scholarly journals Identification of miRNA–mRNA Regulatory Modules Involved in Lipid Metabolism and Seed Development in a Woody Oil Tree (Camellia oleifera)

Cells ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 71
Author(s):  
Bo Wu ◽  
Chengjiang Ruan ◽  
Asad Hussain Shah ◽  
Denghui Li ◽  
He Li ◽  
...  
Keyword(s):  
Lipid Metabolism ◽  
Seed Development ◽  
Seed Oil ◽  
Southern China ◽  
Integrated Analysis ◽  
Camellia Oleifera ◽  
Regulatory Modules ◽  
Oil Biosynthesis ◽  
Regulatory Module ◽  
Early Seed Development

Tea oil camellia (Camellia oleifera), an important woody oil tree, is a source of seed oil of high nutritional and medicinal value that is widely planted in southern China. However, there is no report on the identification of the miRNAs involved in lipid metabolism and seed development in the high- and low-oil cultivars of tea oil camellia. Thus, we explored the roles of miRNAs in the key periods of oil formation and accumulation in the seeds of tea oil camellia and identified miRNA–mRNA regulatory modules involved in lipid metabolism and seed development. Sixteen small RNA libraries for four development stages of seed oil biosynthesis in high- and low-oil cultivars were constructed. A total of 196 miRNAs, including 156 known miRNAs from 35 families, and 40 novel miRNAs were identified, and 55 significantly differentially expressed miRNAs were found, which included 34 upregulated miRNAs, and 21 downregulated miRNAs. An integrated analysis of the miRNA and mRNA transcriptome sequence data revealed that 10 miRNA–mRNA regulatory modules were related to lipid metabolism; for example, the regulatory modules of ath-miR858b–MYB82/MYB3/MYB44 repressed seed oil biosynthesis, and a regulation module of csi-miR166e-5p–S-ACP-DES6 was involved in the formation and accumulation of oleic acid. A total of 23 miRNA–mRNA regulatory modules were involved in the regulation of the seed size, such as the regulatory module of hpe-miR162a_L-2–ARF19, involved in early seed development. A total of 12 miRNA–mRNA regulatory modules regulating growth and development were identified, such as the regulatory modules of han-miR156a_L+1–SPL4/SBP2, promoting early seed development. The expression changes of six miRNAs and their target genes were validated using quantitative real-time PCR, and the targeting relationship of the cpa-miR393_R-1–AFB2 regulatory module was verified by luciferase assays. These data provide important theoretical values and a scientific basis for the genetic improvement of new cultivars of tea oil camellia in the future.

scholarly journals Identification of miRNA-mRNA regulatory modules involved in lipid metabolism and seed development in a woody-oil tree (Camellia oleifera)

2020 ◽  
Author(s):  
Bo Wu ◽  
Chengjiang Ruan ◽  
Asad Hussain Shah ◽  
Sihei Liu
Keyword(s):  
Lipid Metabolism ◽  
Seed Development ◽  
Critical Period ◽  
Seed Oil ◽  
Integrated Analysis ◽  
Camellia Oleifera ◽  
Regulatory Modules ◽  
Oil Biosynthesis ◽  
Regulatory Module ◽  
Early Seed Development

Abstract BackgroundTea oil camellia ( Camellia oleifera ), an important woody oil tree, is a source of seed oil of high nutritional and medicinal values and has been being widely planted in southern China. However, there is no report on the identification of miRNAs involved in lipid metabolism and seed development in high- and low-oil cultivars of tea oil camellia. Thus, we explored the roles of miRNAs in the critical period of oil formation and accumulation in tea oil camellia, and identified miRNA-mRNA regulatory modules involved in lipid metabolism and seed development. ResultsSixteen small RNA libraries for high- and low-oil cultivars of the critical period of oil biosynthesis were constructed. A total of 196 miRNAs, including 156 known miRNAs from 35 families and 40 novel miRNAs, were identified, and 55 significantly differentially expressed miRNAs were found, which included 34 up-regulated miRNAs and 21 down-regulated miRNAs. An integrated analysis of miRNA and mRNA transcriptome sequence data and qRT-PCR-based information was performed and revealed that nine miRNA-mRNA regulatory modules were related to lipid metabolism, such as the negative regulatory modules of ath-miR858b- MYB82 / MYB3 / MYB44 represses seed oil biosynthesis and a positive regulation module of csi-miR166e-5p- S-ACP - DES6 for formation and accumulation of oleic acid. Twenty-tree miRNA-mRNA regulatory modules were involved in the regulation of seed size, such as a negative regulatory module of hpe-miR162a_L-2- ARF19 involved in early seed development. Twelve miRNA-mRNA regulatory modules regulating growth and development were identified, such as the negative regulatory modules of han-miR156a_L+1- SPL4 / SBP2 promoting early seed development. The targeting relationship of the cpa-miR393_R-1-AFB2 regulatory module were verified by luciferase activity assays. ConclusionMultiple microRNAs (miRNAs) were identified to involve in developing seeds of tea oil camellia, especially discovering several miRNA-mRNA regulatory modules involving in seed development and lipid metabolism. These data provide important theoretical value and a scientific basis for the genetic improvement of new varieties of tea oil camellia in the future.

scholarly journals Comparative profiling of microRNA expression in the developing seeds of high- and low-oil tea oil camellia (Camellia oleifera) cultivars

2019 ◽  
Author(s):  
Bo Wu ◽  
Chengjiang Ruan ◽  
Wanchen Zhang ◽  
Asad Hussain Shah ◽  
Sihei Liu
Keyword(s):  
Lipid Metabolism ◽  
Target Genes ◽  
Sequence Data ◽  
Southern China ◽  
Expression Patterns ◽  
Integrated Analysis ◽  
Small Rna Sequencing ◽  
Camellia Oleifera ◽  
Illumina Platform ◽  
Function Modules

Abstract Background Tea oil camellia (Camellia oleifera), an important woody oil tree, is a source of seed oil of high nutritional and medicinal values and has been widely planted in southern China. However, there are few reports on the identification of miRNAs involved in seed lipid metabolism in high- and low-oil cultivars of tea oil camellia. Results An miRNA sequencing database was constructed for an Illumina platform, which was used to perform high-throughput small RNA sequencing of seeds of high- and low-oil cultivars of tea oil camellia at four different developmental stages, and the important relevant miRNAs and their target genes were identified. A total of 196 miRNAs, including 156 known miRNAs from 35 families and 40 novel miRNAs, were identified, and 55 significantly differentially expressed miRNAs were found. An integrated analysis of miRNA and mRNA transcriptome sequence data and qRT-PCR-based information was performed and revealed that 10 miRNA-mRNA function modules were related to lipid metabolism and 23 miRNA-mRNA function modules were involved in the regulation of seed size. Conclusion Mining and studying the expression patterns and functions of miRNAs and their regulatory target genes can not only promote the development of miRNAs related to tea oil camellia in public resource databases but also provide important theoretical value and a scientific basis for the genetic improvement of new varieties of tea oil camellia in the future.

scholarly journals Comparative Transcriptome Analysis of Developing Seeds and Silique Wall Reveals Dynamic Transcription Networks for Effective Oil Production in Brassica napus L.

2019 ◽  
Vol 20 (8) ◽  
pp. 1982 ◽  
Author(s):  
Muhammad Shahid ◽  
Guangqin Cai ◽  
Feng Zu ◽  
Qing Zhao ◽  
Muhammad Uzair Qasim ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Seed Development ◽  
Vegetable Oil ◽  
Oil Content ◽  
Seed Oil ◽  
Seed Oil Content ◽  
Oil Accumulation ◽  
Developing Seeds ◽  
Oil Biosynthesis ◽  
Oil Crops

Vegetable oil is an essential constituent of the human diet and renewable raw material for industrial applications. Enhancing oil production by increasing seed oil content in oil crops is the most viable, environmentally friendly, and sustainable approach to meet the continuous demand for the supply of vegetable oil globally. An in-depth understanding of the gene networks involved in oil biosynthesis during seed development is a prerequisite for breeding high-oil-content varieties. Rapeseed (Brassica napus) is one of the most important oil crops cultivated on multiple continents, contributing more than 15% of the world’s edible oil supply. To understand the phasic nature of oil biosynthesis and the dynamic regulation of key pathways for effective oil accumulation in B. napus, comparative transcriptomic profiling was performed with developing seeds and silique wall (SW) tissues of two contrasting inbred lines with ~13% difference in seed oil content. Differentially expressed genes (DEGs) between high- and low-oil content lines were identified across six key developmental stages, and gene enrichment analysis revealed that genes related to photosynthesis, metabolism, carbohydrates, lipids, phytohormones, transporters, and triacylglycerol and fatty acid synthesis tended to be upregulated in the high-oil-content line. Differentially regulated DEG patterns were revealed for the control of metabolite and photosynthate production in SW and oil biosynthesis and accumulation in seeds. Quantitative assays of carbohydrates and hormones during seed development together with gene expression profiling of relevant pathways revealed their fundamental effects on effective oil accumulation. Our results thus provide insights into the molecular basis of high seed oil content (SOC) and a new direction for developing high-SOC rapeseed and other oil crops.

scholarly journals An integrated omics analysis reveals the gene expression profiles of rapeseed, castor bean, and maize for seed oil biosynthesis

2021 ◽  
Author(s):  
Nian Liu ◽  
Jing Liu ◽  
Shihang Fan ◽  
Hongfang Liu ◽  
Xue-Rong Zhou ◽  
...  
Keyword(s):  
Lipid Metabolism ◽  
Castor Bean ◽  
Oil Content ◽  
Molecular Mechanisms ◽  
Seed Oil ◽  
Lipid Biosynthesis ◽  
Biosynthetic Enzymes ◽  
Seed Oil Content ◽  
Oil Biosynthesis ◽  
Lipid Metabolism Genes

Abstract Background Seed storage lipids are valuable for human diet and for the sustainable development of mankind. In recent decades, many lipid metabolism genes and pathways have been identified, but the molecular mechanisms that underlie species differences in seed oil biosynthesis are not fully understood. Results To investigate the molecular mechanisms of seed oil accumulation in different species, we performed comparative genome and transcriptome analyses of rapeseed and castor bean, which have high seed oil contents, and maize, which has a low seed oil content. The results uncovered the molecular mechanism of the low and high seed oil content in maize and castor bean, respectively. Transcriptome analyses showed that more than 61% of the lipid- and carbohydrate-related genes were regulated in rapeseed and castor bean, but only 20.1% of the lipid-related genes and 22.5% of the carbohydrate-related genes were regulated in maize. Compared to rapeseed and castor bean, fewer lipid biosynthesis genes but more lipid metabolism genes were regulated in the maize embryo. More importantly, most maize genes encoding lipid-related transcription factors, triacylglycerol (TAG) biosynthetic enzymes, pentose phosphate pathway (PPP) and Calvin Cycle proteins were not regulated during seed oil synthesis, despite the presence of many homologs in the maize genome. These results revealed the molecular underpinnings of the low seed oil content in maize. In castor bean, we observed differential regulation of vital oil biosynthetic enzymes and extremely high expression levels of oil biosynthetic genes, which were consistent with the rapid accumulation of oil in castor bean developing seeds. Conclusions Compared to oil seed (rapeseed and castor bean), less oil biosynthetic genes were regulated during the seed development in non-oil seed (maize). These results shed light on molecular mechanisms of lipid biosynthesis in rapeseed, castor bean, and maize. They can provide information on key target genes that may be useful for future experimental manipulation of oil production in oilseed crops.

scholarly journals Integrated analysis of transcriptomic and proteomic data from tree peony (P. ostii) seeds reveals key developmental stages and candidate genes related to oil biosynthesis and fatty acid metabolism

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Xiaojing Wang ◽  
Haiying Liang ◽  
Dalong Guo ◽  
Lili Guo ◽  
Xiangguang Duan ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Seed Development ◽  
Fatty Acid Metabolism ◽  
Proteomic Analysis ◽  
Acid Metabolism ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Tree Peony ◽  
Oil Biosynthesis

Abstract Tree peony (Paeonia section Moutan DC.) seeds are an excellent source of beneficial natural compounds that promote health, and they contain high levels of alpha-linolenic acid (ALA). In recent years, tree peony has been emerging as an oil crop. Therefore, combined analysis of the transcriptome and proteome of tree peony (P. ostii) seeds at 25, 32, 39, 53, 67, 81, 88, 95, and 109 days after pollination (DAP) was conducted to better understand the transcriptional and translational regulation of seed development and oil biosynthesis. A total of 38,482 unigenes and 2841 proteins were identified. A total of 26,912 differentially expressed genes (DEGs) and 592 differentially expressed proteins (DEPs) were clustered into three groups corresponding to the rapid growth, seed inclusion enrichment and conversion, and late dehydration and mature stages of seed development. Fifteen lipid metabolism pathways were identified at both the transcriptome and proteome levels. Pathway enrichment analysis revealed that a period of rapid fatty acid biosynthesis occurred at 53–88 DAP. Furthermore, 211 genes and 35 proteins associated with the fatty acid metabolism pathway, 63 genes and 11 proteins associated with the biosynthesis of unsaturated fatty acids (UFAs), and 115 genes and 24 proteins associated with ALA metabolism were identified. Phylogenetic analysis revealed that 16 putative fatty acid desaturase (FAD)-encoding genes clustered into four FAD groups, eight of which exhibited the highest expression at 53 DAP, suggesting that they play an important role in ALA accumulation. RT-qPCR analysis indicated that the temporal expression patterns of oil biosynthesis genes were largely similar to the RNA-seq results. The expression patterns of fatty acid metabolism- and seed development-related proteins determined by MRM were also highly consistent with the results obtained in the proteomic analysis. Correlation analysis indicated significant differences in the number and abundance of DEGs and DEPs but a high level of consistency in expression patterns and metabolic pathways. The results of the present study represent the first combined transcriptomic and proteomic analysis of tree peony seeds and provide insight into tree peony seed development and oil accumulation.

scholarly journals Characterization of the Volatile Compounds in Camellia oleifera Seed Oil from Different Geographic Origins

Molecules ◽  
2022 ◽  
Vol 27 (1) ◽  
pp. 308
Author(s):  
Jing Wang ◽  
Xuxiao Tang ◽  
Qiulu Chu ◽  
Mengyu Zhang ◽  
Yingzhong Zhang ◽  
...  
Keyword(s):  
Volatile Compounds ◽  
Consumer Choice ◽  
Seed Oil ◽  
Edible Oils ◽  
Solid Phase ◽  
Southern China ◽  
Maturity Stage ◽  
Camellia Oleifera ◽  
Annual Average ◽  
Spectrometer System

Volatile flavor of edible oils is an important quality index and factor affecting consumer choice. The purpose of this investigation was to characterize virgin Camellia oleifera seed oil (VCO) samples from different locations in southern China in terms of their volatile compounds to show the classification of VCO with respect to geography. Different samples from 20 producing VCO regions were collected in 2020 growing season, at almost the same maturity stage, and processed under the same conditions. Headspace solid-phase microextraction (HS-SPME) with a gas chromatography–mass spectrometer system (GC–MS) was used to analyze volatile compounds. A total of 348 volatiles were characterized, including aldehydes, ketones, alcohols, acids, esters, alkenes, alkanes, furans, phenols, and benzene; the relative contents ranged from 7.80–58.68%, 1.73–12.52%, 2.91–37.07%, 2.73–46.50%, 0.99–12.01%, 0.40–14.95%, 0.00–27.23%, 0.00–3.75%, 0.00–7.34%, and 0.00–1.55%, respectively. The VCO geographical origins with the largest number of volatile compounds was Xixiangtang of Guangxi (L17), and the least was Beireng of Hainan (L19). A total of 23 common and 98 unique volatile compounds were detected that reflected the basic and characteristic flavor of VCO, respectively. After PCA, heatmap and PLS-DA analysis, Longchuan of Guangdong (L8), Qingshanhu of Jiangxi (L16), and Panlong of Yunnan (L20) were in one group where the annual average temperatures are relatively low, where annual rainfalls are also low. Guangning of Guangdong (L6), Yunan of Guangdong (L7), Xingning of Guangdong (L9), Tianhe of Guangdong (L10), Xuwen of Guangdong (L11), and Xiuying of Hainan (L18) were in another group where the annual average temperatures are relatively high, and the altitudes are low. Hence, volatile compound distributions confirmed the differences among the VCO samples from these geographical areas, and the provenance difference evaluation can be carried out by flavor.

scholarly journals Transcriptomic Analysis Reveals Key Genes Involved in Oil and Linoleic Acid Biosynthesis during Artemisia sphaerocephala Seed Development

2021 ◽  
Vol 22 (16) ◽  
pp. 8369
Author(s):  
Shuzhen Nan ◽  
Lijing Zhang ◽  
Xiaowei Hu ◽  
Xiumei Miao ◽  
Xiaoxu Han ◽  
...  
Keyword(s):  
Linoleic Acid ◽  
Seed Development ◽  
Seed Oil ◽  
Critical Role ◽  
Regulatory Mechanisms ◽  
Oil Biosynthesis ◽  
Artemisia Sphaerocephala ◽  
Linoleic Acid Biosynthesis ◽  
Molecular Regulatory Mechanisms ◽  
Mature Seeds

Artemisia sphaerocephala seeds are rich in polysaccharides and linoleic acid (C18:2), which have been widely used as traditional medicine and to improve food quality. The accumulation patterns and molecular regulatory mechanisms of polysaccharides during A. sphaerocephala seed development have been studied. However, the related research on seed oil and C18:2 remain unclear. For this study, A. sphaerocephala seeds at seven different development stages at 10, 20, 30, 40, 50, 60, and 70 days after flowering (designated as S1~S7), respectively, were employed as experimental samples, the accumulation patterns of oil and fatty acids (FA) and the underlying molecular regulatory mechanisms were analyzed. The results revealed that oil content increased from 10.1% to 20.0% in the early stages of seed development (S1~S2), and up to 32.0% in mature seeds, of which C18:2 accounted for 80.6% of the total FA. FA and triacylglycerol biosynthesis-related genes jointly involved in the rapid accumulation of oil in S1~S2. Weighted gene co-expression network analysis showed that transcription factors FUS3 and bHLH played a critical role in the seed oil biosynthesis. The perfect harmonization of the high expression of FAD2 with the extremely low expression of FAD3 regulated the accumulation of C18:2. This study uncovered the gene involved in oil biosynthesis and molecular regulatory mechanisms of high C18:2 accumulation in A. sphaerocephala seeds; thus, advancing research into unsaturated fatty acid metabolism in plants while generating valuable genetic resources for optimal C18:2 breeding.

scholarly journals The characteristics of circRNA as competing endogenous RNA in pathogenesis of acute myeloid leukemia

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Siyuan Zhang
Keyword(s):  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Expression Profiles ◽  
Gene Expression Omnibus ◽  
The Novel ◽  
Competing Endogenous Rna ◽  
Regulatory Modules ◽  
Cerna Network ◽  
Regulatory Module ◽  
Acute Myeloid

Abstract Background As one of the novel molecules, circRNA has been identified closely involved in the pathogenesis of many diseases. However, the function of circRNA in acute myeloid leukemia (AML) still remains unknown. Methods In the current study, the RNA expression profiles were obtained from Gene Expression Omnibus (GEO) datasets. The differentially expressed RNAs were identified using R software and the competing endogenous RNA (ceRNA) network was constructed using Cytoscape. Functional and pathway enrichment analyses were performed to identify the candidate circRNA-mediated aberrant signaling pathways. The hub genes were identified by MCODE and CytoHubba plugins of Cytoscape, and then a subnetwork regulatory module was established. Results A total of 27 circRNA-miRNA pairs and 208 miRNA-mRNA pairs, including 12 circRNAs, 24 miRNAs and 112 mRNAs were included in the ceRNA network. Subsequently, a subnetwork, including 4 circRNAs, 5 miRNAs and 6 mRNAs, was established based on related circRNA-miRNA-mRNA regulatory modules. Conclusions In summary, this work analyzes the characteristics of circRNA as competing endogenous RNA in AML pathogenesis, which would provide hints for developing novel prognostic, diagnostic and therapeutic strategy for AML.

scholarly journals Dog colour patterns explained by modular promoters of ancient canid origin

2021 ◽  
Author(s):  
Danika L. Bannasch ◽  
Christopher B. Kaelin ◽  
Anna Letko ◽  
Robert Loechel ◽  
Petra Hug ◽  
...  
Keyword(s):  
Colour Pattern ◽  
Hair Cycle ◽  
Temporal And Spatial Distribution ◽  
Multiple Alleles ◽  
Haplotype Combination ◽  
Regulatory Modules ◽  
Regulatory Module ◽  
Temporal And Spatial ◽  
Selection For ◽  
Colour Patterns

AbstractDistinctive colour patterns in dogs are an integral component of canine diversity. Colour pattern differences are thought to have arisen from mutation and artificial selection during and after domestication from wolves but important gaps remain in understanding how these patterns evolved and are genetically controlled. In other mammals, variation at the ASIP gene controls both the temporal and spatial distribution of yellow and black pigments. Here, we identify independent regulatory modules for ventral and hair cycle ASIP expression, and we characterize their action and evolutionary origin. Structural variants define multiple alleles for each regulatory module and are combined in different ways to explain five distinctive dog colour patterns. Phylogenetic analysis reveals that the haplotype combination for one of these patterns is shared with Arctic white wolves and that its hair cycle-specific module probably originated from an extinct canid that diverged from grey wolves more than 2 million years ago. Natural selection for a lighter coat during the Pleistocene provided the genetic framework for widespread colour variation in dogs and wolves.

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