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Identification of genes associated with ricinoleic acid accumulation in Hiptage benghalensis via transcriptome analysis.

ABSTRACT: Background:Ricinoleic acid is a high-value hydroxy fatty acid with broad industrial applications. Hiptage benghalensis seed oil contains a high amount of ricinoleic acid (~?80%) and represents an emerging source of this unusual fatty acid. However, the mechanism of ricinoleic acid accumulation in H. benghalensis is yet to be explored at the molecular level, which hampers the exploration of its potential in ricinoleic acid production. Results:To explore the molecular mechanism of ricinoleic acid biosynthesis and regulation, H. benghalensis seeds were harvested at five developing stages (13, 16, 19, 22, and 25 days after pollination) for lipid analysis. The results revealed that the rapid accumulation of ricinoleic acid occurred at the early-mid-seed development stages (16-22 days after pollination). Subsequently, the gene transcription profiles of the developing seeds were characterized via a comprehensive transcriptome analysis with second-generation sequencing and single-molecule real-time sequencing. Differential expression patterns were identified in 12,555 transcripts, including 71 enzymes in lipid metabolic pathways, 246 putative transcription factors (TFs) and 124 long noncoding RNAs (lncRNAs). Twelve genes involved in diverse lipid metabolism pathways, including fatty acid biosynthesis and modification (hydroxylation), lipid traffic, triacylglycerol assembly, acyl editing and oil-body formation, displayed high expression levels and consistent expression patterns with ricinoleic acid accumulation in the developing seeds, suggesting their primary roles in ricinoleic acid production. Subsequent co-expression network analysis identified 57 TFs and 35 lncRNAs, which are putatively involved in the regulation of ricinoleic acid biosynthesis. The transcriptome data were further validated by analyzing the expression profiles of key enzyme-encoding genes, TFs and lncRNAs with quantitative real-time PCR. Finally, a network of genes associated with ricinoleic acid accumulation in H. benghalensis was established. Conclusions:This study was the first step toward the understating of the molecular mechanisms of ricinoleic acid biosynthesis and oil accumulation in H. benghalensis seeds and identified a pool of novel genes regulating ricinoleic acid accumulation. The results set a foundation for developing H. benghalensis into a novel ricinoleic acid feedstock at the transcriptomic level and provided valuable candidate genes for improving ricinoleic acid production in other plants.

SUBMITTER: Tian B

PROVIDER: S-EPMC6340187 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Identification of genes associated with ricinoleic acid accumulation in <i>Hiptage benghalensis</i> via transcriptome analysis.

Tian Bo B Lu Tianquan T Xu Yang Y Wang Ruling R Chen Guanqun G

Biotechnology for biofuels 20190121

<h4>Background</h4>Ricinoleic acid is a high-value hydroxy fatty acid with broad industrial applications. <i>Hiptage benghalensis</i> seed oil contains a high amount of ricinoleic acid (~ 80%) and represents an emerging source of this unusual fatty acid. However, the mechanism of ricinoleic acid accumulation in <i>H. benghalensis</i> is yet to be explored at the molecular level, which hampers the exploration of its potential in ricinoleic acid production.<h4>Results</h4>To explore the molecular ...[more]

PMID: 30679955

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Project description:BackgroundPaeonia lactiflora 'Hangshao' is widely cultivated in China as a traditional Chinese medicine 'Radix Paeoniae Alba'. Due to the abundant unsaturated fatty acids in its seed, it can also be regarded as a new oilseed plant. However, the process of the biosynthesis of unsaturated fatty acids in it has remained unknown. Therefore, transcriptome analysis is helpful to better understand the underlying molecular mechanisms.ResultsFive main fatty acids were detected, including stearic acid, palmitic acid, oleic acid, linoleic acid and α-linolenic acid, and their absolute contents first increased and then decreased during seed development. A total of 150,156 unigenes were obtained by transcriptome sequencing. There were 15,005 unigenes annotated in the seven functional databases, including NR, NT, GO, KOG, KEGG, Swiss-Prot and InterPro. Based on the KEGG database, 1766 unigenes were annotated in the lipid metabolism. There were 4635, 12,304, and 18,291 DEGs in Group I (60 vs 30 DAF), Group II (90 vs 60 DAF) and Group III (90 vs 30 DAF), respectively. A total of 1480 DEGs were detected in the intersection of the three groups. In 14 KEGG pathways of lipid metabolism, 503 DEGs were found, belonging to 111 enzymes. We screened out 123 DEGs involved in fatty acid biosynthesis (39 DEGs), fatty acid elongation (33 DEGs), biosynthesis of unsaturated fatty acid (24 DEGs), TAG assembly (17 DEGs) and lipid storage (10 DEGs). Furthermore, qRT-PCR was used to analyze the expression patterns of 16 genes, including BBCP, BC, MCAT, KASIII, KASII, FATA, FATB, KCR, SAD, FAD2, FAD3, FAD7, GPAT, DGAT, OLE and CLO, most of which showed the highest expression at 45 DAF, except for DGAT, OLE and CLO, which showed the highest expression at 75 DAF.ConclusionsWe predicted that MCAT, KASIII, FATA, SAD, FAD2, FAD3, DGAT and OLE were the key genes in the unsaturated fatty acid biosynthesis and oil accumulation in herbaceous peony seed. This study provides the first comprehensive genomic resources characterizing herbaceous peony seed gene expression at the transcriptional level. These data lay the foundation for elucidating the molecular mechanisms of fatty acid biosynthesis and oil accumulation for herbaceous peony.

Project description:Organic acids and sugars are the primary components that determine the quality and flavor of loquat fruits. In the present study, major organic acids, sugar content, enzyme activities, and the expression of related genes were analyzed during fruit development in two loquat cultivars, 'JieFangZhong' (JFZ) and 'BaiLi' (BL). Our results showed that the sugar content increased during fruit development in the two cultivars; however, the organic acid content dramatically decreased in the later stages of fruit development. The differences in organic acid and sugar content between the two cultivars primarily occured in the late stage of fruit development and the related enzymes showed dynamic changes in activies during development. Phosphoenolpyruvate carboxylase (PEPC) and mNAD malic dehydrogenase (mNAD-MDH) showed higher activities in JFZ at 95 days after flowering (DAF) than in BL. However, NADP-dependent malic enzyme (NADP-ME) activity was the lowest at 95 DAF in both JFZ and BL with BL showing higher activity compared with JFZ. At 125 DAF, the activity of fructokinase (FRK) was significantly higher in JFZ than in BL. The activity of sucrose synthase (SUSY) in the sucrose cleavage direction (SS-C) was low at early stages of fruit development and increased at 125 DAF. SS-C activity was higher in JFZ than in BL. vAI and sucrose phosphate synthase (SPS) activities were similar in the two both cultivars and increased with fruit development. RNA-sequencing was performed to determine the candidate genes for organic acid and sugar metabolism. Our results showed that the differentially expressed genes (DEGs) with the greated fold changes in the later stages of fruit development between the two cultivars were phosphoenolpyruvate carboxylase 2 (PEPC2), mNAD-malate dehydrogenase (mNAD-MDH), cytosolic NADP-ME (cyNADP-ME2), aluminum-activated malate transporter (ALMT9), subunit A of vacuolar H+-ATPase (VHA-A), vacuolar H+-PPase (VHP1), NAD-sorbitol dehydrogenase (NAD-SDH), fructokinase (FK), sucrose synthase in sucrose cleavage (SS-C), sucrose-phosphate synthase 1 (SPS1), neutral invertase (NI), and vacuolar acid invertase (vAI). The expression of 12 key DEGs was validated by quantitative reverese transcription PCR (RT-qPCR). Our findings will help understand the molecular mechanism of organic acid and sugar formation in loquat, which will aid in breeding high-quality loquat cultivars.

Project description:The sperm storage tubules located in the mucosal folds of the uterovaginal junction (UVJ) are the primary site of sperm storage in chicken hens after natural mating or artificial insemination (AI). The short-term sperm storage (24 h after mating or AI) in hens was highly associated with immunity and pH-related pathway genes. However, the underlying mechanism of longer duration of sperm storage in female birds remains largely unclear. In the present study, transcriptome analysis was applied to uncover the dynamic gene expression changes in chicken UVJ tissues at two time points (day 3 and day 9) after AI. A total of 574 differentially expressed genes (DEG) were enriched, including 266 upregulated and 308 downregulated DEG. The validation of 5 DEG using quantitative PCR showed a similar expression tendency with RNA sequencing results. The gene ontology terms of DEG were highly enriched in heparin binding (9 genes including COMP, CTGF, and IMPG2), glycosaminoglycan binding (10 genes including PCOLCE, POSTN, and RSPO3), and response to estradiol and ion transport (AREG, RAMP3, SFRP1, and SSTR1). Kyoto encyclopedia of genes and genomes pathway-enrichment analyses of DEG revealed 10 significant pathways (P < 0.05) represented by calcium signaling pathway (7 genes including CACNA1G, PDE1C, PDGFRB, and SLC8A1) and glycosaminoglycan biosynthesis (B3GNT7, CSGALNACT1, GLCE, and ST3GAL1). Protein-protein interaction network of DEG established the connection-regulating epithelial cell or cell-matrix adhesion and migration. The enriched pathways and genes were highly correlated with temporary sperm storage in and possibly sequential sperm release from chicken UVJ overtime after AI. Of these, HIP1, PDE1C, and calcium-related genes were the most interesting candidates associated with sperm storage duration. This report provided a global gene expression profile of the chicken UVJ regarding the capacity of sperm storage overtime after AI. The outcome of this study will contribute to further understanding of the long-term sperm maintenance in avian females and eventually improving the duration of fertile egg performance by selected chicken breeding.

Project description:BackgroundAdvancement in gene profiling techniques makes it possible to measure expressions of thousands of genes and identify genes associated with development and progression of cancer. The identified cancer-associated genes can be used for diagnosis, prognosis prediction, and treatment selection. Most existing cancer microarray studies have been focusing on the identification of genes associated with a specific type of cancer. Recent biomedical studies suggest that different cancers may share common susceptibility genes. A comprehensive description of the associations between genes and cancers requires identification of not only multiple genes associated with a specific type of cancer but also genes associated with multiple cancers.ResultsIn this article, we propose the Mc.TGD (Multi-cancer Threshold Gradient Descent), an integrative analysis approach capable of analyzing multiple microarray studies on different cancers. The Mc.TGD is the first regularized approach to conduct "two-dimensional" selection of genes with joint effects on cancer development. Simulation studies show that the Mc.TGD can more accurately identify genes associated with multiple cancers than meta analysis based on "one-dimensional" methods. As a byproduct, identification accuracy of genes associated with only one type of cancer may also be improved. We use the Mc.TGD to analyze seven microarray studies investigating development of seven different types of cancers. We identify one gene associated with six types of cancers and four genes associated with five types of cancers. In addition, we also identify 11, 9, 18, and 17 genes associated with 4 to 1 types of cancers, respectively. We evaluate prediction performance using a Leave-One-Out cross validation approach and find that only 4 (out of 570) subjects cannot be properly predicted.ConclusionThe Mc.TGD can identify a short list of genes associated with one or multiple types of cancers. The identified genes are considerably different from those identified using meta analysis or analysis of marginal effects.

Dataset Information

Identification of genes associated with ricinoleic acid accumulation in Hiptage benghalensis via transcriptome analysis.

Publications

Identification of genes associated with ricinoleic acid accumulation in <i>Hiptage benghalensis</i> via transcriptome analysis.

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