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Li G, Cheng J, Yang L, Chen P, Duan X. Ethanol extract of Rubia yunnanensis inhibits carotid atherosclerosis via the PI3K/AKT signaling pathway. Biomed Rep 2024; 20:19. [PMID: 38170026 PMCID: PMC10758924 DOI: 10.3892/br.2023.1707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 11/13/2023] [Indexed: 01/05/2024] Open
Abstract
Atherosclerosis is a multifactorial vascular disease caused by endothelial dysfunction. Because of adverse reactions to drugs used to treat atherosclerosis. For example, statins, which significantly reduce the burden of atherosclerotic disease, have been associated with muscle toxicity. There is a need to identify novel drugs for the prevention and treatment of atherosclerosis Rubia yunnanensis is a herbs commonly used in Asian countries for its protective effects against cardiovascular diseases. However, the mechanism of action of R. yunnanensis extract in carotid artery atherosclerosis has not been found. The carotid artery is usually used as a site for clinical evaluation of atherosclerosis. The present study aimed to determine the mechanism of action of R. yunnanensis extract in the inhibition of carotid atherosclerosis in apolipoprotein E gene knockout (ApoE-/-) mice. The mechanism of atherosclerosis inhibition was elucidated by detecting the blood lipid level, carotid artery pathology, and the protein expression of PI3K and AKT. The present study demonstrated that ethanol extract of R. yunnanensis reduced lipid levels, intima damage and carotid lipid accumulation and increased p-PI3K/PI3K and p-AKT/AKT protein levels in ApoE-/- mice fed high-fat diet for 12 weeks. It was hypothesized that the effects of R. yunnanensis extract may be achieved by regulation of the phosphatidylinositol-3-kinase/protein kinase B signaling pathway. Ethanol extract of R. yunnanensis decreased carotid atherosclerosis in ApoE-/- mice fed a high-fat diet via the phosphatidylinositol-3-kinase/protein kinase B signaling pathway. Therefore, R. yunnanensis may be a promising option for treating atherosclerosis in the future.
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Affiliation(s)
- Gaoyizhou Li
- Yunnan Key Laboratory of Dai and Yi Medicines, Yunnan University of Chinese Medicine, Kunming, Yunnan 650500, P.R. China
| | - Jianghao Cheng
- Yunnan Key Laboratory of Dai and Yi Medicines, Yunnan University of Chinese Medicine, Kunming, Yunnan 650500, P.R. China
| | - Liping Yang
- Yunnan Key Laboratory of Dai and Yi Medicines, Yunnan University of Chinese Medicine, Kunming, Yunnan 650500, P.R. China
| | - Pu Chen
- Yunnan Key Laboratory of Dai and Yi Medicines, Yunnan University of Chinese Medicine, Kunming, Yunnan 650500, P.R. China
| | - Xiaohua Duan
- Yunnan Key Laboratory of Dai and Yi Medicines, Yunnan University of Chinese Medicine, Kunming, Yunnan 650500, P.R. China
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2
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de Sousa PRC, da Silva ASM, de Ponte CGG, Nogueira LL, Frota CC, Antas PRZ. Commentary: Identification of optimal reference genes for gene expression normalization in human osteosarcoma cell lines under proliferative conditions. Front Genet 2024; 15:1342447. [PMID: 38333617 PMCID: PMC10850317 DOI: 10.3389/fgene.2024.1342447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/02/2024] [Indexed: 02/10/2024] Open
Affiliation(s)
- Paulo R. C. de Sousa
- Programa de Pós-Graduação em Patologia, Universidade Federal do Ceará, Fortaleza, Brazil
| | | | | | - Lucas L. Nogueira
- Programa de Pós-Graduação em Patologia, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Cristiane C. Frota
- Programa de Pós-Graduação em Patologia, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Paulo R. Z. Antas
- Programa de Pós-Graduação em Patologia, Universidade Federal do Ceará, Fortaleza, Brazil
- Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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3
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Zhang J, He X, Zhou J, Dong Z, Yu H, Tang Q, Yuan L, Peng S, Zhong X, He Y. Selection and Verification of Standardized Reference Genes of Angelica dahurica under Various Abiotic Stresses by Real-Time Quantitative PCR. Genes (Basel) 2024; 15:79. [PMID: 38254968 PMCID: PMC10815136 DOI: 10.3390/genes15010079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
In traditional Chinese medicine, Angelica dahurica is a valuable herb with numerous therapeutic applications for a range of ailments. There have not yet been any articles on the methodical assessment and choice of the best reference genes for A. dahurica gene expression studies. Real-time quantitative PCR (RT-qPCR) is widely employed as the predominant method for investigating gene expression. In order to ensure the precise determination of target gene expression outcomes in RT-qPCR analysis, it is imperative to employ stable reference genes. In this study, a total of 11 candidate reference genes including SAND family protein (SAND), polypyrimidine tract-binding protein (PTBP), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), actin (ACT), TIP41-like protein (TIP41), cyclophilin 2 (CYP2), elongation factor 1 α (EF1α), ubiquitin-protein ligase 9 (UBC9), tubulin β-6 (TUB6), thioredoxin-like protein YLS8 (YLS8), and tubulin-α (TUBA) were selected from the transcriptome of A. dahurica. Subsequently, three statistical algorithms (geNorm, NormFinder, and BestKeeper) were employed to assess the stability of their expression patterns across seven distinct stimulus treatments. The outcomes obtained from these analyses were subsequently amalgamated into a comprehensive ranking using RefFinder. Additionally, one target gene, phenylalanine ammonia-lyase (PAL), was used to confirm the effectiveness of the selected reference genes. According to the findings of this study, the two most stable reference genes for normalizing the expression of genes in A. dahurica are TIP41 and UBC9. Overall, our research has determined the appropriate reference genes for RT-qPCR in A. dahurica and provides a crucial foundation for gene screening and identifying genes associated with the biosynthesis of active ingredients in A. dahurica.
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Affiliation(s)
- Jing Zhang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Xinyi He
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Jun Zhou
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Zhuang Dong
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Han Yu
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Qi Tang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Lei Yuan
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Siqing Peng
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Xiaohong Zhong
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Yuedong He
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
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Chen J, Wang Y, Yang Z, Liu D, Jin Y, Li X, Deng Y, Wang B, Zhang Z, Ma Y. Identification and validation of the reference genes in the echiuran worm Urechis unicinctus based on transcriptome data. BMC Genomics 2023; 24:248. [PMID: 37165306 PMCID: PMC10170059 DOI: 10.1186/s12864-023-09358-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/05/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Real-time quantitative PCR (RT-qPCR) is a crucial and widely used method for gene expression analysis. Selecting suitable reference genes is extremely important for the accuracy of RT-qPCR results. Commonly used reference genes are not always stable in various organisms or under different environmental conditions. With the increasing application of high-throughput sequencing, transcriptome analysis has become an effective method for identifying novel stable reference genes. RESULTS In this study, we identified candidate reference genes based on transcriptome data covering embryos and larvae of early development, normal adult tissues, and the hindgut under sulfide stress using the coefficient of variation (CV) method in the echiuran Urechis unicinctus, resulting in 6834 (15.82%), 7110 (16.85%) and 13880 (35.87%) candidate reference genes, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the candidate reference genes were significantly enriched in cellular metabolic process, protein metabolic process and ribosome in early development and normal adult tissues as well as in cellular localization and endocytosis in the hindgut under sulfide stress. Subsequently, ten genes including five new candidate reference genes and five commonly used reference genes, were validated by RT-qPCR. The expression stability of the ten genes was analyzed using four methods (geNorm, NormFinder, BestKeeper, and ∆Ct). The comprehensive results indicated that the new candidate reference genes were more stable than most commonly used reference genes. The commonly used ACTB was the most unstable gene. The candidate reference genes STX12, EHMT1, and LYAG were the most stable genes in early development, normal adult tissues, and hindgut under sulfide stress, respectively. The log2(TPM) of the transcriptome data was significantly negatively correlated with the Ct values of RT-qPCR (Ct = - 0.5405 log2(TPM) + 34.51), which made it possible to estimate the Ct value before RT-qPCR using transcriptome data. CONCLUSION Our study is the first to select reference genes for RT-qPCR from transcriptome data in Echiura and provides important information for future gene expression studies in U. unicinctus.
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Affiliation(s)
- Jiao Chen
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yunjian Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhi Yang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Danwen Liu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yao Jin
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xixi Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuhang Deng
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Boya Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhifeng Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Yubin Ma
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
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Yi S, Lu H, Tian C, Xu T, Song C, Wang W, Wei P, Gu F, Liu D, Cai Y, Han B. Selection of Suitable Reference Genes for Gene Expression Normalization Studies in Dendrobium huoshanense. Genes (Basel) 2022; 13:genes13081486. [PMID: 36011396 PMCID: PMC9408602 DOI: 10.3390/genes13081486] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
Dendrobium huoshanense is a kind of precious herb with important medicinal and edible value in China, which is widely used in traditional Chinese medicine for various diseases. Recent studies have paid close attention to the genetic expression of the biosynthetic pathway of the main active components (polysaccharides, alkaloids, and flavonoids), and real-time polymerase chain reaction (qPCR) is one of the most widely used methods for doing so. However, so far, no reference gene selections have been reported in D. huoshanense. In this study, 15 reference gene candidates (GAPDH, eIF, EF-1α, PP2A, UBCE, RPL5, TBP, APT1, MDH, PTBP3, PEPC, CYP71, NCBP2, TIP41, and F-box) were selected and evaluated for their expression stability in D. huoshanense under various experimental conditions, including in different tissues (root, stem, and leaf), abiotic stresses (oxidative, drought, cold, and UV), and hormone treatment (methyl jasmonate) using three statistical programs (geNorm, NormFinder, and BestKeeper). Then, the RefFinder program was employed to comprehensively validate the stability of the selected reference genes. Finally, the expression profiles of the CESA and GMPP genes were further analyzed, and these results indicated that TBP, NCBP2, and CYP71 were the top three most stable reference genes after comprehensive comparison, which could be used as stable reference genes for normalizing the genes expression in D. huoshanense. This study described here provides the first data regarding on reference gene selection in D. huoshanense, which will be extremely beneficial for future research on the gene expression normalization in D. huoshanense.
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Affiliation(s)
- Shanyong Yi
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Haibo Lu
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Chuanjun Tian
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
| | - Tao Xu
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Cheng Song
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Wei Wang
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Peipei Wei
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Fangli Gu
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Dong Liu
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Yongping Cai
- College of Life Sciences, Anhui Agricultural University, Hefei 230036, China
- Correspondence: (Y.C.); (B.H.); Tel.: +86-564-3307060 (B.H.)
| | - Bangxing Han
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
- Correspondence: (Y.C.); (B.H.); Tel.: +86-564-3307060 (B.H.)
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Yang J, Han F, Yang L, Wang J, Jin F, Luo A, Zhao F. Identification of Reference Genes for RT-qPCR Analysis in Gleditsia microphylla under Abiotic Stress and Hormone Treatment. Genes (Basel) 2022; 13:genes13071227. [PMID: 35886010 PMCID: PMC9315665 DOI: 10.3390/genes13071227] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 11/25/2022] Open
Abstract
Gleditsia microphylla is an important galactomannan gums source plant with characteristics of drought resistance, barren tolerance, and good adaptability. However, the underlying molecular mechanisms of the biological process are not yet fully understood. Real-time quantitative PCR (RT-qPCR) is an accurate and convenient method to quantify the gene expression level and transcription abundance of suitable reference genes. This study aimed to screen the best internal reference genes in G. microphylla under abiotic stresses, hormone treatments, and different tissues. Based on the transcriptome data, twelve candidate reference genes were selected, and ultimately, nine of them were further evaluated by the geNorm, NormFinder, BestKeeper, and RefFinder algorithms. These results show that TATA-binding protein 1 (TBP1)and Eukaryotic translation initiation factor 4A1 (EIF4A1)were the two most stable reference genes, and glyceraldehyde-3-phosphate dehydrogenase A subunit, chloroplastic (GAPA)and glyceraldehyde-3-phosphate dehydrogenase B subunit, chloroplastic (GAPB)were the two most unstable reference genes across all samples under the given experimental conditions. Meanwhile, the most stable reference genes varied among the different groups and tissues. Therefore, this study suggests that it is better to use a specific reference gene for a particular case rather than using a common reference gene.
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Wang W, Xu T, Song X, Chen C, Liu D, Han B, Yi S. Sequencing of the complete chloroplast genome of Rubia yunnanensis Diels and its phylogenetic analysis. Mitochondrial DNA B Resour 2022; 7:1087-1089. [PMID: 35756430 PMCID: PMC9225772 DOI: 10.1080/23802359.2022.2086496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Rubia yunnanensis Diels, an important medicinal herb, is mainly distributed in Yunnan province, Southwest China. In this study, the complete chloroplast genome of R. yunnanensis was successfully sequenced. The assembled chloroplast genome was 155,108 bp in length with an overall GC content of 36.98%, including a pair of inverted repeat (IR) regions (26,573 bp, each), respectively, a large single-copy (LSC) region (84,848 bp) and a small single-copy (SSC) region (17,114 bp). The genome contained 131 genes, comprising 85 protein-coding genes, 37 tRNA genes, eight rRNA genes, and one pseudogene. The phylogenetic analysis indicated that R. yunnanensis was closely related to R. cordifolia.
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Affiliation(s)
- Wei Wang
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, P.R. China
| | - Tao Xu
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, P.R. China
| | - Xiangwen Song
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, P.R. China
| | - Cunwu Chen
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, P.R. China
| | - Dong Liu
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, P.R. China
| | - Bangxing Han
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, P.R. China
| | - Shanyong Yi
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, P.R. China
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8
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De Novo Transcriptome Analysis Reveals Putative Genes Involved in Anthraquinone Biosynthesis in Rubia yunnanensis. Genes (Basel) 2022; 13:genes13030521. [PMID: 35328075 PMCID: PMC8954821 DOI: 10.3390/genes13030521] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 02/18/2022] [Accepted: 02/18/2022] [Indexed: 02/01/2023] Open
Abstract
Rubia yunnanensis Diels (R. yunnanensis), a Chinese perennial plant, is well-known for its medicinal values such as rheumatism, contusion, and anemia. It is rich in bioactive anthraquinones, but the biosynthetic pathways of anthraquinones in R. yunnanensis remain unknown. To investigate genes involved in anthraquinone biosynthesis in R. yunnanensis, we generated a de novo transcriptome of R. yunnanensis using the Illumina HiSeq 2500 sequencing platform. A total of 636,198 transcripts were obtained, in which 140,078 transcripts were successfully annotated. A differential gene expression analysis identified 15 putative genes involved in anthraquinone biosynthesis. Additionally, the hairy roots of R. yunnanensis were treated with 200 µM Methyl Jasmonate (MeJA). The contents of six bioactive anthraquinones and gene expression levels of 15 putative genes were measured using ultra performance liquid chromatography coupled with mass spectrometry (UPLC-MS/MS) and real-time quantitative polymerase chain reaction (RT-qPCR), respectively. The results showed that the expressions levels for 11 of the 15 genes and the contents of two of six anthraquinones significantly increased by MeJA treatment. Pearson’s correlation analyses indicated that the expressions of 4 of the 15 putative genes were positively correlated with the contents of rubiquinone (Q3) and rubiquinone-3-O-β-d-xylopranosyl-(1→6)-β-d-glucopyranoside (Q20). This study reported the first de novo transcriptome of R. yunnanensis and shed light on the anthraquinone biosynthesis and genetic information for R. yunnanensis.
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Nizan IEF, Kamaruddin K, Ong PW, Ramli Z, Singh R, Rose RJ, Chan PL. Overexpression of Oil Palm Early Nodulin 93 Protein Gene (EgENOD93) Enhances In Vitro Shoot Regeneration in Arabidopsis thaliana. Mol Biotechnol 2022; 64:743-757. [PMID: 35107753 DOI: 10.1007/s12033-022-00450-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 01/04/2022] [Indexed: 11/28/2022]
Abstract
EgENOD93 was first identified in a cDNA microarray study of oil palm tissue culture where it was highly expressed in leaf explants with embryogenic potential. Functional characterization via an RNA interference study of its orthologue in Medicago truncatula demonstrated a significant role of this gene in somatic embryo formation. In this study, EgENOD93 was overexpressed in the important model plant Arabidopsis thaliana to investigate the embryogenic potential of EgENOD93 transgenic Arabidopsis explants compared to explants from control plants (pMDC140 and WT). Experiments using leaf explants revealed higher numbers of regenerated shoots at day 27 in all the homozygous transgenic Arabidopsis cultures (Tg01, Tg02 and Tg03) compared to controls. The expression level of EgENOD93 in Arabidopsis cultures was quantified using reverse transcription quantitative real-time PCR (RT-qPCR). The results supported the overexpression of this gene in transgenic Arabidopsis cultures, with 6 and 10 times higher expression of EgENOD93 in callus at Day 9 and Day 20, respectively. Overall, the results support the role of EgENOD93 in the enhancement of shoot regeneration in transgenic Arabidopsis. This together with the previous results observed in oil palm and Medicago truncatula suggests that ENOD93 plays a key role in the induction of somatic embryogenesis. A similarity to early nodulation-like ontogeny is possible.
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Affiliation(s)
- Intan Ernieza Farhana Nizan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Katialisa Kamaruddin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Pei-Wen Ong
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia.,Institute of Plant Biology, National Taiwan University, No. 1, Section 4, Roosevelt Road, 10617, Taipei, Taiwan, ROC
| | - Zubaidah Ramli
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Rajinder Singh
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Ray J Rose
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Pek-Lan Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia.
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10
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Tong J, Hu M, Han B, Ji Y, Wang B, Liang H, Liu M, Wu Z, Liu N. Determination of reliable reference genes for gene expression studies in Chinese chive (Allium tuberosum) based on the transcriptome profiling. Sci Rep 2021; 11:16558. [PMID: 34400673 PMCID: PMC8367972 DOI: 10.1038/s41598-021-95849-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/22/2021] [Indexed: 12/31/2022] Open
Abstract
Chinese chive (Allium tuberosum) is widely cultivated around the world for its unique flavor, nutrient, and medicinal values, yet its molecular mechanism on flavor formation and other metabolic pathways remains intangible. The elucidation of these complex processes begins with investigating the expression of the genes of interest, however the appropriate reference genes (RGs) for normalizing the gene expression are still unavailable in A. tuberosum. To fill this lacuna, transcriptome-wide screening was undertaken to identify the most stable genes according to the analysis of their FPKM values. The expression stability of the RGs was further evaluated using geNorm, NormFinder, BestKeeper, and RefFinder algorithms. The comprehensive analysis showed that GLY1 and SKP1, instead of two traditionally used RGs (eIF1α and ACT2), were the most stable genes across diverse A. tuberosum tissues, indicating the necessity to carefully validate the stability of RGs prior to their use for normalizations. As indicated by geNorm, the normalizations with at least two RGs could give more accurate results. qRT-PCR experiments were conducted with randomly selected genes, demonstrating that normalization with a combination of GLY1 and SKP1 resulted in reliable normalization results. Our finding represents the first attempt toward establishing a standardized qRT-PCR analysis in this economically important vegetable.
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Affiliation(s)
- Jing Tong
- Key Laboratory of Urban Agriculture (North) of Minstry of Agriculture and Rural Affairs, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.,National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Manman Hu
- Key Laboratory of Urban Agriculture (North) of Minstry of Agriculture and Rural Affairs, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.,National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Beibei Han
- Key Laboratory of Urban Agriculture (North) of Minstry of Agriculture and Rural Affairs, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.,National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yanhai Ji
- Key Laboratory of Urban Agriculture (North) of Minstry of Agriculture and Rural Affairs, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.,National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Baoju Wang
- Key Laboratory of Urban Agriculture (North) of Minstry of Agriculture and Rural Affairs, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.,National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Hao Liang
- Key Laboratory of Urban Agriculture (North) of Minstry of Agriculture and Rural Affairs, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.,National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Mingchi Liu
- Key Laboratory of Urban Agriculture (North) of Minstry of Agriculture and Rural Affairs, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.,National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Zhanhui Wu
- Key Laboratory of Urban Agriculture (North) of Minstry of Agriculture and Rural Affairs, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China. .,National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Ning Liu
- Key Laboratory of Urban Agriculture (North) of Minstry of Agriculture and Rural Affairs, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China. .,National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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