was significantly correlated with low-temperature stress in M. falcata. Electrolyte leakage was correlated with most genetic modules and verified that electrolyte leakage can be used as a direct stress marker in physiological assays to indicate cell membrane damage from low-temperature stress. The consistency between the qRT-PCR results and RNA-seq analyses confirmed the validity of the RNA-seq data and the analysis of the regulatory mechanism of low-temperature stress on the basis of the transcriptome. Conclusions The full-length transcripts generated in this study provide a full characterization of the transcriptome of M. falcata and may be useful for mining new low-temperature stress-related genes specific to M. falcata. These new findings could facilitate the understanding of the low-temperature-tolerance mechanism of M. falcata.

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Morpho-Physiological Characterization of Diverse Rice Genotypes for Seedling Stage High- and Low-Temperature Tolerance

Agronomy ◽

10.3390/agronomy11010112 ◽

2021 ◽

Vol 11 (1) ◽

pp. 112

Author(s):

Kambham Raja Reddy ◽

Akanksha Seghal ◽

Salah Jumaa ◽

Raju Bheemanahalli ◽

Naqeebullah Kakar ◽

...

Keyword(s):

High Temperature ◽

Low Temperature ◽

Developmental Plasticity ◽

Temperature Response ◽

Temperature Tolerance ◽

Seedling Stage ◽

Response Index ◽

High Temperature Tolerance ◽

Early Seedling ◽

Rice Genotypes

Extreme temperatures are considered one of the main constraints that limit the growth and development of rice. We elucidated the root and shoot developmental plasticity of 64 rice genotypes during early seedling establishment, using the sunlit plant growth chambers at 22/14 (low), 30/22 (optimum), and 38/30 °C (high) day/night temperatures. Low temperature severely inhibited 23 traits, such as shoot (68%), root (57%), and physiological (35%) attributes. On the contrary, the high temperature positively affected most of the shoot (48%) and root (31%) traits, except root diameter and root/shoot ratio, compared with the optimum. Alternatively, leaf chlorophyll fluorescence-associated parameters declined under low (34%) and high (8%) temperatures. A weak correlation between cumulative high-temperature response index (CHTRI) and cumulative low-temperature response index (CLTRI) indicates the operation of different low- and high-temperature tolerance mechanisms at the early seedling stage. Groups of distinct rice genotypes associated with low or high-temperature tolerance were selected based on CHTRI and CLTRI. The genotypes that commonly performed well under low and high temperatures (IR65600-81-5-2-3, CT18593-1-7-2-2-5, RU1504114, RU1504122, Bowman, and INIA Tacuari) will be valuable genetic resources for breeders in developing early-season high- and low-temperature-tolerant genotypes for a broad range of both tropical and temperate rice-growing environments.

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An Update to the TraVA Database: Time Series of Capsella bursa-pastoris Shoot Apical Meristems during Transition to Flowering

Data ◽

10.3390/data5030058 ◽

2020 ◽

Vol 5 (3) ◽

pp. 58

Author(s):

Anna V. Klepikova ◽

Artem S. Kasianov

Keyword(s):

Time Series ◽

Gene Networks ◽

Expression Profiles ◽

Data Extraction ◽

Differential Expression Analysis ◽

Gene Expression Profiles ◽

Apical Meristems ◽

Shoot Apical Meristems ◽

Transcriptome Variation ◽

Transition To Flowering

Transition to flowering is a crucial part of plant life directly affecting the fitness of a plant. Time series of transcriptomes is a useful tool for the investigation of process dynamics and can be used for the identification of novel genes and gene networks involved in the process. We present a detailed time series of polyploid Capsella bursa-pastoris shoot apical meristems created with RNA-seq. The time series covers transition to flowering and can be used for thorough analysis of the process. To make the data easy to access, we uploaded them in our database Transcriptome Variation Analysis (TraVA), which provides a convenient depiction of the gene expression profiles, the differential expression analysis between the homeologs and quick data extraction.

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Full-length transcriptome sequencing reveals a low-temperature-tolerance mechanism in Medicago falcata roots

10.21203/rs.2.12899/v1 ◽

2019 ◽

Author(s):

Guowen Cui ◽

Hua Chai ◽

Hang Yin ◽

Mei Yang ◽

Guofu Hu ◽

...

Keyword(s):

Low Temperature ◽

Temperature Stress ◽

Electrolyte Leakage ◽

Temperature Tolerance ◽

Low Temperature Stress ◽

Full Length ◽

Rna Seq ◽

Tolerance Mechanism ◽

Medicago Falcata ◽

Low Temperature Tolerance

Abstract Background Low temperature is one of the main environmental factors that limits crop growth, development and production. Medicago falcata is an economically and ecologically important legume that is closely related to alfalfa and exhibits better tolerance to low temperature than alfalfa. Understanding the low-temperature-tolerance mechanism of M. falcata is important for the genetic improvement of alfalfa. Results In this study, we explored the transcriptomic changes in low-temperature-treated M. falcata roots by combining SMRT and NGS technologies. A total of 115,153 nonredundant sequences were obtained, and 8,849 AS events, 73,149 SSRs and 4,189 LncRNAs were predicted. A total of 111,587 genes from SMRT were annotated, and 11,369 DEGs were identified in this paper that are involved in plant hormone signal transduction, protein processing in endoplasmic reticulum, carbon metabolism, glycolysis/gluconeogenesis, starch and sucrose metabolism, and endocytosis pathways. We characterized 1,538 TF genes into 45 TF gene families, and the most abundant TF family was WRKY, followed by ERF, MYB, bHLH and NAC. A total of 134 genes were differentially coexpressed at all five temperature points, including 101 upregulated genes and 33 downregulated genes. PB40804, PB75011, PB110405 and PB108808 were found to play crucial roles in the tolerance of M. falcata to low temperature. The WGCNA results showed that the MEbrown module was significantly correlated with low-temperature stress in M. falcata. Electrolyte leakage was correlated with most genetic modules and corroborated that electrolyte leakage can be used as direct stress markers to reflect cell membrane damage from low-temperature stress in physiological assays. The consistency between the qRT-PCR results and RNA-Seq analyses confirm the validity of the RNA-Seq data and the analysis of the regulation of low-temperature stress in the transcriptome. Conclusions The full-length transcripts generated in this study provided a full characterization of the gene transcription of M. falcata and are useful for mining new low-temperature stress-related genes specific to M. falcata. These new findings facilitate the understanding of low-temperature-tolerance mechanisms in M. falcata.

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Exogenous DA-6 Improves the Low Night Temperature Tolerance of Tomato Through Regulating Cytokinin

Frontiers in Plant Science ◽

10.3389/fpls.2020.599111 ◽

2021 ◽

Vol 11 ◽

Author(s):

Jiazhi Lu ◽

Pengxiao Guan ◽

Jiamao Gu ◽

Xiaolong Yang ◽

Feng Wang ◽

...

Keyword(s):

Low Temperature ◽

Plant Growth ◽

Defense Mechanisms ◽

Negative Impact ◽

Temperature Response ◽

Chlorophyll Synthesis ◽

Temperature Tolerance ◽

Photochemical Activity ◽

Night Temperature ◽

Cold Response

Low night temperature (LNT) causes environmental stress and has a severe and negative impact on plant growth and productivity. Synthetic elicitors can regulate plant growth and induce defense mechanisms from this type of stress. Here, we evaluated the effect of the exogenous growth regulator diethyl aminoethyl hexanoate (DA-6) in tomato leaf response to LNT stress. Our results showed that exogenous DA-6 activates the expression of chlorophyll synthesis and photosystem-related genes, and results in higher photosynthetic activity and chlorophyll production. Furthermore, DA-6 can regulate the synthesis of endogenous cytokinin (CTK) and the expression of decomposition genes to stabilize chloroplast structure, reduce oxidative damage, and maintain the photochemical activity of tomato leaves under LNT stress. DA-6 maintains a high level of ABA content and induces the expression of CBF genes, indicating that DA-6 may participate in the cold response signaling pathway and induce the expression of downstream low temperature response genes and accumulation of compatible osmolytes. This study unravels a mode of action by which plant growth regulators can improve low temperature tolerance and provides important considerations for their application to alleviate the harmful effects of cold stress.

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Integrated Transcriptomics and Metabolomics Analysis Reveal Key Metabolism Pathways Contributing to Cold Tolerance in Peanut

Frontiers in Plant Science ◽

10.3389/fpls.2021.752474 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xin Wang ◽

Yue Liu ◽

Zhongkui Han ◽

Yuning Chen ◽

Dongxin Huai ◽

...

Keyword(s):

Low Temperature ◽

Cold Tolerance ◽

Gene Networks ◽

Cold Resistance ◽

Chilling Stress ◽

Soluble Sugar ◽

Growth Yield ◽

Limiting Factors ◽

Accumulation Pattern ◽

Cold Tolerant

Low temperature (non-freezing) is one of the major limiting factors in peanut (Arachis hypogaea L.) growth, yield, and geographic distribution. Due to the complexity of cold-resistance trait in peanut, the molecular mechanism of cold tolerance and related gene networks were largely unknown. In this study, metabolomic analysis of two peanut cultivars subjected to chilling stress obtained a set of cold-responsive metabolites, including several carbohydrates and polyamines. These substances showed a higher accumulation pattern in cold-tolerant variety SLH than cold-susceptible variety ZH12 under cold stress, indicating their importance in protecting peanut from chilling injuries. In addition, 3,620 cold tolerance genes (CTGs) were identified by transcriptome sequencing, and the CTGs were most significantly enriched in the “phenylpropanoid biosynthesis” pathway. Two vital modules and several novel hub genes were obtained by weighted gene co-expression network analysis (WGCNA). Several key genes involved in soluble sugar, polyamine, and G-lignin biosynthetic pathways were substantially higher and/or responded more quickly in SLH (cold tolerant) than ZH12 (cold susceptible) under low temperature, suggesting they might be crucial contributors during the adaptation of peanut to low temperature. These findings will not only provide valuable resources for study of cold resistance in peanut but also lay a foundation for genetic modification of cold regulators to enhance stress tolerance in crops.

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Full-length transcriptome sequencing reveals the low-temperature-tolerance mechanism of Medicago falcata roots

10.21203/rs.2.12899/v2 ◽

2019 ◽

Author(s):

Guowen Cui ◽

Hua Chai ◽

Hang Yin ◽

Mei Yang ◽

Guofu Hu ◽

...

Keyword(s):

Low Temperature ◽

Temperature Stress ◽

Electrolyte Leakage ◽

Temperature Tolerance ◽

Low Temperature Stress ◽

Full Length ◽

Rna Seq ◽

Smrt Sequencing ◽

Tolerance Mechanism ◽

Low Temperature Tolerance

Abstract Background: Low temperature is one of the main environmental factors that limits crop growth, development, and production. Medicago falcata is an important leguminous herb that is widely distributed worldwide. M. falcata is related to alfalfa but is more tolerant to low temperature than alfalfa. Understanding the low temperature tolerance mechanism of M. falcata is important for the genetic improvement of alfalfa. Results: In this study, we explored the transcriptomic changes in the roots of low-temperature-treated M. falcata plants by combining SMRT sequencing and NGS technologies. A total of 115,153 nonredundant sequences were obtained, and 8,849 AS events, 73,149 SSRs, and 4,189 lncRNAs were predicted. A total of 111,587 genes from SMRT sequencing were annotated, and 11,369 DEGs involved in plant hormone signal transduction, protein processing in endoplasmic reticulum, carbon metabolism, glycolysis/gluconeogenesis, starch and sucrose metabolism, and endocytosis pathways were identified. We characterized 1,538 TF genes into 45 TF gene families, and the most abundant TF family was the WRKY family, followed by the ERF, MYB, bHLH and NAC families. A total of 134 genes, including 101 whose expression was upregulated and 33 whose expression was downregulated, were differentially coexpressed at all five temperature points. PB40804, PB75011, PB110405 and PB108808 were found to play crucial roles in the tolerance of M. falcata to low temperature. WGCNA revealed that the MEbrown module was significantly correlated with low-temperature stress in M. falcata. Electrolyte leakage was correlated with most genetic modules and verified that electrolyte leakage can be used as a direct stress marker in physiological assays to indicate cell membrane damage from low-temperature stress. The consistency between the qRT-PCR results and RNA-seq analyses confirmed the validity of the RNA-seq data and the analysis of the regulatory mechanism of low-temperature stress on the basis of the transcriptome. Conclusions: The full-length transcripts generated in this study provide a full characterization of the transcriptome of M. falcata and may be useful for mining new low-temperature stress-related genes specific to M. falcata. These new findings could facilitate the understanding of the low-temperature-tolerance mechanism of M. falcata.

Download Full-text