Metabolomic and transcriptomic analyses reveal the regulation of pigmentation in the purple variety of Dendrobium officinale

Zhan, Xinqiao; Qi, Jufeng; Zhou, Bin; Mao, Bizeng

doi:10.1038/s41598-020-74789-0

Cited by 25 publications

(32 citation statements)

References 63 publications

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“…All samples were acquired by using the LC-MS system according to the direction of the instrument. All chromatographic separations were performed following the protocol as previously described in the study of ( 28 ) using an ultra-performance liquid chromatography system (SCIEX, UK). A high-resolution tandem mass spectrometer TripleTOF5600plus (SCIEX) was used to identify metabolites eluted from the column according to the procedure previously described by Xiang et al ( 15 ).…”

Section: Methodsmentioning

confidence: 99%

Dietary Amylose/Amylopectin Ratio Modulates Cecal Microbiota and Metabolites in Weaned Goats

et al. 2021

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Increasing the ratio of amylose in the diet can increase the quantity of starch that flows to the large intestine for microbial fermentation. This leads to the alteration of microbiota and metabolite of the hindgut, where the underlying mechanism is not clearly understood. The present study used a combination of 16S amplicon sequencing technology and metabolomics technique to reveal the effects of increasing ratios of amylose/amylopectin on cecal mucosa- and digesta-associated microbiota and their metabolites in young goats. Twenty-seven Xiangdong black female goats with average body weights (9.00 ± 1.12 kg) were used in this study. The goats were randomly allocated to one of the three diets containing starch with 0% amylose corn (T1), 50% high amylose corn (T2), and 100% high amylose corn (T3) for 35 days. Results showed that cecal valerate concentration was higher (P < 0.05) in the T2 group than those in the T1 and T3 groups. The levels of tumor necrosis factor-α (TNF-α) and interleukin (IL)-6 were decreased (P < 0.05) in cecal tissue while IL-10 was increased (P < 0.05) in the T2 group when compared with T1 or T3 groups. At the phylum level, the proportion of mucosa-associated Spirochaetes was increased (P < 0.05), while Proteobacteria was deceased by feeding high amylose ratios (P < 0.05). The abundance of Verrucomicrobia was decreased (P < 0.05) in the T3 group compared with the T1 and T2 groups. The abundance of digesta-associated Firmicutes was increased (P < 0.05) while Verrucomicrobia and Tenericutes were deceased (P < 0.05) with the increment of amylose/amylopectin ratios. The LEfSe analysis showed that a diet with 50% high amylose enriched the abundance of beneficial bacteria such as Faecalibacterium and Lactobacillus in the digesta and Akkermansia in the mucosa compared with the T1 diet. The metabolomics results revealed that feeding a diet containing 50% high amylose decreased the concentration of fatty acyls-related metabolites, including dodecanedioic acid, heptadecanoic acid, and stearidonic acid ethyl ester compared with the T1 diet. The results suggested that a diet consisting of 50% high amylose could maintain a better cecal microbiota composition and host immune function.

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Section: Methodsmentioning

confidence: 99%

Dietary Amylose/Amylopectin Ratio Modulates Cecal Microbiota and Metabolites in Weaned Goats

et al. 2021

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“…The indication that flavonoids/anthocyanins are one major class of plant chromogenic compounds is probably why researchers tended to conduct targeted metabolomics measurements covering the flavonoids and/or anthocyanins in plant-color-related cases ( Shi et al., 2020b ; Jiao et al., 2020 ; Qiu et al., 2020 ). Subsequently, differential metabolites and corresponding responsible candidate genes were collected to explain the molecular mechanisms of color variation at the metabolomic and, probably, the transcriptomic levels ( Li et al., 2020 ; Zhan et al., 2020 ).…”

Section: Delineating the Metabolic Pathways Is Essential To Explain Or Explore The Connections Betwmentioning

confidence: 99%

Exploring the genic resources underlying metabolites through mGWAS and mQTL in wheat: From large-scale gene identification and pathway elucidation to crop improvement

Chen

Xue

Liu

et al. 2021

Plant Communications

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Common wheat ( Triticum aestivum L.) is a leading cereal crop, but has lagged behind with respect to the interpretation of the molecular mechanisms of phenotypes compared with other major cereal crops such as rice and maize. The recently available genome sequence of wheat affords the pre-requisite information for efficiently exploiting the potential molecular resources for decoding the genetic architecture of complex traits and identifying valuable breeding targets. Meanwhile, the successful application of metabolomics as an emergent large-scale profiling methodology in several species has demonstrated this approach to be accessible for reaching the above goals. One such productive avenue is combining metabolomics approaches with genetic designs. However, this trial is not as widespread as that for sequencing technologies, especially when the acquisition, understanding, and application of metabolic approaches in wheat populations remain more difficult and even arguably underutilized. In this review, we briefly introduce the techniques used in the acquisition of metabolomics data and their utility in large-scale identification of functional candidate genes. Considerable progress has been made in delivering improved varieties, suggesting that the inclusion of information concerning these metabolites and genes and metabolic pathways enables a more explicit understanding of phenotypic traits and, as such, this procedure could serve as an -omics-informed roadmap for executing similar improvement strategies in wheat and other species.

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“…The wax synthesis that was evidenced by the glassy wax coating on the V. darrowii leaves was probably due to high number of DEGs involved in wax and fatty acid biosynthesis pathway. DEGs in several non-enzymatic antioxidant biosynthesis pathways (flavonoid, anthocyanin, carotenoid, and other secondary metabolites) and their essential role in the scavenging of ROS to overcome the heat stress impacts is evidenced by the accumulation of antioxidant compounds under heat stress in plants [81,82]. DEGs were identified in the valine, leucine, and isoleucine biosynthesis pathways and their induction in response to osmoregulation under heat stress [83].…”

Section: Dynamics Of Key Pathways Involved In Response To Heat Stressmentioning

confidence: 99%

Differential Morpho-Physiological and Transcriptomic Responses to Heat Stress in Two Blueberry Species

Callwood

Melmaiee

Kulkarni

et al. 2021

IJMS

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Blueberries (Vaccinium spp.) are highly vulnerable to changing climatic conditions, especially increasing temperatures. To gain insight into mechanisms underpinning the response to heat stress, two blueberry species were subjected to heat stress for 6 and 9 h at 45 °C, and leaf samples were used to study the morpho-physiological and transcriptomic changes. As compared with Vaccinium corymbosum, Vaccinium darrowii exhibited thermal stress adaptation features such as small leaf size, parallel leaf orientation, waxy leaf coating, increased stomatal surface area, and stomatal closure. RNAseq analysis yielded ~135 million reads and identified 8305 differentially expressed genes (DEGs) during heat stress against the control samples. In V. corymbosum, 2861 and 4565 genes were differentially expressed at 6 and 9 h of heat stress, whereas in V. darrowii, 2516 and 3072 DEGs were differentially expressed at 6 and 9 h, respectively. Among the pathways, the protein processing in the endoplasmic reticulum (ER) was the highly enriched pathway in both the species: however, certain metabolic, fatty acid, photosynthesis-related, peroxisomal, and circadian rhythm pathways were enriched differently among the species. KEGG enrichment analysis of the DEGs revealed important biosynthesis and metabolic pathways crucial in response to heat stress. The GO terms enriched in both the species under heat stress were similar, but more DEGs were enriched for GO terms in V. darrowii than the V. corymbosum. Together, these results elucidate the differential response of morpho-physiological and molecular mechanisms used by both the blueberry species under heat stress, andhelp in understanding the complex mechanisms involved in heat stress tolerance.

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Metabolomic and transcriptomic analyses reveal the regulation of pigmentation in the purple variety of Dendrobium officinale

Cited by 25 publications

References 63 publications

Dietary Amylose/Amylopectin Ratio Modulates Cecal Microbiota and Metabolites in Weaned Goats

Dietary Amylose/Amylopectin Ratio Modulates Cecal Microbiota and Metabolites in Weaned Goats

Exploring the genic resources underlying metabolites through mGWAS and mQTL in wheat: From large-scale gene identification and pathway elucidation to crop improvement

Differential Morpho-Physiological and Transcriptomic Responses to Heat Stress in Two Blueberry Species

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