Transcriptome-wide identification of WRKY family genes and their expression under cold acclimation in Eucalyptus globulus

Aguayo, Paula; Lagos, Catalina; Conejera, Daniel; Medina, Diego L.; Fernández, M; Valenzuela, Sofía

doi:10.1007/s00468-019-01860-3

Cited by 15 publications

(6 citation statements)

References 63 publications

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“…Several transcription factor (TF) families have been reported to regulate cold responses in plants including bZIP in B. rapa [ 29 ], WRKY in Eucalyptus globulus [ 30 ], NAC in Oryza sativa [ 31 ], and Malus domestica [ 32 ], among others. To this regard, we found that TFs belonging to 15 families were differentially expressed in the two genotypes under the influence of cold-stress treatment ( Figure 5 A–C).…”

Section: Resultsmentioning

confidence: 99%

Combined Transcriptome and Metabolome Profiling Provide Insights into Cold Responses in Rapeseed (Brassica napus L.) Genotypes with Contrasting Cold-Stress Sensitivity

Liu

Wei

Tian

et al. 2022

IJMS

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Low temperature is a major environmental factor, which limits rapeseed (Brassica napus L.) growth, development, and productivity. So far, the physiological and molecular mechanisms of rapeseed responses to cold stress are not fully understood. Here, we explored the transcriptome and metabolome profiles of two rapeseed genotypes with contrasting cold responses, i.e., XY15 (cold-sensitive) and GX74 (cold-tolerant). The global metabolome profiling detected 545 metabolites in siliques of both genotypes before (CK) and after cold-stress treatment (LW). The contents of several sugar metabolites were affected by cold stress with the most accumulated saccharides being 3-dehydro-L-threonic acid, D-xylonic acid, inositol, D-mannose, D-fructose, D-glucose, and L-glucose. A total of 1943 and 5239 differentially expressed genes were identified from the transcriptome sequencing in XY15CK_vs_XY15LW and GX74CK_vs_GX74LW, respectively. We observed that genes enriched in sugar metabolism and biosynthesis-related pathways, photosynthesis, reactive oxygen species scavenging, phytohormone, and MAPK signaling were highly expressed in GX74LW. In addition, several genes associated with cold-tolerance-related pathways, e.g., the CBF-COR pathway and MAPK signaling, were specifically expressed in GX74LW. Contrarily, genes in the above-mentioned pathways were mostly downregulated in XY15LW. Thus, our results indicate the involvement of these pathways in the differential cold-stress responses in XY15 and GX74.

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Section: Resultsmentioning

confidence: 99%

Combined Transcriptome and Metabolome Profiling Provide Insights into Cold Responses in Rapeseed (Brassica napus L.) Genotypes with Contrasting Cold-Stress Sensitivity

Liu

Wei

Tian

et al. 2022

IJMS

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“…There were 11 EglWRKY genes in the leaf tissues that were regulated during cold acclimation. 17 Comparative transcriptome analysis of anther development in rice in cold regions under cold stress demonstrated that starch metabolism and sucrose metabolism were the only important pathways (including 47 DEGs) that were annotated during the cold periods. 18 The basic helix-loop-helix (bHLH) transcription factors are involved in several abiotic stress responses.…”

Section: Low Temperature and High Temperature Stressesmentioning

confidence: 99%

Advances in Transcriptomics in the Response to Stress in Plants

Wang

Li²,

et al. 2020

Global Medical Genetics

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Adverse stress influences the normal growth and development of plants. With the development of molecular biology technology, understanding the molecular mechanism of plants in response to adverse stress has gradually become an important topic for academic exploration. The expression of the transcriptome is dynamic, which reflects the level of expression of all genes in a particular cell, tissue, or organ of an individual organism at a particular stage of growth and development. Transcriptomics can disclose the expression at the whole genome level under stress from the whole transcriptional level, which can be useful in understanding the complex regulatory network associated with the adaptability and tolerance of plants to stress. In this article, we review the application of transcriptomics in understanding the response of plants to biotic stresses such as diseases and insect infestation and abiotic stresses such as water, temperature, salt, and heavy metals to provide a guideline for related research.

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“…In recent years, transcriptome sequencing has been widely recognized as an effective method for the identification of plant transcription factor families under specific conditions for species such as S. integra, whose genome data have not yet been published. For example, transcriptome-wide identification and expression analysis of the MYB, ERKY, and CCCH families of Pinus massoniana under abiotic stress, such as phosphorus deficiency [22][23][24], the WRKY family of Eucalyptus globulus under cold acclimation [25], and the R2R3-MYB family of barley under boron stress [26] have been completed. Full-length transcriptome sequencing (also known as third-generation sequencing, or NGS) technology based on the PacBio platform has been developed in recent years to provide longer read lengths and higher accuracy [27] than next-generation sequencing (NGS) technology.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome-Wide Identification and Response Pattern Analysis of the Salix integra NAC Transcription Factor in Response to Pb Stress

Yue

Huang

et al. 2023

IJMS

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The NAC (NAM-ATAF1/2-CUC) transcription factor family is one of the largest plant-specific transcription factor families, playing an important role in plant growth and development and abiotic stress response. As a short-rotation woody plant, Salix integra (S. integra) has high lead (Pb) phytoremediation potential. To understand the role of NAC in S. integra Pb tolerance, 53 SiNAC transcripts were identified using third-generation and next-generation transcriptomic data from S. integra exposed to Pb stress, and a phylogenetic analysis revealed 11 subfamilies. A sequence alignment showed that multiple subfamilies represented by TIP and ATAF had a gene that produced more than one transcript under Pb stress, and different transcripts had different responses to Pb. By analyzing the expression profiles of SiNACs at 9 Pb stress time points, 41 of 53 SiNACs were found to be significantly responsive to Pb. Short time-series expression miner (STEM) analysis revealed that 41 SiNACs had two significant Pb positive response patterns (early and late), both containing 10 SiNACs. The SiNACs with the most significant Pb response were mainly from the ATAF and NAP subfamilies. Therefore, 4 and 3 SiNACs from the ATAF and NAP subfamilies, respectively, were selected as candidate Pb-responsive SiNACs for further structural and functional analysis. The RT-qPCR results of 7 transcripts also confirmed the different Pb response patterns of the ATAF and NAP subfamilies. SiNAC004 and SiNAC120, which were randomly selected from two subfamilies, were confirmed to be nuclear localization proteins by subcellular localization experiments. Functional prediction analysis of the associated transcripts of seven candidate SiNACs showed that the target pathways of ATAF subfamily SiNACs were “sulfur metabolism” and “glutathione metabolism”, and the target pathways of NAP subfamily SiNACs were “ribosome” and “phenylpropanoid biosynthesis”. This study not only identified two NAC subfamilies with different Pb response patterns but also identified Pb-responsive SiNACs that could provide a basis for subsequent gene function verification.

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Transcriptome-wide identification of WRKY family genes and their expression under cold acclimation in Eucalyptus globulus

Cited by 15 publications

References 63 publications

Combined Transcriptome and Metabolome Profiling Provide Insights into Cold Responses in Rapeseed (Brassica napus L.) Genotypes with Contrasting Cold-Stress Sensitivity

Combined Transcriptome and Metabolome Profiling Provide Insights into Cold Responses in Rapeseed (Brassica napus L.) Genotypes with Contrasting Cold-Stress Sensitivity

Advances in Transcriptomics in the Response to Stress in Plants

Transcriptome-Wide Identification and Response Pattern Analysis of the Salix integra NAC Transcription Factor in Response to Pb Stress

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