Potential regulatory genes of light induced anthocyanin accumulation in sweet cherry identified by combining transcriptome and metabolome analysis

Zhang, Yao; Chen, Chaoqun; Cui, Yiling; Du, Qinsong; Tang, Wenjing; Yang, Wenlong; Kou, Guanqiong; Tang, Wanjia; Chen, Hongxu; Gong, Ronggao

doi:10.3389/fpls.2023.1238624

Cited by 3 publications

(1 citation statement)

References 81 publications

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“…When assessing the clustering of the CPDAGs, based on their SHD to all other CPDAGs, and the percentage of common directed edges (or directed and directed that turned into bidirected) with all other CPDAGs, it was found that in the transcriptomic case, this expectation was not satisfied (Figures 1 and A1). Indeed, in a transcriptomic analysis of quality changes during sweet cherry fruit development, the transcriptome of the organs has been found to exhibit strong differentiation depending on the developmental stage [50,51].…”

Section: Discussionmentioning

confidence: 99%

Exploring the Robustness of Causal Structures in Omics Data: A Sweet Cherry Proteogenomic Perspective

Ganopoulou,

Xanthopoulou,

Michailidis

et al. 2023

Agronomy

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Causal discovery is a highly promising tool with a broad perspective in the field of biology. In this study, a causal structure robustness assessment algorithm is proposed and employed on the causal structures obtained, based on transcriptomic, proteomic, and the combined datasets, emerging from a quantitative proteogenomic atlas of 15 sweet cherry (Prunus avium L.) cv. ‘Tragana Edessis’ tissues. The algorithm assesses the impact of intervening in the datasets of the causal structures, using various criteria. The results showed that specific tissues exhibited an intense impact on the causal structures that were considered. In addition, the proteogenomic case demonstrated that biologically related tissues that referred to the same organ induced a similar impact on the causal structures considered, as was biologically expected. However, this result was subtler in both the transcriptomic and the proteomic cases. Furthermore, the causal structures based on a single omic analysis were found to be impacted to a larger extent, compared to the proteogenomic case, probably due to the distinctive biological features related to the proteome or the transcriptome. This study showcases the significance and perspective of assessing the causal structure robustness based on omic databases, in conjunction with causal discovery, and reveals advantages when employing a multiomics (proteogenomic) analysis compared to a single-omic (transcriptomic, proteomic) analysis.

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Section: Discussionmentioning

confidence: 99%

Exploring the Robustness of Causal Structures in Omics Data: A Sweet Cherry Proteogenomic Perspective

Ganopoulou,

Xanthopoulou,

Michailidis

et al. 2023

Agronomy

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Metabolomics and transcriptomics analysis revealed the response mechanism of alfalfa to combined cold and saline‐alkali stress

Liu,

Si,

Zhang

et al. 2024

The Plant Journal

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SUMMARYCold and saline‐alkali stress are frequently encountered by plants, and they often occur simultaneously in saline‐alkali soils at mid to high latitudes, constraining forage crop distribution and production. However, the mechanisms by which forage crops respond to the combination of cold and saline‐alkali stress remain unknown. Alfalfa (Medicago sativa L.) is one of the most essential forage grasses in the world. In this study, we analyzed the complex response mechanisms of two alfalfa species (Zhaodong [ZD] and Blue Moon [BM]) to combined cold and saline‐alkali stress using multi‐omics. The results revealed that ZD had a greater ability to tolerate combined stress than BM. The tricarboxylic acid cycles of the two varieties responded positively to the combined stress, with ZD accumulating more sugars, amino acids, and jasmonic acid. The gene expression and flavonoid content of the flavonoid biosynthesis pathway were significantly different between the two varieties. Weighted gene co‐expression network analysis and co‐expression network analysis based on RNA‐Seq data suggested that the MsMYB12 gene may respond to combined stress by regulating the flavonoid biosynthesis pathway. MsMYB12 can directly bind to the promoter of MsFLS13 and promote its expression. Moreover, MsFLS13 overexpression can enhance flavonol accumulation and antioxidant capacity, which can improve combined stress tolerance. These findings provide new insights into improving alfalfa resistance to combined cold and saline‐alkali stress, showing that flavonoids are essential for plant resistance to combined stresses, and provide theoretical guidance for future breeding programs.

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Metabolic Profiling and Transcriptome Analysis Provide Insights into the Anthocyanin Types and Biosynthesis in Zingiber striolatum Diels Flower Buds in Three Planting Modes

Zhou,

Wang,

Zhao

et al. 2024

Agronomy

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The flower buds of Zingiber striolatum Diels are considered a special vegetable in China, and they are rich in anthocyanins. However, the detailed composition types and the molecular mechanism of anthocyanin biosynthesis in Z. striolatum flower buds are still unclear. In this study, targeted metabolites were used to analyze and identify the anthocyanin types of Z. striolatum in three planting modes: monoculture (CK), intercropping with maize (ZP), and intercropping with soybean (SP). A total of 48 anthocyanins were identified with significant differential accumulation in Z. striolatum flower buds. Among them, cyanidin-3-O-glucoside was the main composition type of anthocyanins. Furthermore, the composition types of blue anthocyanin were identified in flower buds. A total of 15 structure genes were obtained from the transcriptome database of Z. striolatum flower buds. The qRT-PCR results revealed that the expression levels of ZsC4H-1, ZsC4H-2, ZsCHS-2, ZsCHI, ZsF3H, ZsF3’H, ZsDFR, ZsF3’5’H-3, and ZsANS genes were the highest in the ZP model. This study showed that the ZP model contributes to anthocyanin synthesis and accumulation of Z. striolatum flower buds among the three planting modes of Z. striolatum. These findings provide valuable information for research on the planting model and anthocyanin biosynthesis in Z. striolatum flower buds.

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Potential regulatory genes of light induced anthocyanin accumulation in sweet cherry identified by combining transcriptome and metabolome analysis

Cited by 3 publications

References 81 publications

Exploring the Robustness of Causal Structures in Omics Data: A Sweet Cherry Proteogenomic Perspective

Exploring the Robustness of Causal Structures in Omics Data: A Sweet Cherry Proteogenomic Perspective

Metabolomics and transcriptomics analysis revealed the response mechanism of alfalfa to combined cold and saline‐alkali stress

Metabolic Profiling and Transcriptome Analysis Provide Insights into the Anthocyanin Types and Biosynthesis in Zingiber striolatum Diels Flower Buds in Three Planting Modes

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