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Eshaghi M, Rashidi-Monfared S. Co-regulatory network analysis of the main secondary metabolite (SM) biosynthesis in Crocus sativus L. Sci Rep 2024; 14:15839. [PMID: 38982154 PMCID: PMC11233700 DOI: 10.1038/s41598-024-65870-z] [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: 11/16/2023] [Accepted: 06/25/2024] [Indexed: 07/11/2024] Open
Abstract
Saffron (Crocus sativus L.) is being embraced as the most important medicinal plant and the commercial source of saffron spice. Despite the beneficial economic and medicinal properties of saffron, the regulatory mechanism of the correlation of TFs and genes related to the biosynthesis of the apocarotenoids pathway is less obvious. Realizing these regulatory hierarchies of gene expression networks related to secondary metabolites production events is the main challenge owing to the complex and extensive interactions between the genetic behaviors. Recently, high throughput expression data have been highly feasible for constructing co-regulation networks to reveal the regulated processes and identifying novel candidate hub genes in response to complex processes of the biosynthesis of secondary metabolites. Herein, we performed Weighted Gene Co-expression Network Analysis (WGCNA), a systems biology method, to identify 11 regulated modules and hub TFs related to secondary metabolites. Three specialized modules were found in the apocarotenoids pathway. Several hub TFs were identified in notable modules, including MADS, C2H2, ERF, bZIP, HD-ZIP, and zinc finger protein MYB and HB, which were potentially associated with apocarotenoid biosynthesis. Furthermore, the expression levels of six hub TFs and six co-regulated genes of apocarotenoids were validated with RT-qPCR. The results confirmed that hub TFs specially MADS, C2H2, and ERF had a high correlation (P < 0.05) and a positive effect on genes under their control in apocarotenoid biosynthesis (CCD2, GLT2, and ADH) among different C. sativus ecotypes in which the metabolite contents were assayed. Promoter analysis of the co-expressed genes of the modules involved in apocarotenoids biosynthesis pathway suggested that not only are the genes co-expressed, but also share common regulatory motifs specially related to hub TFs of each module and that they may describe their common regulation. The result can be used to engineer valuable secondary metabolites of C. sativus by manipulating the hub regulatory TFs.
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Affiliation(s)
- Mahsa Eshaghi
- Department of Plant Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Sajad Rashidi-Monfared
- Department of Plant Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
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Qin T, Wang Y, Pu Z, Shi N, Dormatey R, Wang H, Sun C. Comprehensive Transcriptome and Proteome Analyses Reveal the Drought Responsive Gene Network in Potato Roots. PLANTS (BASEL, SWITZERLAND) 2024; 13:1530. [PMID: 38891338 PMCID: PMC11175002 DOI: 10.3390/plants13111530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024]
Abstract
The root system plays a decisive role in the growth and development of plants. The water requirement of a root system depends strongly on the plant species. Potatoes are an important food and vegetable crop grown worldwide, especially under irrigation in arid and semi-arid regions. However, the expected impact of global warming on potato yields calls for an investigation of genes related to root development and drought resistance signaling pathways in potatoes. In this study, we investigated the molecular mechanisms of different drought-tolerant potato root systems in response to drought stress under controlled water conditions, using potato as a model. We analyzed the transcriptome and proteome of the drought-sensitive potato cultivar Atlantic (Atl) and the drought-tolerant cultivar Qingshu 9 (Q9) under normal irrigation (CK) and weekly drought stress (D). The results showed that a total of 14,113 differentially expressed genes (DEGs) and 5596 differentially expressed proteins (DEPs) were identified in the cultivars. A heat map analysis of DEGs and DEPs showed that the same genes and proteins in Atl and Q9 exhibited different expression patterns under drought stress. Weighted gene correlation network analysis (WGCNA) showed that in Atl, Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG)-enriched pathways were related to pyruvate metabolism and glycolysis, as well as cellular signaling and ion transmembrane transporter protein activity. However, GO terms and KEGG-enriched pathways related to phytohormone signaling and the tricarboxylic acid cycle were predominantly enriched in Q9. The present study provides a unique genetic resource to effectively explore the functional genes and uncover the molecular regulatory mechanism of the potato root system in response to drought stress.
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Affiliation(s)
- Tianyuan Qin
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (T.Q.); (Y.W.); (Z.P.); (N.S.); (H.W.)
| | - Yihao Wang
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (T.Q.); (Y.W.); (Z.P.); (N.S.); (H.W.)
| | - Zhuanfang Pu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (T.Q.); (Y.W.); (Z.P.); (N.S.); (H.W.)
| | - Ningfan Shi
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (T.Q.); (Y.W.); (Z.P.); (N.S.); (H.W.)
| | - Richard Dormatey
- CSIR—Crops Research Institute, P.O. Box 3785, Kumasi 00233, Ghana;
| | - Huiqiong Wang
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (T.Q.); (Y.W.); (Z.P.); (N.S.); (H.W.)
| | - Chao Sun
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (T.Q.); (Y.W.); (Z.P.); (N.S.); (H.W.)
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Zhao X, Zhang Y, Wang J, Zhao X, Li Y, Teng W, Han Y, Zhan Y. GWAS and WGCNA Analysis Uncover Candidate Genes Associated with Oil Content in Soybean. PLANTS (BASEL, SWITZERLAND) 2024; 13:1351. [PMID: 38794422 PMCID: PMC11125034 DOI: 10.3390/plants13101351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/10/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024]
Abstract
Soybean vegetable oil is an important source of the human diet. However, the analysis of the genetic mechanism leading to changes in soybean oil content is still incomplete. In this study, a total of 227 soybean materials were applied and analyzed by a genome-wide association study (GWAS). There are 44 quantitative trait nucleotides (QTNs) that were identified as associated with oil content. A total of six, four, and 34 significant QTN loci were identified in Xiangyang, Hulan, and Acheng, respectively. Of those, 26 QTNs overlapped with or were near the known oil content quantitative trait locus (QTL), and 18 new QTNs related to oil content were identified. A total of 594 genes were located near the peak single nucleotide polymorphism (SNP) from three tested environments. These candidate genes exhibited significant enrichment in tropane, piperidine, and pyridine alkaloid biosynthesiss (ko00960), ABC transporters (ko02010), photosynthesis-antenna proteins (ko00196), and betalain biosynthesis (ko00965). Combined with the GWAS and weighted gene co-expression network analysis (WGCNA), four candidate genes (Glyma.18G300100, Glyma.11G221100, Glyma.13G343300, and Glyma.02G166100) that may regulate oil content were identified. In addition, Glyma.18G300100 was divided into two main haplotypes in the studied accessions. The oil content of haplotype 1 is significantly lower than that of haplotype 2. Our research findings provide a theoretical basis for improving the regulatory mechanism of soybean oil content.
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Affiliation(s)
| | | | | | | | | | | | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin 150030, China; (X.Z.); (Y.Z.); (J.W.); (X.Z.); (Y.L.); (W.T.)
| | - Yuhang Zhan
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin 150030, China; (X.Z.); (Y.Z.); (J.W.); (X.Z.); (Y.L.); (W.T.)
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Zhang R, Bai X, Chen Z, Chen M, Li X, Zeng B, Hu B. Physiological, Biochemical, and Molecular Analyses Reveal Dark Heartwood Formation Mechanism in Acacia melanoxylon. Int J Mol Sci 2024; 25:4974. [PMID: 38732191 PMCID: PMC11084464 DOI: 10.3390/ijms25094974] [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: 02/23/2024] [Revised: 04/23/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
Acacia melanoxylon is highly valued for its commercial applications, with the heartwood exhibiting a range of colors from dark to light among its various clones. The underlying mechanisms contributing to this color variation, however, have not been fully elucidated. In an effort to understand the factors that influence the development of dark heartwood, a comparative analysis was conducted on the microstructure, substance composition, differential gene expression, and metabolite profiles in the sapwood (SW), transition zone (TZ), and heartwood (HW) of two distinct clones, SR14 and SR25. A microscopic examination revealed that heartwood color variations are associated with an increased substance content within the ray parenchyma cells. A substance analysis indicated that the levels of starches, sugars, and lignin were more abundant in SP compared to HW, while the concentrations of phenols, flavonoids, and terpenoids were found to be higher in HW than in SP. Notably, the dark heartwood of the SR25 clone exhibited greater quantities of phenols and flavonoids compared to the SR14 clone, suggesting that these compounds are pivotal to the color distinction of the heartwood. An integrated analysis of transcriptome and metabolomics data uncovered a significant accumulation of sinapyl alcohol, sinapoyl aldehyde, hesperetin, 2', 3, 4, 4', 6'-peptahydroxychalcone 4'-O-glucoside, homoeriodictyol, and (2S)-liquiritigenin in the heartwood of SR25, which correlates with the up-regulated expression of CCRs (evm.TU.Chr3.1751, evm.TU.Chr4.654_667, evm.TU.Chr4.675, evm.TU.Chr4.699, and evm.TU.Chr4.704), COMTs (evm.TU.Chr13.3082, evm.TU.Chr13.3086, and evm.TU.Chr7.1411), CADs (evm.TU.Chr10.2175, evm.TU.Chr1.3453, and evm.TU.Chr8.1600), and HCTs (evm.TU.Chr4.1122, evm.TU.Chr4.1123, evm.TU.Chr8.1758, and evm.TU.Chr9.2960) in the TZ of A. melanoxylon. Furthermore, a marked differential expression of transcription factors (TFs), including MYBs, AP2/ERFs, bHLHs, bZIPs, C2H2s, and WRKYs, were observed to be closely linked to the phenols and flavonoids metabolites, highlighting the potential role of multiple TFs in regulating the biosynthesis of these metabolites and, consequently, influencing the color variation in the heartwood. This study facilitates molecular breeding for the accumulation of metabolites influencing the heartwood color in A. melanoxylon, and offers new insights into the molecular mechanisms underlying heartwood formation in woody plants.
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Affiliation(s)
| | | | | | | | | | - Bingshan Zeng
- Key Laboratory of State Forestry and Grassland Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China; (R.Z.); (X.B.); (Z.C.); (M.C.); (X.L.)
| | - Bing Hu
- Key Laboratory of State Forestry and Grassland Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China; (R.Z.); (X.B.); (Z.C.); (M.C.); (X.L.)
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Zhu Z, Chen D, Sun M, Xiao M, Huang P, Ren D, Yang Y, Zhang Z, Zhao Q, Li R. Integrative analysis of the metabolome and transcriptome provides insights into the mechanisms of lignan biosynthesis in Herpetospermum pedunculosum (Cucurbitaceae). BMC Genomics 2024; 25:421. [PMID: 38684979 PMCID: PMC11059704 DOI: 10.1186/s12864-024-10306-1] [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: 01/08/2024] [Accepted: 04/12/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Herpetospermum pedunculosum (Ser.) C. B. Clarke is a traditional Chinese herbal medicine that heavily relies on the lignans found in its dried ripe seeds (Herpetospermum caudigerum), which have antioxidant and hepatoprotective functions. However, little is known regarding the lignan biosynthesis in H. pedunculosum. In this study, we used metabolomic (non-targeted UHPLC-MS/MS) and transcriptome (RNA-Seq) analyses to identify key metabolites and genes (both structural and regulatory) associated with lignan production during the green mature (GM) and yellow mature (YM) stages of H. pedunculosum. RESULTS The contents of 26 lignan-related metabolites and the expression of 30 genes involved in the lignan pathway differed considerably between the GM and YM stages; most of them were more highly expressed in YM than in GM. UPLC-Q-TOF/MS confirmed that three Herpetospermum-specific lignans (including herpetrione, herpetotriol, and herpetin) were found in YM, but were not detected in GM. In addition, we proposed a lignan biosynthesis pathway for H. pedunculosum based on the fundamental principles of chemistry and biosynthesis. An integrated study of the transcriptome and metabolome identified several transcription factors, including HpGAF1, HpHSFB3, and HpWOX1, that were highly correlated with the metabolism of lignan compounds during seed ripening. Furthermore, functional validation assays revealed that the enzyme 4-Coumarate: CoA ligase (4CL) catalyzes the synthesis of hydroxycinnamate CoA esters. CONCLUSION These results will deepen our understanding of seed lignan biosynthesis and establish a theoretical basis for molecular breeding of H. pedunculosum.
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Affiliation(s)
- Ziwei Zhu
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu University, 610106, Chengdu, China
- Institute for Advanced Study, Chengdu University, 610106, Chengdu, China
| | - Daihan Chen
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China
| | - Min Sun
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu University, 610106, Chengdu, China
- Institute for Advanced Study, Chengdu University, 610106, Chengdu, China
| | - Maotao Xiao
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu University, 610106, Chengdu, China
- School of Food and Biological Engineering, Chengdu University, 610106, Chengdu, China
| | - Peng Huang
- Tibet Rhodiola Pharmaceutical Holding Company, 850000, Lhasa, China
| | - Dongsheng Ren
- Tibet Rhodiola Pharmaceutical Holding Company, 850000, Lhasa, China
| | - Yixi Yang
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu University, 610106, Chengdu, China
- School of Food and Biological Engineering, Chengdu University, 610106, Chengdu, China
| | - Zhen Zhang
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu University, 610106, Chengdu, China
- School of Food and Biological Engineering, Chengdu University, 610106, Chengdu, China
| | - Qi Zhao
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu University, 610106, Chengdu, China.
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China.
- School of Food and Biological Engineering, Chengdu University, 610106, Chengdu, China.
| | - Rui Li
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu University, 610106, Chengdu, China.
- School of Food and Biological Engineering, Chengdu University, 610106, Chengdu, China.
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Zhang R, Zhang Z, Yan C, Chen Z, Li X, Zeng B, Hu B. Comparative physiological, biochemical, metabolomic, and transcriptomic analyses reveal the formation mechanism of heartwood for Acacia melanoxylon. BMC PLANT BIOLOGY 2024; 24:308. [PMID: 38644502 PMCID: PMC11034122 DOI: 10.1186/s12870-024-04884-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/04/2024] [Indexed: 04/23/2024]
Abstract
Acacia melanoxylon is well known as a valuable commercial tree species owing to its high-quality heartwood (HW) products. However, the metabolism and regulatory mechanism of heartwood during wood development remain largely unclear. In this study, both microscopic observation and content determination proved that total amount of starches decreased and phenolics and flavonoids increased gradually from sapwood (SW) to HW. We also obtained the metabolite profiles of 10 metabolites related to phenolics and flavonoids during HW formation by metabolomics. Additionally, we collected a comprehensive overview of genes associated with the biosynthesis of sugars, terpenoids, phenolics, and flavonoids using RNA-seq. A total of ninety-one genes related to HW formation were identified. The transcripts related to plant hormones, programmed cell death (PCD), and dehydration were increased in transition zone (TZ) than in SW. The results of RT-PCR showed that the relative expression level of genes and transcription factors was also high in the TZ, regardless of the horizontal or vertical direction of the trunk. Therefore, the HW formation took place in the TZ for A. melanoxylon from molecular level, and potentially connected to plant hormones, PCD, and cell dehydration. Besides, the increased expression of sugar and terpenoid biosynthesis-related genes in TZ further confirmed the close connection between terpenoid biosynthesis and carbohydrate metabolites of A. melanoxylon. Furthermore, the integrated analysis of metabolism data and RNA-seq data showed the key transcription factors (TFs) regulating flavonoids and phenolics accumulation in HW, including negative correlation TFs (WRKY, MYB) and positive correlation TFs (AP2, bZIP, CBF, PB1, and TCP). And, the genes and metabolites from phenylpropanoid and flavonoid metabolism and biosynthesis were up-regulated and largely accumulated in TZ and HW, respectively. The findings of this research provide a basis for comprehending the buildup of metabolites and the molecular regulatory processes of HW formation in A. melanoxylon.
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Affiliation(s)
- Ruping Zhang
- Key Laboratory of State Forestry Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Zhiwei Zhang
- Key Laboratory of State Forestry Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Caizhen Yan
- Sihui fengfu forestry development co., ltd, Sihui, 526299, China
| | - Zhaoli Chen
- Key Laboratory of State Forestry Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Xiangyang Li
- Key Laboratory of State Forestry Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Bingshan Zeng
- Key Laboratory of State Forestry Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China.
| | - Bing Hu
- Key Laboratory of State Forestry Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China.
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Yang J, Huang J, Wu X, Xu Y, Gu Z, Chen Y, Zhang Y, Ren Y, Miao Y. NtMYB1 and NtNCED1/2 control abscisic acid biosynthesis and tepal senescence in Chinese narcissus (Narcissus tazetta). JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6505-6521. [PMID: 37625033 DOI: 10.1093/jxb/erad311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023]
Abstract
Chinese narcissus (Narcissus tazetta var. chinensis cv. 'Jinzhanyintai') is one of the 10 most famous traditional flowers of China, having a beautiful and highly ornamental flower with a rich fragrance. However, the flower longevity affects its commercial appeal. While petal senescence in Narcissus is ethylene-independent and abscisic acid-dependent, the regulatory mechanism has yet to be determined. In this study, we identified a R2R3-MYB gene (NtMYB1) from Narcissus tazetta and generated oeNtMYB1 and Ntmyb1 RNA interference mutants in Narcissus as well as an oeNtMYB1 construct in Arabidopsis. Overexpressing NtMYB1 in Narcissus or Arabidopsis led to premature leaf yellowing, an elevated level of total carotenoid, a reduced level of chlorophyll b, and a decrease in photosystem II fluorescence (Fv/Fm). A dual-luciferase assay and chromatin immunoprecipitation-quantitative PCR revealed that NtMYB1 directly binds to the promoter of NtNCED1 or NtNCED2 and activates NtNCED1/2 gene expression both in vitro and in vivo. Moreover, overexpressing NtMYB1 accelerated abscisic acid biosynthesis, up-regulated the content of zeatin and abscisic acid, and down-regulated the level of β-carotene and gibberellin A1, leading to petal senescence and leaf yellowing in Narcissus. This study revealed a regulatory process that is fundamentally different between non-photosynthetic organs and leaves.
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Affiliation(s)
- Jingwen Yang
- Fujian Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiazhi Huang
- Fujian Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xi Wu
- Fujian Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yun Xu
- Fujian Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zheng Gu
- Fujian Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yajue Chen
- Fujian Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yu Zhang
- Fujian Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yujun Ren
- Fujian Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ying Miao
- Fujian Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Wang R, Wang Y, Yao W, Ge W, Jiang T, Zhou B. Transcriptome Sequencing and WGCNA Reveal Key Genes in Response to Leaf Blight in Poplar. Int J Mol Sci 2023; 24:10047. [PMID: 37373194 DOI: 10.3390/ijms241210047] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Leaf blight is a fungal disease that mainly affects the growth and development of leaves in plants. To investigate the molecular mechanisms of leaf blight defense in poplar, we performed RNA-Seq and enzyme activity assays on the Populus simonii × Populus nigra leaves inoculated with Alternaria alternate fungus. Through weighted gene co-expression network analysis (WGCNA), we obtained co-expression gene modules significantly associated with SOD and POD activities, containing 183 and 275 genes, respectively. We then constructed a co-expression network of poplar genes related to leaf blight resistance based on weight values. Additionally, we identified hub transcription factors (TFs) and structural genes in the network. The network was dominated by 15 TFs, and four out of them, including ATWRKY75, ANAC062, ATMYB23 and ATEBP, had high connectivity in the network, which might play important functions in leaf blight defense. In addition, GO enrichment analysis revealed a total of 44 structural genes involved in biotic stress, resistance, cell wall and immune-related biological processes in the network. Among them, there were 16 highly linked structural genes in the central part, which may be directly involved in poplar resistance to leaf blight. The study explores key genes associated with leaf blight defense in poplar, which further gains an understanding of the molecular mechanisms of biotic stress response in plants.
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Affiliation(s)
- Ruiqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Yuting Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Wenjing Yao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Wengong Ge
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Boru Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
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Yang Z, Zhu Y, Zhang X, Zhang H, Zhang X, Liu G, Zhao Q, Bao Z, Ma F. Volatile secondary metabolome and transcriptome analysis reveals distinct regulation mechanism of aroma biosynthesis in Syringa oblata and S. vulgaris. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:965-973. [PMID: 36889235 DOI: 10.1016/j.plaphy.2023.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/13/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
Lilacs have high ornamental value due to their strong aroma. However, the molecular regulatory mechanisms of aroma biosynthesis and metabolism in lilac were largely unclear. In this study, two varieties with distinct aroma, Syringa oblata 'Zi Kui' (faint aroma) and Syringa vulgaris 'Li Fei' (strong aroma), were used for exploring the regulation mechanism of aroma difference. Via GC-MS analysis, a total of 43 volatile components were identified. Terpene volatiles was the most abundant volatiles constituting the aroma of two varieties. Notably, 3 volatile secondary metabolites were unique in 'Zi Kui' and 30 volatile secondary metabolites were unique in 'Li Fei'. Then, a transcriptome analysis was performed to clarify the regulation mechanism of aroma metabolism difference between these two varieties, and identified 6411 differentially expressed genes (DEGs). Interestingly, ubiquinone and other terpenoid-quinone biosynthesis genes were significantly enriched in DEGs. We further conducted a correlation analysis between the volatile metabolome and transcriptome and found that TPS, GGPPS, and HMGS genes might be the key contributors to the differences in floral fragrance composition between the two lilac varieties. Our study improves the understanding in the regulation mechanism of Lilac aroma and would help improve the aroma of ornamental crops by metabolic engineering.
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Affiliation(s)
- Zhiying Yang
- Weifang Academy of Agricultural Sciences, Weifang, 261071, Shandong, China
| | - Yuanyuan Zhu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Xu Zhang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Hailiang Zhang
- Weifang Academy of Agricultural Sciences, Weifang, 261071, Shandong, China
| | - Xiaoyu Zhang
- Weifang Academy of Agricultural Sciences, Weifang, 261071, Shandong, China
| | - Genzhong Liu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Qingzhu Zhao
- Weifang Academy of Agricultural Sciences, Weifang, 261071, Shandong, China.
| | - Zhilong Bao
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China.
| | - Fangfang Ma
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China.
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Transcriptomics and Selection Pressure Analysis Reveals the Influence Mechanism of PLIN1 Protein on the Development of Small Size in Min Pigs. Int J Mol Sci 2023; 24:ijms24043947. [PMID: 36835359 PMCID: PMC9960057 DOI: 10.3390/ijms24043947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023] Open
Abstract
Body size is an important biological phenotypic trait that has attracted substantial attention. Small domestic pigs can serve as excellent animal models for biomedicine and also help meet sacrificial culture needs in human societies. Although the mechanisms underlying vertebral development regulating body size variation in domestic pigs during the embryonic period have been well described, few studies have examined the genetic basis of body size variation in post embryonic developmental stages. In this study, seven candidate genes-PLIN1, LIPE, PNPLA1, SCD, FABP5, KRT10 and IVL-significantly associated with body size were identified in Min pigs, on the basis of weighted gene co-expression network analysis (WGCNA), and most of their functions were found to be associated with lipid deposition. Six candidate genes except for IVL were found to have been subjected to purifying selection. PLIN1 had the lowest ω value (0.139) and showed heterogeneous selective pressure among domestic pig lineages with different body sizes (p < 0.05). These results suggested that PLIN1 is an important genetic factor regulating lipid deposition and consequently affecting body size variation in pigs. The culture of whole pig sacrifice in Manchu during the Qing Dynasty in China might have contributed to the strong artificial domestication and selection of Hebao pigs.
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Yang J, Wu X, Aucapiña CB, Zhang D, Huang J, Hao Z, Zhang Y, Ren Y, Miao Y. NtMYB12 requires for competition between flavonol and (pro)anthocyanin biosynthesis in Narcissus tazetta tepals. MOLECULAR HORTICULTURE 2023; 3:2. [PMID: 37789446 PMCID: PMC10515073 DOI: 10.1186/s43897-023-00050-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 01/19/2023] [Indexed: 10/05/2023]
Abstract
The color of flowers is one of the main characteristics adopted for plants to attract pollinators to ensure the reproductive success of the plant, they are also important in their ornamental appeal in Narcissus plant. In this study, we identified a NtMYB12 locus encoding an R2R3-MYB transcription factor. Comparative transcriptome analysis of loss- and gain- of NtMYB12 tissue relative to wild-type narcissus showed NtMYB12 was mainly involved in flavonol and phenylpropanoid metabolic pathways. Biochemical evidences of dual-luciferase activity and chromatin immunoprecipitation assay supported that MYB12 directly bound to promoters of NtFLS, NtLAR, and NtDFR that were cloned by genome walking assay, and activated NtFLS and NtLAR expression but repressed NtDFR expression. More interestingly, NtMYB12 can interact with NtbHLH1 and NtWD40-1 proteins via R3 domain that were selected by transcriptome-based WGCNA and confirmed by yeast two hybrid, bimolecular fluorescence complementation and coimmunoprecipitation assay. Interaction of NtMYB12 with NtbHLH1 and NtWD40-1 forming MYB-bHLH-WD40 triplex specially activated NtDFR and NtANS expression and promoted (pro)anthocyanin accumulation, while NtMYB12 alone activated NtFLS and NtLAR expression and accumulated flavonols, but repressed NtDFR expression. These results indicated that NtMYB12 alone or NtMYB12-bHLH1-WD40-1 triplex requires for competition of metabolism fluxes between flavonol and (pro)anthocyanin biosynthesis. NtMYB12 dually functions on flavonol and proanthocyanin biogenesis via physically binding to NtFLS and NtLAR promoter activating their expression and on (pro)anthocyanin biosynthesis via NtMYB12-NtWD40-NtbHLH (MBW) triplex activating NtDFR and NtANS expression. Requirement of NtMYB12 alone or MBW complex for the competition between flavonol and anthocyanin biosynthesis results in narcissus colorized petal traits.
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Affiliation(s)
- Jingwen Yang
- Fujian Provincial Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xi Wu
- Fujian Provincial Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Cristina belen Aucapiña
- Fujian Provincial Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Deyu Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jiazhi Huang
- Fujian Provincial Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Ziyuan Hao
- Fujian Provincial Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yu Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yujun Ren
- Fujian Provincial Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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12
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Ma Y, Devi MJ, Feng X, Li Y, Song L, Gao H, Cao B. Transcriptome analysis reveals the fruit color variation in Ailanthus altissima. PHYSIOLOGIA PLANTARUM 2023; 175:e13867. [PMID: 36708240 DOI: 10.1111/ppl.13867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Anthocyanins are responsible for the intensity of color in plants; however, the systematic mechanisms underlying the color differences in the fruit of Ailanthus altissima remain unknown. Therefore, this study aims to analyze the transcriptomes of the white and red fruit of A. altissima by screening and validating the key genes involved in flavonoid and anthocyanin biosynthesis. Samples of A. altissima fruit were collected 30, 45, and 60 days after flowering, and their pigment and sugar content were determined. The anthocyanin content was significantly higher in red than in white fruits. Transcriptome analysis was also performed on the fruit samples, 73,807 unigenes were assembled and annotated to seven databases. Twenty-one co-expressed modules were identified via weighted gene co-expression network analysis, of which two were associated with flavonoids and anthocyanins. Furthermore, in three growth stages, 126, 30, and 124 differentially expressed genes were screened between white and red fruit. Genes involved in flavonoid and anthocyanin metabolism were identified. AaDFR (A. altissima bifunctional dihydroflavonol 4-reductase/flavanone 4-reductase) and AaANS (A. altissima anthocyanidin synthase) were associated with flavonoid and anthocyanin metabolism. Members of the AaDFR and AaANS families were also identified, and their basic physicochemical characteristics, conserved domains, motif compositions, phylogenetics, and expression levels were analyzed. The overexpression of AaDFR and AaANS in transgenic Arabidopsis significantly increased the content of seed and foliar flavonoids and anthocyanins. The study elucidated the different mechanisms underlying fruit color development and provided insight into A. altissima plants breeding with commercially desirable properties.
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Affiliation(s)
- Yaping Ma
- School of Agriculture, Ningxia University, Yinchuan, China
- College of Forestry, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Mura Jyostna Devi
- USDA-ARS, Vegetable Crops Research Unit, Madison, Wisconsin, USA
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Xuerui Feng
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yunmao Li
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Lihua Song
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Handong Gao
- College of Forestry, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Southern Tree Seed Inspection Center, Nanjing, China
| | - Bing Cao
- School of Agriculture, Ningxia University, Yinchuan, China
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13
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Chen L, Xia B, Li Z, Liu X, Bai Y, Yang Y, Gao W, Meng Q, Xu N, Sun Y, Li Q, Yue L, He M, Zhou Y. Syringa oblata genome provides new insights into molecular mechanism of flower color differences among individuals and biosynthesis of its flower volatiles. FRONTIERS IN PLANT SCIENCE 2022; 13:1078677. [PMID: 36618636 PMCID: PMC9811319 DOI: 10.3389/fpls.2022.1078677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Syringa oblata is a high ornamental value tree owing to its elegant colors, unique aromas and wide adaptability, however, studies on the molecular mechanism underlying the formation of its ornamental traits are still lacking. Here, we presented a chromosome-scale genome assembly of S. oblata and the final genome size was 1.11 Gb with a contig N50 of 4.75 Mb, anchored on 23 chromosomes and was a better reference for S. oblata transcriptome assembly. Further by integrating transcriptomic and metabolic data, it was concluded that F3H, F3'H, 4CL and PAL, especially the F3'H, were important candidates involved in the formation of floral color differences among S. oblata individuals. Genome-wide identification and analysis revealed that the TPS-b subfamily was the most abundant subfamily of TPS family in S. oblata, which together with the CYP76 family genes determined the formation of the major floral volatiles of S. oblata. Overall, our results provide an important reference for mechanistic studies on the main ornamental traits and molecular breeding in S. oblata.
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Affiliation(s)
- Lifei Chen
- College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Bin Xia
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - Ziwei Li
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - Xiaowei Liu
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - Yun Bai
- College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Yujia Yang
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - Wenjie Gao
- School of Ecological Technology and Engineering, Shanghai Institute of Technology University, Shanghai, China
| | - Qingran Meng
- School of Perfume and Aroma Technology, Shanghai Institute of Technology University, Shanghai, China
| | - Ning Xu
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Ying Sun
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - Qiang Li
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - Liran Yue
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - Miao He
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - Yunwei Zhou
- College of Horticulture, Jilin Agricultural University, Changchun, China
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Integrating Metabolomics and Transcriptomics to Unveil Atisine Biosynthesis in Aconitum gymnandrum Maxim. Int J Mol Sci 2022; 23:ijms232113463. [DOI: 10.3390/ijms232113463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/16/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Diterpene alkaloids (DAs) are characteristic compounds in Aconitum, which are classified into four skeletal types: C18, C19, C20, and bisditerpenoid alkaloids. C20-DAs are thought to be the precursor of the other types. Their biosynthetic pathway, however, is largely unclear. Herein, we combine metabolomics and transcriptomics to unveil the methyl jasmonate (MJ) inducible biosynthesis of DAs in the sterile seedling of A. gymnandrum, the only species in the Subgenus Gymnaconitum (Stapf) Rapaics. Target metabolomics based on root and aerial portions identified 51 C19-DAs and 15 C20-DAs, with 40 inducible compounds. The highest content of C20-DA atisine was selected for further network analysis. PacBio Isoform sequencing integrated with RNA sequencing not only provided the full-length transcriptome but also their response to induction, revealing 1994 genes that exhibited up-regulated expression. Further, 38 genes involved in terpenoid biosynthesis were identified, including 7 diterpene synthases. In addition to the expected function of the four diterpene synthases, AgCPS5 was identified to be a new ent-8,13-CPP synthase in Aconitum and could also combine with AgKSL1 to form the C20-DAs precursor ent-atiserene. Combined with multiple network analyses, six CYP450 and seven 2-ODD genes predicted to be involved in the biosynthesis of atisine were also identified. This study not only sheds light on diterpene synthase evolution in Aconitum but also provides a rich dataset of full-length transcriptomes, systemic metabolomes, and gene expression profiles, setting the groundwork for further investigation of the C20-DAs biosynthesis pathway.
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15
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Shi S, Zhang S, Wu J, Liu X, Zhang Z. Identification of long non-coding RNAs involved in floral scent of Rosa hybrida. FRONTIERS IN PLANT SCIENCE 2022; 13:996474. [PMID: 36267940 PMCID: PMC9577252 DOI: 10.3389/fpls.2022.996474] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Long non-coding RNAs (lncRNAs) were found to play important roles in transcriptional, post-transcriptional, and epigenetic gene regulation in various biological processes. However, lncRNAs and their regulatory roles remain poorly studied in horticultural plants. Rose is economically important not only for their wide use as garden and cut flowers but also as important sources of natural fragrance for perfume and cosmetics industry, but presently little was known about the regulatory mechanism of the floral scent production. In this paper, a RNA-Seq analysis with strand-specific libraries, was performed to rose flowers in different flowering stages. The scented variety 'Tianmidemeng' (Rosa hybrida) was used as plant material. A total of 13,957 lncRNAs were identified by mining the RNA-Seq data, including 10,887 annotated lncRNAs and 3070 novel lncRNAs. Among them, 10,075 lncRNAs were predicted to possess a total of 29,622 target genes, including 54 synthase genes and 24 transcription factors related to floral scent synthesis. 425 lncRNAs were differentially expressed during the flowering process, among which 19 were differentially expressed among all the three flowering stages. Using weighted correlation network analysis (WGCNA), we correlate the differentially-expressed lncRNAs to synthesis of individual floral scent compounds. Furthermore, regulatory function of one of candidate lncRNAs for floral scent synthesis was verified using VIGS method in the rose. In this study, we were able to show that lncRNAs may play important roles in floral scent production in the rose. This study also improves our understanding of how plants regulate their secondary metabolism by lncRNAs.
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Affiliation(s)
- Shaochuan Shi
- Vegetable Research Institute, Shandong Academy of Agricultural Science, Jinan, China
| | - Shiya Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Jie Wu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Xintong Liu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Zhao Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
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16
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Integrated Analysis of Transcriptome and Small RNAome Reveals the Regulatory Network for Rapid Growth in Mikania micrantha. Int J Mol Sci 2022; 23:ijms231810596. [PMID: 36142547 PMCID: PMC9501215 DOI: 10.3390/ijms231810596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/17/2022] Open
Abstract
M. micrantha has caused huge ecological damage and economic losses worldwide due to its rapid growth and serious invasion. However, the underlying molecular mechanisms of its rapid growth and environmental adaption remain unclear. Here, we performed transcriptome and small RNA sequencing with five tissues of M. micrantha to dissect miRNA-mediated regulation in M. micrantha. WGCNA and GO enrichment analysis of transcriptome identified the gene association patterns and potential key regulatory genes for plant growth in each tissue. The genes highly correlated with leaf and stem tissues were mainly involved in the chlorophyll synthesis, response to auxin, the CAM pathway and other photosynthesis-related processes, which promoted the fast growth of M. micrantha. Importantly, we identified 350 conserved and 192 novel miRNAs, many of which displayed differential expression patterns among tissues. PsRNA target prediction analysis uncovered target genes of both conserved and novel miRNAs, including GRFs and TCPs, which were essential for plant growth and development. Further analysis revealed that miRNAs contributed to the regulation of tissue-specific gene expression in M. micrantha, such as mmi-miR396 and mmi-miR319. Taken together, our study uncovered the miRNA-mRNA regulatory networks and the potential vital roles of miRNAs in modulating the rapid growth of M. micrantha.
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17
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Wang J, Li B, Yang X, Liang C, Raza SHA, Pan Y, Zhang K, Zan L. Integration of RNA-seq and ATAC-seq identifies muscle-regulated hub genes in cattle. Front Vet Sci 2022; 9:925590. [PMID: 36032309 PMCID: PMC9404375 DOI: 10.3389/fvets.2022.925590] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
As the main product of livestock, muscle itself plays an irreplaceable role in maintaining animal body movement and regulating metabolism. Therefore, it is of great significance to explore its growth, development and regeneration to improve the meat yield and quality of livestock. In this study, we attempted to use RNA-seq and ATAC-seq techniques to identify differentially expressed genes (DEGs) specifically expressed in bovine skeletal muscle as potential candidates for studying the regulatory mechanisms of muscle development. Microarray data from 8 tissue samples were selected from the GEO database for analysis. First, we obtained gene modules related to each tissue through WGCNA analysis. Through Gene Ontology (GO) functional annotation, the module of lightyellow (MElightyellow) was closely related to muscle development, and 213 hub genes were screened as follow-up research targets. Further, the difference analysis showed that, except for PREB, all other candidate hub genes were up-regulated (muscle group vs. other-group). ATAC-seq analysis showed that muscle-specific accessible chromatin regions were mainly located in promoter of genes related to muscle structure development (GO:0061061), muscle cell development (GO:0055001) and muscle system process (GO:0003012), which were involved in cAMP, CGMP-PKG, MAPK, and other signaling pathways. Next, we integrated the results of RNA-seq and ATAC-seq analysis, and 54 of the 212 candidate hub genes were identified as key regulatory genes in skeletal muscle development. Finally, through motif analysis, 22 of the 54 key genes were found to be potential target genes of transcription factor MEF2C. Including CAPN3, ACTN2, MB, MYOM3, SRL, CKM, ALPK3, MAP3K20, UBE2G1, NEURL2, CAND2, DOT1L, HRC, MAMSTR, FSD2, LRRC2, LSMEM1, SLC29A2, FHL3, KLHL41, ATXN7L2, and PDRG1. This provides a potential reference for studying the molecular mechanism of skeletal muscle development in mammals.
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Affiliation(s)
- Jianfang Wang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Bingzhi Li
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Xinran Yang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Chengcheng Liang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | | | - Yueting Pan
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Ke Zhang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
- National Beef Cattle Improvement Center, Northwest A&F University, Xianyang, China
- *Correspondence: Linsen Zan
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18
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Response of Anthocyanin Accumulation in Pepper (Capsicum annuum) Fruit to Light Days. Int J Mol Sci 2022; 23:ijms23158357. [PMID: 35955513 PMCID: PMC9369206 DOI: 10.3390/ijms23158357] [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: 07/01/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 12/02/2022] Open
Abstract
Light is the key factor affecting the synthesis of anthocyanins in pepper. In this study, pepper fruit under different light days was used as experimental material to explore the synthesis of anthocyanins in purple pepper. A total of 38 flavonoid metabolites were identified in the purple pepper germplasm HNUCA21 by liquid chromatography–tandem mass spectrometry (LC-MS/MS), of which 30 belong to anthocyanins. The detected anthocyanin with the highest content was Delphinidin-3-O-glucoside (17.13 µg/g), which reached the maximum after 168 h of light treatment. Through weighted gene co-expression network analysis (WGCNA), the brown module was identified to be related to the early synthesis of anthocyanins. This module contains many structural genes related to flavonoid synthesis, including chalcone synthase (CHS 107871256, 107864266), chalcone isomerase (CHI 107871144, 107852750), dihydroflavonol 4-reductase (DFR 107860031), flavonoid 3′ 5′-hydroxylase (F3’5’H 107848667), flavonoid 3′-monooxygenase (F3M 107862334), leucoanthocyanidin dioxygenase (LDOX 107866341), and trans-cinnamate 4-monooxygenase (TCM 107875406, 107875407). The module also contained some genes related to anthocyanin transport function, such as glutathione S-transferase (GST 107861273), anthocyanidin 3-O-glucosyltransferase (UDPGT 107861697, 107843659), and MATE (107863234, 107844661), as well as some transcription factors, such as EGL1 (107865400), basic helix-loop-helix 104 (bHLH104 107864591), and WRKY44 (107843538, 107843524). The co-expression regulatory network indicated the involvement of CHS, DFR, CHI, and EGL1, as well as two MATE and two WRKY44 genes in anthocyanin synthesis. The identified genes involved in early, middle, and late light response provided a reference for the further analysis of the regulatory mechanism of anthocyanin biosynthesis in pepper.
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Jiao C, Wei M, Fan H, Song C, Wang Z, Cai Y, Jin Q. Transcriptomic analysis of genes related to alkaloid biosynthesis and the regulation mechanism under precursor and methyl jasmonate treatment in Dendrobium officinale. FRONTIERS IN PLANT SCIENCE 2022; 13:941231. [PMID: 35937364 PMCID: PMC9355482 DOI: 10.3389/fpls.2022.941231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
Dendrobium officinale is both a traditional herbal medicine and a plant of high ornamental and medicinal value. Alkaloids, especially terpenoid indole alkaloids (TIAs), with pharmacological activities are present in the tissues of D. officinale. A number of genes involved in alkaloid biosynthetic pathways have been identified. However, the regulatory mechanisms underlying the precursor and methyl jasmonate (MeJA)-induced accumulation of alkaloids in D. officinale are poorly understood. In this study, we collected D. officinale protocorm-like bodies (PLBs) and treated them with TIA precursors (tryptophan and secologanin) and MeJA for 0 (T0), 4 (T4) and 24 h (T24); we also established control samples (C4 and C24). Then, we measured the total alkaloid content of the PLBs and performed transcriptome sequencing using the Illumina HiSeq 2,500 system. The total alkaloid content increased significantly after 4 h of treatment. Go and KEGG analysis suggested that genes from the TIA, isoquinoline alkaloid, tropane alkaloid and jasmonate (JA) biosynthetic pathways were significantly enriched. Weighted gene coexpression network analysis (WGCNA) uncovered brown module related to alkaloid content. Six and seven genes related to alkaloid and JA bisosynthetic pathways, respectively, might encode the key enzymes involved in alkaloid biosynthesis of D. officinale. Moreover, 13 transcription factors (TFs), which mostly belong to AP2/ERF, WRKY, and MYB gene families, were predicted to regulate alkaloid biosynthesis. Our data provide insight for studying the regulatory mechanism underlying TIA precursor and MeJA-induced accumulation of three types of alkaloids in D. officinale.
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Affiliation(s)
- Chunyan Jiao
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Mengke Wei
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Honghong Fan
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Cheng Song
- College of Biological and Pharmaceutical Engineering, West Anhui University, Luan, China
| | - Zhanjun Wang
- College of Life Sciences, Hefei Normal University, Hefei, China
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Qing Jin
- School of Life Sciences, Anhui Agricultural University, Hefei, China
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20
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Fu J, Huang S, Qian J, Qing H, Wan Z, Cheng H, Zhang C. Genome-Wide Identification of Petunia HSF Genes and Potential Function of PhHSF19 in Benzenoid/Phenylpropanoid Biosynthesis. Int J Mol Sci 2022; 23:ijms23062974. [PMID: 35328393 PMCID: PMC8951162 DOI: 10.3390/ijms23062974] [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: 02/14/2022] [Revised: 03/04/2022] [Accepted: 03/08/2022] [Indexed: 11/17/2022] Open
Abstract
Volatile benzenoids/phenylpropanoids are the main flower scent compounds in petunia (Petunia hybrida). Heat shock factors (HSFs), well known as the main regulator of heat stress response, have been found to be involved in the biosynthesis of benzenoid/phenylpropanoid and other secondary metabolites. In order to figure out the potential function of HSFs in the regulation of floral scent in petunia, we systematically identified the genome-wide petunia HSF genes and analyzed their expression and then the interaction between the key petunia HSF gene with target gene involved in benzenoid/phenylpropanoid biosynthesis. The results revealed that 34 HSF gene family members were obtained in petunia, and most petunia HSFs contained one intron. The phylogenetic analysis showed that 23 petunia HSFs were grouped into the largest subfamily HSFA, while only two petunia HSFs were in HSFC subfamily. The DBD domain and NLS motif were well conserved in most petunia HSFs. Most petunia HSF genes’ promoters contained STRE motifs, the highest number of cis-acting element. PhHSF19 is highly expressed in petal tubes, followed by peduncles and petal limbs. During flower development, the expression level of PhHSF19 was dramatically higher at earlier flower opening stages than that at the bud stage, suggesting that PhHSF19 may have potential roles in regulating benzenoid/phenylpropanoid biosynthesis. The expression pattern of PhHSF19 is positively related with PhPAL2, which catalyzes the first committed step in the phenylpropanoid pathway. In addition, there are three STRE elements in the promoter of PhPAL2. PhHSF19 was proven to positively regulate the expression of PhPAL2 according to the yeast one hybrid and dual luciferase assays. These results lay a theoretical foundation for further studies of the regulation of HSFs on plant flower scent biosynthesis.
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21
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Yu X, Liu Z, Pan Y, Cui X, Zhao X, Li D, Xue X, Fu J. Co-expression network analysis for identification of novel biomarkers of bronchopulmonary dysplasia model. Front Pediatr 2022; 10:946747. [PMID: 36440350 PMCID: PMC9696732 DOI: 10.3389/fped.2022.946747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 10/11/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Bronchopulmonary dysplasia (BPD) is the most common neonatal chronic lung disease. However, its exact molecular pathogenesis is not understood. We aimed to identify relevant gene modules that may play crucial roles in the occurrence and development of BPD by weighted gene co-expression network analysis (WGCNA). METHODS We used RNA-Seq data of BPD and healthy control rats from our previous studies, wherein data from 30 samples was collected at days 1, 3, 7, 10, and 14. Data for preprocessing analysis included 17,613 differentially expressed genes (DEGs) with false discovery rate <0.05. RESULTS We grouped the highly correlated genes into 13 modules, and constructed a network of mRNA gene associations, including the 150 most associated mRNA genes in each module. Lgals8, Srpra, Prtfdc1, and Thap11 were identified as the key hub genes. Enrichment analyses revealed Golgi vesicle transport, coated vesicle, actin-dependent ATPase activity and endoplasmic reticulum pathways associated with these genes involved in the pathological process of BPD in module. CONCLUSIONS This is a study to analyze data obtained from BPD animal model at different time-points using WGCNA, to elucidate BPD-related susceptibility modules and disease-related genes.
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Affiliation(s)
- Xuefei Yu
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Ziyun Liu
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yuqing Pan
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xuewei Cui
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xinyi Zhao
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Danni Li
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xindong Xue
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Jianhua Fu
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
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