Identification of key genes and modules in response to Cadmium stress in different rice varieties and stem nodes by weighted gene co-expression network analysis

Wang, Qi; Zeng, Xianmin; Song, Qiulai; Sun, Yu; Feng, Yang; Lai, Yongcai

doi:10.1038/s41598-020-66132-4

Cited by 30 publications

(24 citation statements)

References 48 publications

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“…analyses (DalCorso et al, 2010;Huang et al, 2012;Yu et al, 2012;Deng et al, 2020;Wang et al, 2020). Usually, the regulatory networks consist of rapidly activated ROS production and calcium (Ca) oscillation, which can be perceived by Ca-binding proteins and magnified via kinases and further downstream pathways such as phytohormones, transport systems, and ROS scavenging, are precisely modulated to induce an appropriately reactive physiological response (Deng et al, 2020).…”

Section: Regulatory Components Of Ja-responsive Signaling Pathways In Response To Toxic Elementsmentioning

confidence: 99%

Molecular Interaction and Evolution of Jasmonate Signaling With Transport and Detoxification of Heavy Metals and Metalloids in Plants

et al. 2021

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An increase in environmental pollution resulting from toxic heavy metals and metalloids [e.g., cadmium (Cd), arsenic (As), and lead (Pb)] causes serious health risks to humans and animals. Mitigation strategies need to be developed to reduce the accumulation of the toxic elements in plant-derived foods. Natural and genetically-engineered plants with hyper-tolerant and hyper-accumulating capacity of toxic minerals are valuable for phytoremediation. However, the molecular mechanisms of detoxification and accumulation in plants have only been demonstrated in very few plant species such as Arabidopsis and rice. Here, we review the physiological and molecular aspects of jasmonic acid and the jasmonate derivatives (JAs) in response to toxic heavy metals and metalloids. Jasmonates have been identified in, limiting the accumulation and enhancing the tolerance to the toxic elements, by coordinating the ion transport system, the activity of antioxidant enzymes, and the chelating capacity in plants. We also propose the potential involvement of Ca2+ signaling in the stress-induced production of jasmonates. Comparative transcriptomics analyses using the public datasets reveal the key gene families involved in the JA-responsive routes. Furthermore, we show that JAs may function as a fundamental phytohormone that protects plants from heavy metals and metalloids as demonstrated by the evolutionary conservation and diversity of these gene families in a large number of species of the major green plant lineages. Using ATP-Binding Cassette G (ABCG) transporter subfamily of six representative green plant species, we propose that JA transporters in Subgroup 4 of ABCGs may also have roles in heavy metal detoxification. Our paper may provide guidance toward the selection and development of suitable plant and crop species that are tolerant to toxic heavy metals and metalloids.

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Section: Regulatory Components Of Ja-responsive Signaling Pathways In Response To Toxic Elementsmentioning

confidence: 99%

Molecular Interaction and Evolution of Jasmonate Signaling With Transport and Detoxification of Heavy Metals and Metalloids in Plants

et al. 2021

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“…Finally, we tested for associations with climate terms between, within, and variably across clusters for FLC/SOC1 expression, these residual gene expression PCs, and S1. Congruence of 13 genomic clusters identified and used in this study with the ancestry groups found by the 1001 Genomes Consortium [39]. Percentages indicate the percent of a given genomic cluster in each ancestry group, color coded by the number of accessions in a given group.…”

Section: Gene Expression and Flowering Timementioning

confidence: 99%

“…Thus, another effective method for more deeply examining signals of local adaptation is by interrogating environmental associations among genes with co-varying expression levels clustered into gene co-expression networks (33). With sufficient data, gene co-expression modules can then be connected to environmental agents of selection through clinal analysis (34)(35)(36)(37), to underlying polymorphisms through association mapping (38), and to organismal phenotypes through correlational tests or analyses of enrichment for particular gene functions (39,40). Moreover, different co-expression modules may orthogonally influence variation in subcomponents of a more integrated trait or trait syndrome.…”

Section: Introductionmentioning

confidence: 99%

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The scales and signatures of climate adaptation by theArabidopsistranscriptome

Colicchio¹,

Akman²,

Blackman³

2020

Preprint

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Clines in allele frequency and trait variation can be highly informative for understanding how populations have historically adapted to climate variation across landscapes. However, as a consequence of the many complexities inherent to this process, these climate-associated differentiation patterns can be confounded, misleading, or obscured. Molecular phenotypes like gene expression levels are a potentially valuable means for resolving these complexities. Their intermediate position between genomes and organismal traits and their interrelatedness structured by gene regulatory networks can help parse how different climatic factors contribute to unique components of range-wide or region-specific diversity patterns. Here, we demonstrate these explanatory values of gene expression variation through integrative analyses of transcriptomic data from 665 Arabidopsis thaliana accessions. Differentiation of co-expressed genes is often associated with source site climate. Although some patterns hold range-wide, many other gene expression clines are specific to particular ancestry groups, reflecting how broad-scale and local combinations of selective agents differentially resolve functional interrelationships between plant defense, drought tolerance, and life history traits. We also extend these analyses to parse how different factors explain climate-associated variation in flowering time and its plasticity. Expression of key regulators FLC and SOC1 strongly predicts time to flower, consistent with previous work, but our results also highlight novel relationships that indicate as yet unexplored climate-related connections between defense signaling and flowering. Finally, we show that integrative models combining genotype and gene expression information predict variation in flowering time under ecologically realistic conditions more accurately than models based on either source alone.

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“…Gene co-expression networks derived through WCNA analysis have emerged as a robust systems biology approach to discover associations within biomolecules [41][42][43][44][45][46][47][48]. As demonstrated by the guilt-of-association concept, genes with similar expression patterns are most likely to be associated with a similar biological process [49,50].…”

Section: Network-based Characterization Of Transcriptome and Metabolome Relationships In Mallotus Japonicusmentioning

confidence: 99%

Gene-Metabolite Network Analysis Revealed Tissue-Specific Accumulation of Therapeutic Metabolites in Mallotus japonicus

Rai

Mori

et al. 2021

IJMS

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Mallotus japonicus is a valuable traditional medicinal plant in East Asia for applications as a gastrointestinal drug. However, the molecular components involved in the biosynthesis of bioactive metabolites have not yet been explored, primarily due to a lack of omics resources. In this study, we established metabolome and transcriptome resources for M. japonicus to capture the diverse metabolite constituents and active transcripts involved in its biosynthesis and regulation. A combination of untargeted metabolite profiling with data-dependent metabolite fragmentation and metabolite annotation through manual curation and feature-based molecular networking established an overall metabospace of M. japonicus represented by 2129 metabolite features. M. japonicus de novo transcriptome assembly showed 96.9% transcriptome completeness, representing 226,250 active transcripts across seven tissues. We identified specialized metabolites biosynthesis in a tissue-specific manner, with a strong correlation between transcripts expression and metabolite accumulations in M. japonicus. The correlation- and network-based integration of metabolome and transcriptome datasets identified candidate genes involved in the biosynthesis of key specialized metabolites of M. japonicus. We further used phylogenetic analysis to identify 13 C-glycosyltransferases and 11 methyltransferases coding candidate genes involved in the biosynthesis of medicinally important bergenin. This study provides comprehensive, high-quality multi-omics resources to further investigate biological properties of specialized metabolites biosynthesis in M. japonicus.

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Identification of key genes and modules in response to Cadmium stress in different rice varieties and stem nodes by weighted gene co-expression network analysis

Cited by 30 publications

References 48 publications

Molecular Interaction and Evolution of Jasmonate Signaling With Transport and Detoxification of Heavy Metals and Metalloids in Plants

Molecular Interaction and Evolution of Jasmonate Signaling With Transport and Detoxification of Heavy Metals and Metalloids in Plants

The scales and signatures of climate adaptation by theArabidopsistranscriptome

Gene-Metabolite Network Analysis Revealed Tissue-Specific Accumulation of Therapeutic Metabolites in Mallotus japonicus

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