Identification of core genes associated with different phosphorus levels in quinoa seedlings by weighted gene co-expression network analysis

Zhang, Shan; Liu, Jian; Shi, Lei; Wang, Qianchao; Zhang, Ping; Wang, Hongxin; Liu, Junna; Li, Hanxue; Li, Li; Huang, Lei; Qin, Peng

doi:10.1186/s12864-023-09507-x

Cited by 3 publications

(1 citation statement)

References 44 publications

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“…Acid phosphatase plays important roles in metabolism such as hydrolysis of phospholipid materials, participation in autophagy processes, and endomembrane recycling [ 48 ]. The up-regulation of acid phosphatase could also be observed in many plant transcriptome studies under conditions of phosphorus deficiency, such as peanut [ 39 ], quinoa [ 49 ], rice [ 50 ], and soybean [ 51 ]. Phospholipase plays central roles in the maintenance and remodeling of the cell membrane by hydrolyzing membrane phospholipids [ 52 ].…”

Section: Discussionmentioning

confidence: 99%

Transcriptomic Analysis of the Response of the Toxic Dinoflagellate Prorocentrum lima to Phosphorous Limitation

Wan,

Yao,

Wang

et al. 2023

Microorganisms

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Some dinoflagellates cause harmful algal blooms, releasing toxic secondary metabolites, to the detriment of marine ecosystems and human health. Phosphorus (P) is a limiting macronutrient for dinoflagellate growth in the ocean. Previous studies have been focused on the physiological response of dinoflagellates to ambient P changes. However, the whole-genome’s molecular mechanisms are poorly understood. In this study, RNA-Seq was utilized to compare the global gene expression patterns of a marine diarrheic shellfish poisoning (DSP) toxin-producing dinoflagellate, Prorocentrum lima, grown in inorganic P-replete and P-deficient conditions. A total of 148 unigenes were significantly up-regulated, and 30 unigenes were down-regulated under 1/4 P-limited conditions, while 2708 unigenes were significantly up-regulated, and 284 unigenes were down-regulated under 1/16 P-limited conditions. KEGG enrichment analysis of the differentially expressed genes shows that genes related to ribosomal proteins, glycolysis, fatty acid biosynthesis, phagosome formation, and ubiquitin-mediated proteolysis are found to be up-regulated, while most of the genes related to photosynthesis are down-regulated. Further analysis shows that genes encoding P transporters, organic P utilization, and endocytosis are significantly up-regulated in the P-limited cells, indicating a strong ability of P. lima to utilize dissolved inorganic P as well as intracellular organic P. These transcriptomic data are further corroborated by biochemical and physiological analyses, which reveals that under P deficiency, cellular contents of starch, lipid, and toxin increase, while photosynthetic efficiency declines. Our results indicate that has P. lima evolved diverse strategies to acclimatize to low P environments. The accumulation of carbon sources and DSP toxins could provide protection for P. lima to cope with adverse environmental conditions.

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Section: Discussionmentioning

confidence: 99%

Transcriptomic Analysis of the Response of the Toxic Dinoflagellate Prorocentrum lima to Phosphorous Limitation

Wan,

Yao,

Wang

et al. 2023

Microorganisms

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Using Bacillus megaterium as a bio-fertilizer alleviates salt stress, improves phosphorus nutrition, and increases cauliflower yield

Shalaby

2023

Journal of Plant Nutrition

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Identification and core gene-mining of Weighted Gene Co-expression Network Analysis-based co-expression modules related to flood resistance in quinoa seedlings

Wang,

Bai,

Zhang

et al. 2024

BMC Genomics

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Background As an emerging food crop with high nutritional value, quinoa has been favored by consumers in recent years; however, flooding, as an abiotic stress, seriously affects its growth and development. Currently, reports on the molecular mechanisms related to quinoa waterlogging stress responses are lacking; accordingly, the core genes related to these processes were explored via Weighted Gene Co-expression Network Analysis (WGCNA). Results Based on the transcriptome data, WGCNA was used to construct a co-expression network of weighted genes associated with flooding resistance-associated physiological traits and metabolites. Here, 16 closely related co-expression modules were obtained, and 10 core genes with the highest association with the target traits were mined from the two modules. Functional annotations revealed the biological processes and metabolic pathways involved in waterlogging stress, and four candidates related to flooding resistance, specifically AP2/ERF, MYB, bHLH, and WRKY-family TFs, were also identified. Conclusions These results provide clues to the identification of core genes for quinoa underlying quinoa waterlogging stress responses. This could ultimately provide a theoretical foundation for breeding new quinoa varieties with flooding tolerance. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-024-10638-y.

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Identification of core genes associated with different phosphorus levels in quinoa seedlings by weighted gene co-expression network analysis

Cited by 3 publications

References 44 publications

Transcriptomic Analysis of the Response of the Toxic Dinoflagellate Prorocentrum lima to Phosphorous Limitation

Transcriptomic Analysis of the Response of the Toxic Dinoflagellate Prorocentrum lima to Phosphorous Limitation

Using Bacillus megaterium as a bio-fertilizer alleviates salt stress, improves phosphorus nutrition, and increases cauliflower yield

Identification and core gene-mining of Weighted Gene Co-expression Network Analysis-based co-expression modules related to flood resistance in quinoa seedlings

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