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Lemus-Conejo A, Villanueva-Lazo A, Martin ME, Millan F, Millan-Linares MC. Sacha Inchi ( Plukenetia volubilis L.) Protein Hydrolysate as a New Ingredient of Functional Foods. Foods 2024; 13:2045. [PMID: 38998552 PMCID: PMC11241537 DOI: 10.3390/foods13132045] [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: 06/07/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/14/2024] Open
Abstract
Sacha inchi (Plukenetia volubilis L.) is an under-exploited crop with great potential due to its nutritional and medicinal characteristics. A Sacha inchi protein isolate (SII), obtained from defatted Sacha inchi flour (SIF), was hydrolyzed by Bioprotease LA 660 under specific conditions. The hydrolysates were characterized chemically, and their digestibility and antioxidant capacity were evaluated by in vitro cell-free experiments to select the hydrolysate with major antioxidant activity. Sacha inchi protein hydrolysate at 20 min (SIH20B) was selected, and the anti-inflammatory capacity was evaluated by RT-qPCR and ELISA techniques, using two different doses in monocytes THP-1 stimulated with lipopolysaccharide (LPS). The results obtained showed that the in vitro administration of SIH20B down-regulated the TNF-α gene and reduced the release of this cytokine, whereas the anti-inflammatory cytokines IL-10 and IL-4 were up-regulated in LPS-stimulated monocytes and co-administrated with SIH20B. The peptides contained in SIH20B were identified, and the 20 more relatively abundant peptides with a mass by 1 kDa were subjected to in silico analysis to hypothesize those that could be responsible for the bioactivity reported in the hydrolysate. From the identified peptides, the peptides AAGALKKFL and LGVKFKGGL, among others, are proposed as the most biologically actives. In conclusion, SIH20B is a novel, natural source of high-value-added biopeptides that could be used as an ingredient in formulations of food or nutraceutical compounds.
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Affiliation(s)
- Ana Lemus-Conejo
- Foundation Centre for Research and Development of Functional Food-CIDAF, Avda del Conocimiento 37, 18100 Granade, Spain
| | - Alvaro Villanueva-Lazo
- Food Protein and Immunonutrition Group, Department of Food and Health, Instituto de la Grasa, CSIC, Campus Universitario Pablo de Olavide, Edificio 46, Ctra. de Utrera, Km. 1, 41013 Seville, Spain
| | - Maria E Martin
- Department of Cell Biology, Faculty of Biology, University of Seville, Av. Reina Mercedes s/n, 41012 Seville, Spain
| | - Francisco Millan
- Food Protein and Immunonutrition Group, Department of Food and Health, Instituto de la Grasa, CSIC, Campus Universitario Pablo de Olavide, Edificio 46, Ctra. de Utrera, Km. 1, 41013 Seville, Spain
| | - Maria C Millan-Linares
- Food Protein and Immunonutrition Group, Department of Food and Health, Instituto de la Grasa, CSIC, Campus Universitario Pablo de Olavide, Edificio 46, Ctra. de Utrera, Km. 1, 41013 Seville, Spain
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Yang T, Niu Q, Dai H, Tian X, Ma J, Pritchard HW, Lin L, Yang X. The transcription factor MYB1 activates DGAT2 transcription to promote triacylglycerol accumulation in sacha inchi (Plukenetia volubilis L.) leaves under heat stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108517. [PMID: 38503190 DOI: 10.1016/j.plaphy.2024.108517] [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: 12/07/2023] [Revised: 02/17/2024] [Accepted: 03/08/2024] [Indexed: 03/21/2024]
Abstract
Triacylglycerol (TAG) accumulation is frequently triggered in vegetative tissues experiencing heat stress, which may increases plant basal plant thermo-tolerance by sequestering the toxic lipid intermediates that contribute to membrane damage or cell death under stress conditions. However, stress-responsive TAG biosynthesis and the underlying regulatory mechanisms are not fully understood. Here, we investigated the lipidomic and transcriptomic landscape under heat stress in the leaves of sacha inchi (Plukenetia volubilis L.), an important oilseed crop in tropical regions. Under heat stress (45 °C), the content of polyunsaturated TAGs (e.g., TAG18:2 and TAG18:3) and total TAGs were significantly higher, while those of unsaturated sterol esters, including ZyE 28:4, SiE 18:2 and SiE 18:3, were dramatically lower. Transcriptome analysis showed that the expression of PvDGAT2-2, encoding a type II diacylglycerol acyltransferase (DGAT) that is critical for TAG biosynthesis, was substantially induced under heat stress. We confirmed the function of PvDGAT2-2 in TAG production by complementing a yeast mutant defective in TAG biosynthesis. Importantly, we also identified the heat-induced transcription factor PvMYB1 as an upstream activator of PvDGAT2-2 transcription. Our findings on the molecular mechanism leading to TAG biosynthesis in leaves exposed to heat stress have implications for improving the biotechnological production of TAGs in vegetative tissues, offering an alternative to seeds.
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Affiliation(s)
- Tianquan Yang
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Qian Niu
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China
| | - Huan Dai
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Xiaoling Tian
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming, 650500, China
| | - Junchao Ma
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Hugh W Pritchard
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Liang Lin
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | - Xiangyun Yang
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
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Fu Y, Huo K, Pei X, Liang C, Meng X, Song X, Wang J, Niu J. Full-length transcriptome revealed the accumulation of polyunsaturated fatty acids in developing seeds of Plukenetia volubilis. PeerJ 2022; 10:e13998. [PMID: 36157055 PMCID: PMC9504451 DOI: 10.7717/peerj.13998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 08/12/2022] [Indexed: 01/19/2023] Open
Abstract
Background Plukenetia volubilis is cultivated as a valuable oilseed crop, and its mature seeds are rich in polyunsaturated fatty acids (FAs), which are widely used in food and pharmaceutical industries. Recently, next-generation sequencing (NGS) transcriptome studies in P. volubilis indicated that some candidate genes were involved in oil biosynthesis. The NGS were inaccuracies in assembly of some candidate genes, leading to unknown errors in date analyses. However, single molecular real-time (SMRT) sequencing can overcome these assembled errors. Unfortunately, this technique has not been reported in P. volubilis. Methods The total oil content of P. volubilis seed (PVS) was determined using Soxhlet extraction system. The FA composition were analyzed by gas chromatography. Combining PacBio SMRT and Illumina technologies, the transcriptome analysis of developing PVS was performed. Functional annotation and differential expression were performed by BLAST software (version 2.2.26) and RSEM software (version 1.2.31), respectively. The lncRNA-targeted transcripts were predicted in developing PVS using LncTar tool. Results By Soxhlet extraction system, the oil content of superior plant-type (SPT) was 13.47% higher than that of inferior plant-type (IPT) at mature PVS. The most abundant FAs were C18:2 and C18:3, among which C18:3 content of SPT was 1.11-fold higher than that of IPT. Combined with PacBio and Illumina platform, 68,971 non-redundant genes were obtained, among which 7,823 long non-coding RNAs (lncRNAs) and 7,798 lncRNA-targeted genes were predicted. In developing seed, the expressions of 57 TFs showed a significantly positive correlation with oil contents, including WRI1-like1, LEC1-like1, and MYB44-like. Comparative analysis of expression profiles between SPT and IPT implied that orthologs of FAD3, PDCT, PDAT, and DAGT2 were possibly important for the accumulation of polyunsaturated FAs. Together, these results provide a reference for oil biosynthesis of P. volubilis and genetic improvement of oil plants.
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Affiliation(s)
- Yijun Fu
- College of Forestry, Hainan University, Haikou, Hainan, China
| | - Kaisen Huo
- College of Forestry, Hainan University, Haikou, Hainan, China
| | - Xingjie Pei
- College of Forestry, Hainan University, Haikou, Hainan, China
| | - Chongjun Liang
- College of Forestry, Hainan University, Haikou, Hainan, China
| | - Xinya Meng
- College of Forestry, Hainan University, Haikou, Hainan, China
| | - Xiqiang Song
- College of Forestry, Hainan University, Haikou, Hainan, China
| | - Jia Wang
- College of Forestry, Hainan University, Haikou, Hainan, China
| | - Jun Niu
- College of Forestry, Hainan University, Haikou, Hainan, China
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Integrated Transcriptome and Proteome Analysis Provides Insight into the Ribosome Inactivating Proteins in Plukenetia volubilis Seeds. Int J Mol Sci 2022; 23:ijms23179562. [PMID: 36076961 PMCID: PMC9455912 DOI: 10.3390/ijms23179562] [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: 07/25/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 11/17/2022] Open
Abstract
Plukenetia volubilis is a highly promising plant with high nutritional and economic values. In our previous studies, the expression levels of ricin encoded transcripts were the highest in the maturation stage of P. volubilis seeds. The present study investigated the transcriptome and proteome profiles of seeds at two developmental stages (Pv-1 and Pv-2) using RNA-Seq and iTRAQ technologies. A total of 53,224 unigenes and 6026 proteins were identified, with functional enrichment analyses, including GO, KEGG, and KOG annotations. At two development stages of P. volubilis seeds, 8815 unique differentially expressed genes (DEGs) and 4983 unique differentially abundant proteins (DAPs) were identified. Omics-based association analysis showed that ribosome-inactivating protein (RIP) transcripts had the highest expression and abundance levels in Pv-2, and those DEGs/DAPs of RIPs in the GO category were involved in hydrolase activity. Furthermore, 21 RIP genes and their corresponding amino acid sequences were obtained from libraries produced with transcriptome analysis. The analysis of physicochemical properties showed that 21 RIPs of P. volubilis contained ricin, the ricin_B_lectin domain, or RIP domains and could be divided into three subfamilies, with the largest number for type II RIPs. The expression patterns of 10 RIP genes indicated that they were mostly highly expressed in Pv-2 and 4 transcripts encoding ricin_B_like lectins had very low expression levels during the seed development of P. volubilis. This finding would represent valuable evidence for the safety of oil production from P. volubilis for human consumption. It is also notable that the expression level of the Unigene0030485 encoding type I RIP was the highest in roots, which would be related to the antiviral activity of RIPs. This study provides a comprehensive analysis of the physicochemical properties and expression patterns of RIPs in different organs of P. volubilis and lays a theoretical foundation for further research and utilization of RIPs in P. volubilis.
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Lipid composition of the Amazonian 'Mountain Sacha Inchis' including Plukenetia carolis-vegae Bussmann, Paniagua & C.Téllez. Sci Rep 2022; 12:6450. [PMID: 35440613 PMCID: PMC9018825 DOI: 10.1038/s41598-022-10404-8] [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: 11/07/2021] [Accepted: 04/04/2022] [Indexed: 11/30/2022] Open
Abstract
Several Amazonian species of Plukenetia are remarkably rich sources of polyunsaturated fatty acids, in particular α-linolenic acid. The lipid composition of the large-seeded, recently described ‘Mountain Sacha Inchi’ Plukenetia carolis-vegae is reported here for the first time, and compared with Plukenetia huayllabambana, two cultivars of Plukenetia volubilis, and a newly developed hybrid between P. volubilis and P. carolis-vegae. All species and cultivars had a very high content of polyunsaturated fatty acids, 82.6–86.7% of total fatty acids, and at least 46.6% α-linolenic acid of total fatty acids. The highest content was found in P. carolis-vegae which had 57.4%. The exceptionally high α-linolenic acid content suggests that P. carolis-vegae may be an important plant-derived dietary source of this essential fatty acid and that the species has considerable potential for further domestication and commercialisation of its seeds and seed oil. A TAG analysis was carried out for the two P. volubilis cultivars, in which LLnLn and LnLL were most prevalent, and for P. huayllabambana, in which LLnLn constituted the largest fraction, followed by LnLnLn, indicating that this large-seeded species also has interesting dietary properties.
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Liu G, Wu Z, Shang X, Peng Y, Gao L. Overexpression of PvFAD3 Gene from Plukenetia volubilis Promotes the Biosynthesis of α-Linolenic Acid in Transgenic Tobacco Seeds. Genes (Basel) 2022; 13:450. [PMID: 35328004 PMCID: PMC8951128 DOI: 10.3390/genes13030450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 02/25/2022] [Accepted: 02/25/2022] [Indexed: 11/17/2022] Open
Abstract
The ω-3 fatty acid desaturase (FAD3) gene encodes a rate-limiting enzyme in the synthesis of α-linolenic acid. In this study, homologous cloning was used to obtain the full-length sequence of the PvFAD3 gene of Plukenetia volubilis. The full-length DNA sequence was 1871 bp long, with 8 exons and 7 introns. The structural analysis of the amino acid sequence revealed that the PvFAD3 protein contained three histidine-conserved regions and an endoplasmic reticulum retention signal. The real-time reverse transcription-polymerase chain reaction performed for determining the expression patterns of the PvFAD3 gene in different tissues of P. volubilis showed that PvFAD3 expression was highly expressed in the fast oil accumulation stage of seed. The analysis of subcellular localization assay in epidermal cells of tobacco (Nicotiana benthamiana) leaves showed that the PvFAD3 protein was mainly localized in the endoplasmic reticulum. Seed-specific overexpression vectors were constructed, and Agrobacterium-mediated genetic transformation was performed to obtain transgenic tobacco plants overexpressing PvFAD3. The results of fatty acid assays performed using harvested seeds showed a significant increase in α-linolenic acid content, a dramatic decrease in linoleic acid content, and an obvious increase in oil content in transgenic tobacco seeds. Collectively, the PvFAD3 gene of P. volubilis was confirmed as a key enzyme gene for α-linolenic acid synthesis; thus, indicating that the PvFAD3 gene can be used for fatty acid fraction improvement in oilseed plants.
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Affiliation(s)
- Guo Liu
- Research Institute of Fast-Growing Trees, Chinese Academy of Forestry, 30 Mid Renmin Avenue, Zhanjiang 524022, China; (Z.W.); (X.S.); (Y.P.); (L.G.)
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Wu B, Li Y, Li J, Xie Z, Luan M, Gao C, Shi Y, Chen S. Genome-Wide Analysis of Alternative Splicing and Non-Coding RNAs Reveal Complicated Transcriptional Regulation in Cannabis sativa L. Int J Mol Sci 2021; 22:ijms222111989. [PMID: 34769433 PMCID: PMC8584933 DOI: 10.3390/ijms222111989] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/21/2021] [Accepted: 10/26/2021] [Indexed: 12/26/2022] Open
Abstract
It is of significance to mine the structural genes related to the biosynthetic pathway of fatty acid (FA) and cellulose as well as explore the regulatory mechanism of alternative splicing (AS), microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in the biosynthesis of cannabinoids, FA and cellulose, which would enhance the knowledge of gene expression and regulation at post-transcriptional level in Cannabis sativa L. In this study, transcriptome, small RNA and degradome libraries of hemp 'Yunma No.1' were established, and comprehensive analysis was performed. As a result, a total of 154, 32 and 331 transcripts encoding key enzymes involved in the biosynthesis of cannabinoids, FA and cellulose were predicted, respectively, among which AS occurred in 368 transcripts. Moreover, 183 conserved miRNAs, 380 C. sativa-specific miRNAs and 7783 lncRNAs were predicted. Among them, 70 miRNAs and 17 lncRNAs potentially targeted 13 and 17 transcripts, respectively, encoding key enzymes or transporters involved in the biosynthesis of cannabinoids, cellulose or FA. Finally, the crosstalk between AS and miRNAs or lncRNAs involved in cannabinoids and cellulose was also predicted. In summary, all these results provided insights into the complicated network of gene expression and regulation in C. sativa.
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Affiliation(s)
- Bin Wu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (B.W.); (Y.L.); (J.L.); (Z.X.)
| | - Yanni Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (B.W.); (Y.L.); (J.L.); (Z.X.)
| | - Jishuang Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (B.W.); (Y.L.); (J.L.); (Z.X.)
| | - Zhenzhen Xie
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (B.W.); (Y.L.); (J.L.); (Z.X.)
| | - Mingbao Luan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (M.L.); (C.G.)
| | - Chunsheng Gao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (M.L.); (C.G.)
| | - Yuhua Shi
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China;
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China;
- Correspondence:
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Goyal A, Tanwar B, Kumar Sihag M, Sharma V. Sacha inchi (Plukenetia volubilis L.): An emerging source of nutrients, omega-3 fatty acid and phytochemicals. Food Chem 2021; 373:131459. [PMID: 34731811 DOI: 10.1016/j.foodchem.2021.131459] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/20/2021] [Accepted: 10/20/2021] [Indexed: 12/30/2022]
Abstract
Sacha inchi (Plukenetia volubilis) (SI) is an oleaginous plant producing oil and protein-rich seeds. It has been cultivated for centuries and is native to the tropical rainforest of the Amazon region of South America including parts of Peru and northwestern Brazil. At present, SI seeds are emerging as a potential source of macro- and micronutrients, α-linolenic acid and phytochemicals. This review attempts to elucidate the nutrients, phytonutrients, safety, toxicity, health benefits and food applications of SI seed. Recent scientific studies have associated the consumption of SI seed/oil with reduced risk of chronic inflammatory diseases. However, lack of awareness and in-depth understanding has resulted in it being neglected both at the consumer and industrial level. In all, SI is an underutilized and undervalued oleaginous crop which not only has the potential to mitigate food and nutritional insecurity but also offers humongous opportunities for the development of novel value-added food products.
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Affiliation(s)
- Ankit Goyal
- Department of Dairy Chemistry, Mansinhbhai Institute of Dairy and Food Technology, Mehsana 384002, Gujarat, India.
| | - Beenu Tanwar
- Department of Dairy Technology, Mansinhbhai Institute of Dairy and Food Technology, Mehsana 384002, Gujarat, India.
| | - Manvesh Kumar Sihag
- Department of Dairy Chemistry, College of Dairy Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana 141001, Punjab, India.
| | - Vivek Sharma
- Dairy Chemistry Division, National Dairy Research Institute (ICAR-NDRI), Karnal, Haryana, India.
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Ramos-Escudero F, Morales MT, Ramos Escudero M, Muñoz AM, Cancino Chavez K, Asuero AG. Assessment of phenolic and volatile compounds of commercial Sacha inchi oils and sensory evaluation. Food Res Int 2021; 140:110022. [DOI: 10.1016/j.foodres.2020.110022] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/14/2020] [Accepted: 12/10/2020] [Indexed: 10/22/2022]
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Transcriptome analyses reveals the dynamic nature of oil accumulation during seed development of Plukenetia volubilis L. Sci Rep 2020; 10:20467. [PMID: 33235240 PMCID: PMC7686490 DOI: 10.1038/s41598-020-77177-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/05/2020] [Indexed: 02/06/2023] Open
Abstract
Sacha inchi (Plukenetia volubilis L.) is a shrub native to Amazon rainforests that’s of commercial interest as its seeds contain 35–60% edible oil (dry weight). This oil is one of the healthiest vegetable oils due to its high polyunsaturated fatty acid content and favourable ratio of omega-6 to omega-3 fatty acids. De novo transcriptome assembly and comparative analyses were performed on sacha inchi seeds from five stages of seed development in order to identifying genes associated with oil accumulation and fatty acid production. Of 30,189 unigenes that could be annotated in public databases, 20,446 were differentially expressed unigenes. A total of 14 KEGG pathways related to lipid metabolism were found, and 86 unigenes encoding enzymes involved in α-linolenic acid (ALA) biosynthesis were obtained including five unigenes encoding FATA (Unigene0008403), SAD (Unigene0012943), DHLAT (Unigene0014324), α-CT (Unigene0022151) and KAS II (Unigene0024371) that were significantly up-regulated in the final stage of seed development. A total of 66 unigenes encoding key enzymes involved in the synthesis of triacylglycerols (TAGs) were found, along with seven unigenes encoding PDCT (Unigene0000909), LPCAT (Unigene0007846), Oleosin3 (Unigene0010027), PDAT1 (Unigene0016056), GPDH (Unigene0022660), FAD2 (Unigene0037808) and FAD3 (Unigene0044238); these also proved to be up-regulated in the final stage of seed development.
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Yang T, Wang X, Dong T, Xu W, Liu A. Isolation and functional analyses of PvFAD2 and PvFAD3 involved in the biosynthesis of polyunsaturated fatty acids from Sacha Inchi ( Plukenetia volubilis). PeerJ 2020; 8:e9169. [PMID: 32607277 PMCID: PMC7315619 DOI: 10.7717/peerj.9169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/20/2020] [Indexed: 12/19/2022] Open
Abstract
The development of ω-3 fatty acid-rich vegetable oils is essential to enrich the production of functional foods. Sacha Inchi (Plukenetia volubilis L.) is a unique oilseed crop with much potential. Its seeds contain rich polyunsaturated fatty acids (PUFAs), especially linoleic acid (LA, C18:2) and α-linolenic acid (ALA, C18:3). Endoplasmic reticulum -located ω-6 and ω-3 fatty acid desaturases (FAD) are responsible for the biosynthesis of LA and ALA, respectively, in plant seeds. Here, we isolated two full-length FAD genes from Sacha Inchi, named PvFAD2 and PvFAD3, which encoded predicted amino acid residues of 384 and 379 in protein, respectively. Protein sequence and subcellular localization analysis revealed that they were located in the endoplasmic reticulum (ER). Heterologous expression in Saccharomyces cerevisiae confirmed that PvFAD2 and PvFAD3 could catalyze LA and ALA synthesis, respectively. The stability and catalytic efficiency of the PvFAD3 protein may be closely related to temperature. In transgenic tobacco, using seed-specific expression promoters, PvFAD2 and PvFAD3 significantly promotes the production of LA (from 68% to 70.5%) and ALA (from 0.7% to 3.1%) in seed oil. These results show that PvFAD2 and PvFAD3 do, indeed, function as crucial enzymes for PUFAs biosynthesis, and provide a key gene source for the sustainable production of lipids with tailored fatty acid compositions via genetic engineering in other oil crops.
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Affiliation(s)
- Tianquan Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xiaojuan Wang
- Department of Resources and Environmental Engineering, Henan University of Engineering, Zhengzhou, Henan, China
| | - Tingnan Dong
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Wei Xu
- Department of Economic Plants and Biotechnology, and Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Aizhong Liu
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
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Kodahl N. Sacha inchi (Plukenetia volubilis L.)-from lost crop of the Incas to part of the solution to global challenges? PLANTA 2020; 251:80. [PMID: 32185506 DOI: 10.1007/s00425-020-03377-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 03/11/2020] [Indexed: 05/19/2023]
Abstract
The underutilized, oleaginous crop Plukenetia volubilis L. has a remarkable lipid composition and a large potential for further domestication, alleviation of malnutrition, and integration into sustainable food production systems. Current global challenges include climate change, increasing population size, lack of food security, malnutrition, and degradation of arable lands. In this context, a reformation of our food production systems is imperative. Underutilized crops, or orphan crops, can provide valuable traits for this purpose, e.g., climate change resilience, nutritional benefits, cultivability on marginal lands, and improvement of income opportunities for smallholders. Plukenetia volubilis L. (Euphorbiaceae)-sacha inchi-is a 'lost crop' of the Incas native to the Amazon basin. Its oleaginous seeds are large, with a high content of ω-3, and -6 fatty acids (ca. 50.5, and 34.1%, of the lipid fraction, respectively), protein, and antioxidants. Culinarily, the seeds are nut-like and the crop has been associated with humans since Incan times. Research has particularly been undertaken in seed biochemistry, and to some extent in phylogeny, genetics, and cultivation ecology, but attention has been unevenly distributed, causing knowledge gaps in areas such as ethnobotany, allergenicity, and sustainable cultivation practices. Recently, seed size evolution and molecular drivers of the fatty acid synthesis and composition have been studied, however, further research into the lipid biosynthesis is desirable. Targeted breeding has not been undertaken but might be especially relevant for yield, sensory qualities, and cultivation with low environmental impact. Similarly, studies of integration into sustainable management systems are of highest importance. Here, present knowledge on P. volubilis is reviewed and a general framework for conducting research on underutilized crops with the aim of integration into sustainable food production systems is presented.
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Affiliation(s)
- Nete Kodahl
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.
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Li WY, Wang C, Shi HH, Wang B, Wang JX, Liu YS, Ma JY, Tian SY, Zhang YW. Genome-wide analysis of ethylene-response factor family in adzuki bean and functional determination of VaERF3 under saline-alkaline stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 147:215-222. [PMID: 31869734 DOI: 10.1016/j.plaphy.2019.12.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 12/12/2019] [Accepted: 12/16/2019] [Indexed: 05/24/2023]
Abstract
Ethylene-response factor (ERF) proteins are members of a transcription factor family involved in plant growth and environmental stress responses, but the biological functions of ERF members in adzuki bean (Vigna angularis var. angularis) remain unknown. In addition, it is unclear whether these proteins have a role in regulating responses to abiotic stressors. Here, we identified 47 ERF genes by analyzing the adzuki bean genome. Whole-transcriptome analyses of plants under saline-alkaline stress suggested that the expression of 13 ERF genes was induced in response to saline-alkaline stress. Analysis of the cis-acting elements showed that the promoters of these saline-alkaline stress-inducible ERF genes contained LTRs, DREs, MYBs, ABREs, MYCs, CGTCA-, and TGACG-motifs, which are involved in abiotic stress responses. The expression of VaERF3 was induced by NaHCO3, polyethylene glycol 6000, NaCl, and ABA (abscisic acid), as determined by qRT-PCR. Overexpression of VaERF3 in transgenic Arabidopsis resulted in higher levels of proline accumulation and lower malondialdehyde and reactive oxygen species contents in plants grown under saline-alkaline stress conditions. Moreover, VaERF3 encoded a nuclear-localized transcriptional activator that promoted the expression of stress-responsive genes. Collectively, these results are of great significance in elucidating the mechanisms of saline-alkaline stress responses in adzuki bean.
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Affiliation(s)
- Wei-Yu Li
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Beijing University of Agriculture, Beijing, 102206, China.
| | - Cheng Wang
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Beijing University of Agriculture, Beijing, 102206, China
| | - Heng-Hua Shi
- School of Computer and Information Engineering, Beijing University of Agriculture, Beijing, 102206, China
| | - Bo Wang
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Beijing University of Agriculture, Beijing, 102206, China
| | - Jing-Xuan Wang
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Beijing University of Agriculture, Beijing, 102206, China
| | - Yu-Shu Liu
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Beijing University of Agriculture, Beijing, 102206, China
| | - Jing-Yu Ma
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Beijing University of Agriculture, Beijing, 102206, China
| | - Sen-Ya Tian
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Beijing University of Agriculture, Beijing, 102206, China
| | - Yao-Wen Zhang
- Institute of Crop Sciences, Shanxi Academy of Agricultural Sciences, Taiyuan, 030001, China.
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Tan X, Long W, Zeng L, Ding X, Cheng Y, Zhang X, Zou X. Melatonin-Induced Transcriptome Variation of Rapeseed Seedlings under Salt Stress. Int J Mol Sci 2019; 20:ijms20215355. [PMID: 31661818 PMCID: PMC6862158 DOI: 10.3390/ijms20215355] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 10/16/2019] [Accepted: 10/23/2019] [Indexed: 12/20/2022] Open
Abstract
Salt stress inhibits the production of all crop species, including rapeseed (Brassica napus L.), the second most widely planted oil crop species. Although melatonin was confirmed to alleviate salt stress in rapeseed seedlings recently, the mechanism governing the expression levels remains unknown. Therefore, the melatonin-induced transcriptome variation of salt-stressed seedlings was explored. In this study, the transcriptomes of leaves and roots under control (CK), salt (125 mM NaCl, ST) and melatonin (125 mM NaCl plus 50 µM melatonin, MS) treatments were evaluated by using next-generation sequencing techniques. After conducting comparisons of gene expression in the roots and leaves between MS and ST, the differentially expressed gene (DEG) pools were screened. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses highlighted the significant pathways, which were mainly related to plant hormone synthesis and signal transduction, lignin and fatty acid metabolism. The functional genes in the objective KEGG pathways were identified. Furthermore, members of several transcription factor (TF) families participated in the response process. Combined with the hormone (campesterol (CS), jasmonic acid (JA), and gibberellic acid 3 (GA3)) contents measured in the seedlings, it could be concluded that melatonin induced changes in the intrinsic hormone metabolic network, which promoted seedling growth. Thus, this study identified new candidate genes and pathways active during the interactions between melatonin and salt stress, which provide clues for disclosing melatonin’s function in resistance to salt injury. Our results contribute to developing a practical method for sustainable agriculture on saline lands.
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Affiliation(s)
- Xiaoyu Tan
- Key Lab of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
- College of Plant Science and Technology of Huazhong Agricultural University, Wuhan 430070, China.
| | - Weihua Long
- Key Lab of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
- Key Lab of Cotton and Rapeseed (Nanjing) of Ministry of Agriculture and Rural Affairs, Institute of the Industrial Crops, Jiangsu Academy of Agriculture Sciences, Nanjing 210014, China.
| | - Liu Zeng
- Key Lab of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Xiaoyu Ding
- Key Lab of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Yong Cheng
- Key Lab of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Xuekun Zhang
- Key Lab of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Xiling Zou
- Key Lab of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
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Cardinal-McTeague WM, Wurdack KJ, Sigel EM, Gillespie LJ. Seed size evolution and biogeography of Plukenetia (Euphorbiaceae), a pantropical genus with traditionally cultivated oilseed species. BMC Evol Biol 2019; 19:29. [PMID: 30670006 PMCID: PMC6341577 DOI: 10.1186/s12862-018-1308-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/23/2018] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Plukenetia is a small pantropical genus of lianas and vines with variably sized edible oil-rich seeds that presents an ideal system to investigate neotropical and pantropical diversification patterns and seed size evolution. We assessed the biogeography and seed evolution of Plukenetia through phylogenetic analyses of a 5069 character molecular dataset comprising five nuclear and two plastid markers for 86 terminals in subtribe Plukenetiinae (representing 20 of ~ 23 Plukenetia species). Two nuclear genes, KEA1 and TEB, were used for phylogenetic reconstruction for the first time. Our goals were: (1) produce a robust, time-dependent evolutionary framework for Plukenetia using BEAST; (2) reconstruct its biogeographical history with ancestral range estimation in BIOGEOBEARS; (3) define seed size categories; (4) identify patterns of seed size evolution using ancestral state estimation; and (5) conduct regression analyses with putative drivers of seed size using the threshold model. RESULTS Plukenetia was resolved into two major groups, which we refer to as the pinnately- and palmately-veined clades. Our analyses suggest Plukenetia originated in the Amazon or Atlantic Forest of Brazil during the Oligocene (28.7 Mya) and migrated/dispersed between those regions and Central America/Mexico throughout the Miocene. Trans-oceanic dispersals explain the pantropical distribution of Plukenetia, including from the Amazon to Africa in the Early Miocene (17.4 Mya), followed by Africa to Madagascar and Africa to Southeast Asia in the Late Miocene (9.4 Mya) and Pliocene (4.5 Mya), respectively. We infer a single origin of large seeds in the ancestor of Plukenetia. Seed size fits a Brownian motion model of trait evolution and is moderately to strongly associated with plant size, fruit type/dispersal syndrome, and seedling ecology. Biome shifts were not drivers of seed size, although there was a weak association with a transition to fire prone semi-arid savannas. CONCLUSIONS The major relationships among the species of Plukenetia are now well-resolved. Our biogeographical analyses support growing evidence that many pantropical distributions developed by periodic trans-oceanic dispersals throughout the Miocene and Pliocene. Selection on a combination of traits contributed to seed size variation, while movement between forest edge/light gap and canopy niches likely contributed to the seed size extremes in Plukenetia.
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Affiliation(s)
- Warren M. Cardinal-McTeague
- Department of Biology, University of Ottawa, Gendron Hall, Room 160, 30 Marie Curie, Ottawa, Ontario K1N 6N5 Canada
- Research and Collections, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, Ontario K1P 6P4 Canada
- Department of Botany, MRC-166, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012 USA
| | - Kenneth J. Wurdack
- Department of Botany, MRC-166, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012 USA
| | - Erin M. Sigel
- Department of Biology, University of Louisiana at Lafayette, Billeaud Hall, Room 108, 410 E. St. Mary Blvd, Lafayette, LA 70503 USA
| | - Lynn J. Gillespie
- Department of Biology, University of Ottawa, Gendron Hall, Room 160, 30 Marie Curie, Ottawa, Ontario K1N 6N5 Canada
- Research and Collections, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, Ontario K1P 6P4 Canada
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Zhang Q, Yu R, Sun D, Rahman MM, Xie L, Hu J, He L, Kilaru A, Niu L, Zhang Y. Comparative Transcriptome Analysis Reveals an Efficient Mechanism of α-Linolenic Acid in Tree Peony Seeds. Int J Mol Sci 2018; 20:ijms20010065. [PMID: 30586917 PMCID: PMC6337502 DOI: 10.3390/ijms20010065] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 12/14/2018] [Accepted: 12/21/2018] [Indexed: 01/29/2023] Open
Abstract
Tree peony (Paeonia section Moutan DC.) species are woody oil crops with high unsaturated fatty acid content, including α-linolenic acid (ALA/18:3; >40% of the total fatty acid). Comparative transcriptome analyses were carried out to uncover the underlying mechanisms responsible for high and low ALA content in the developing seeds of P. rockii and P. lutea, respectively. Expression analysis of acyl lipid metabolism genes revealed upregulation of select genes involved in plastidial fatty acid synthesis, acyl editing, desaturation, and triacylglycerol assembly in seeds of P. rockii relative to P. lutea. Also, in association with ALA content in seeds, transcript levels for fatty acid desaturases (SAD, FAD2, and FAD3), which encode enzymes necessary for polyunsaturated fatty acid synthesis, were higher in P. rockii compared to P. lutea. Furthermore, the overexpression of PrFAD2 and PrFAD3 in Arabidopsis increased linoleic and ALA content, respectively, and modulated the final ratio 18:2/18:3 in the seed oil. In conclusion, we identified the key steps and validated the necessary desaturases that contribute to efficient ALA synthesis in a woody oil crop. Together, these results will aid to increase essential fatty acid content in seeds of tree peonies and other crops of agronomic interest.
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Affiliation(s)
- Qingyu Zhang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling 712100, China.
| | - Rui Yu
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling 712100, China.
| | - Daoyang Sun
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling 712100, China.
| | - Md Mahbubur Rahman
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN 37614, USA.
| | - Lihang Xie
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling 712100, China.
| | - Jiayuan Hu
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling 712100, China.
| | - Lixia He
- Gansu Forestry Science and Technology Extend Station, Lanzhou 730046, China.
| | - Aruna Kilaru
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN 37614, USA.
| | - Lixin Niu
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling 712100, China.
| | - Yanlong Zhang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling 712100, China.
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Gan Y, Song Y, Chen Y, Liu H, Yang D, Xu Q, Zheng Z. Transcriptome analysis reveals a composite molecular map linked to unique seed oil profile of Neocinnamomum caudatum (Nees) Merr. BMC PLANT BIOLOGY 2018; 18:303. [PMID: 30477425 PMCID: PMC6258453 DOI: 10.1186/s12870-018-1525-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 11/14/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Neocinnamomum caudatum (Nees) Merr., a biodiesel tree species in the subtropical areas of South China, India and Burma, is distinctive from other species in Lauraceae family and its seed oil is rich in linoleic acid (18:2) and stearic acid (18:0). However, there is little genetic information about this species so far. In this study, a transcriptomic analysis on developing seeds of N. caudatum was conducted in an attempt to discern the molecular mechanisms involving the control of the fatty acid (FA) and triacylglycerol (TAG) biosynthesis. RESULTS Transcriptome analysis revealed 239,703 unigenes with an average length of 436 bp and 137 putative biomarkers that are related to FA formation and TAG biosynthesis. The expression patterns of genes encoding β-ketoacyl-acyl carrier protein synthase I (KASI), β- ketoacyl-acyl carrier protein synthase II (KASII), stearoyl-ACP desaturase (SAD), fatty acid desaturase 2 (FAD2), fatty acid desaturase 8 (FAD8) and acyl-ACP thioesterase A/B (FATA/B) were further validated by qRT-PCR. These genes displayed a very similar expression pattern in two distinct assays. Moreover, sequence analysis of different FATBs from diverse plant species revealed that NcFATB is structurally different from its counterpart in other species in producing medium-chain saturated FAs. Concertedly, heterologous expression of NcFATB in E. coli BL21 (DE3) strain showed that this corresponding expressed protein, NcFATB, prefers long-chain saturated fatty acyl-ACP over medium-chain fatty acyl-ACP as substrate. CONCLUSIONS Transcriptome analysis of developing N. caudatum seeds revealed a composite molecular map linked to the FA formation and oil biosynthesis in this biodiesel tree species. The substrate preference of NcFATB for long-chain saturated FAs is likely to contribute to its unique seed oil profile rich in stearic acid. Our findings demonstrate that in the tree species of Lauraceae family, the FATB enzymes producing long-chain FAs are structurally distinct from those producing medium-chain FAs, thereby suggesting that the FATB genes may serve as a biomarker for the classification of tree species of Lauraceae family.
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Affiliation(s)
- Yi Gan
- School of Agriculture and Food Sciences, Zhejiang A & F University, Zhejiang, 311300 Hangzhou China
| | - Yu Song
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303 Yunnan China
| | - Yadong Chen
- School of Agriculture and Food Sciences, Zhejiang A & F University, Zhejiang, 311300 Hangzhou China
| | - Hongbo Liu
- School of Agriculture and Food Sciences, Zhejiang A & F University, Zhejiang, 311300 Hangzhou China
| | - Dongdong Yang
- School of Agriculture and Food Sciences, Zhejiang A & F University, Zhejiang, 311300 Hangzhou China
| | - Qianyu Xu
- School of Agriculture and Food Sciences, Zhejiang A & F University, Zhejiang, 311300 Hangzhou China
| | - Zhifu Zheng
- School of Agriculture and Food Sciences, Zhejiang A & F University, Zhejiang, 311300 Hangzhou China
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18
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Hu XD, Pan BZ, Fu Q, Niu L, Chen MS, Xu ZF. De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in α-linolenic acid metabolism. BMC Genomics 2018; 19:380. [PMID: 29788925 PMCID: PMC5964912 DOI: 10.1186/s12864-018-4774-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Accepted: 05/09/2018] [Indexed: 12/12/2022] Open
Abstract
Background Sacha Inchi (Plukenetia volubilis L.), which belongs to the Euphorbiaceae, has been considered a new potential oil crop because of its high content of polyunsaturated fatty acids in its seed oil. The seed oil especially contains high amounts of α-linolenic acid (ALA), which is useful for the prevention of various diseases. However, little is known about the genetic information and genome sequence of Sacha Inchi, which has largely hindered functional genomics and molecular breeding studies. Results In this study, a de novo transcriptome assembly based on transcripts sequenced in eight major organs, including roots, stems, shoot apexes, mature leaves, male flowers, female flowers, fruits, and seeds of Sacha Inchi was performed, resulting in a set of 124,750 non-redundant putative transcripts having an average length of 851 bp and an N50 value of 1909 bp. Organ-specific unigenes analysis revealed that the most organ-specific transcripts are found in female flowers (2244 unigenes), whereas a relatively small amount of unigenes are detected to be expressed specifically in other organs with the least in stems (24 unigenes). A total of 42,987 simple sequence repeats (SSRs) were detected, which will contribute to the marker assisted selection breeding of Sacha Inchi. We analyzed expression of genes related to the α-linolenic acid metabolism based on the de novo assembly and annotation transcriptome in Sacha Inchi. It appears that Sacha Inchi accumulates high level of ALA in seeds by strong expression of biosynthesis-related genes and weak expression of degradation-related genes. In particular, the up-regulation of FAD3 and FAD7 is consistent with high level of ALA in seeds of Sacha Inchi compared with in other organs. Meanwhile, several transcription factors (ABI3, LEC1 and FUS3) may regulate key genes involved in oil accumulation in seeds of Sacha Inchi. Conclusions The transcriptome of major organs of Sacha Inchi has been sequenced and de novo assembled, which will expand the genetic information for functional genomic studies of Sacha Inchi. In addition, the identification of candidate genes involved in ALA metabolism will provide useful resources for the genetic improvement of Sacha Inchi and the metabolic engineering of ALA biosynthesis in other plants. Electronic supplementary material The online version of this article (10.1186/s12864-018-4774-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiao-Di Hu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bang-Zhen Pan
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
| | - Qiantang Fu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
| | - Longjian Niu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
| | - Mao-Sheng Chen
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
| | - Zeng-Fu Xu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China.
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Wang WF, Chen P, Lv J, Chen L, Sun YH. Transcriptomic analysis of topping-induced axillary shoot outgrowth in Nicotiana tabacum. Gene 2018; 646:169-180. [PMID: 29292191 DOI: 10.1016/j.gene.2017.12.053] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/11/2017] [Accepted: 12/27/2017] [Indexed: 12/16/2022]
Abstract
Topping is an important agronomic practice that significantly impacts the yield of various crop plants. Topping and the regulation of axillary shoot outgrowth are common agronomic practices in tobacco. However, the effects of topping on gene expression in tobacco remain unknown. We applied the Illumina HiSeq™ 2000 platform and analyzed differentially expressed genes (DEGs) from untopped and topped plants to study the global changes in gene expression in response to topping. We found that the number of DEGs varied from 7609 to 18,770 based on the reads per kilobase per million mapped reads (RPKM) values. The Gene Ontology (GO) enrichment analysis revealed that the cellular carbohydrate metabolic process and the disaccharide metabolic process, which may contribute to starch accumulation and stress/defense, were overrepresented terms for the DEGs. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that many DEGs were involved in starch and sucrose metabolism, glycolysis/gluconeogenesis, pyruvate metabolism, and plant hormone signal transduction, among other processes. The knowledge gained will improve our understanding of the processes of axillary shoot formation and enlargement at the transcriptional level. This study lays a solid foundation for future studies on molecular mechanisms underlying the growth of axillary shoots.
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Affiliation(s)
- Wei-Feng Wang
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Peng Chen
- College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Jing Lv
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Lei Chen
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Yu-He Sun
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
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20
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Fu Q, Niu L, Chen MS, Tao YB, Wang X, He H, Pan BZ, Xu ZF. De novo transcriptome assembly and comparative analysis between male and benzyladenine-induced female inflorescence buds of Plukenetia volubilis. JOURNAL OF PLANT PHYSIOLOGY 2018; 221:107-118. [PMID: 29275214 DOI: 10.1016/j.jplph.2017.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 12/04/2017] [Accepted: 12/04/2017] [Indexed: 05/27/2023]
Abstract
Plukenetia volubilis is a promising oilseed crop due to its seeds being rich in unsaturated fatty acids, especially alpha-linolenic acid. P. volubilis is monoecious, with separate male and female flowers on the same inflorescence. We previously reported that male flowers were converted to female flowers by exogenous cytokinin (6-benzyladenine, 6-BA) treatment in P. volubilis. To identify candidate genes associated with floral sex differentiation of P. volubilis, we performed de novo transcriptome assembly and comparative analysis on control male inflorescence buds (MIB) and female inflorescence buds (FIB) induced by 6-BA using Illumina sequencing technology. A total of 57,664 unigenes with an average length of 979 bp were assembled from 104.1 million clean reads, and 45,235 (78.45%) unigenes were successfully annotated in the public databases. Notably, Gene Ontology analyses revealed that 4193 and 3880 unigenes were enriched in the categories of reproduction and reproductive processes, respectively. Differential expression analysis identified 1385 differentially expressed unigenes between MIB and FIB, of which six unigenes related to cytokinin and auxin signaling pathways and 16 important transcription factor (TF) genes including MADS-box family members were identified. In particular, several unigenes encoding important TFs, such as homologs of CRABS CLAW, RADIALIS-like 1, RADIALIS-like 2, HECATE 2, WUSCHEL-related homeobox 9, and SUPERMAN, were expressed at higher levels in FIB than in MIB. The expression patterns of the 36 selected unigenes revealed by transcriptome analysis were successfully validated by quantitative real-time PCR. This study not only provides comprehensive gene expression profiles of P. volubilis inflorescence buds, but also lays the foundation for research on the molecular mechanism of floral sex determination in P. volubilis and other monoecious plants.
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Affiliation(s)
- Qiantang Fu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
| | - Longjian Niu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
| | - Mao-Sheng Chen
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
| | - Yan-Bin Tao
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
| | - Xiulan Wang
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
| | - Huiying He
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
| | - Bang-Zhen Pan
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
| | - Zeng-Fu Xu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China.
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21
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Yongfeng W, Aiquan Z, Fengli S, Mao L, Kaijie X, Chao Z, Shudong L, Yajun X. Using Transcriptome Analysis to Identify Genes Involved in Switchgrass Flower Reversion. FRONTIERS IN PLANT SCIENCE 2018; 9:1805. [PMID: 30564266 PMCID: PMC6288819 DOI: 10.3389/fpls.2018.01805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 11/20/2018] [Indexed: 05/06/2023]
Abstract
Floral reversion is a process in which differentiated floral organs revert back to vegetative organs. Although this phenomenon has been described for decades, the underlying molecular mechanisms remain unclear. In this study, we found that immature switchgrass (Panicum virgatum) inflorescences can revert to neonatal shoots when incubated on a basal medium with benzylaminopurine. We used anatomical and histological methods to verify that these shoots were formed from floret primordia through flower reversion. To further explore the gene regulation of floral reversion in switchgrass, the transcriptome of reversed, unreversed, and uncultured immature inflorescences were analyzed and 517 genes were identified as participating in flower reversion. Annotation using non-redundant databases revealed that these genes are involved in plant hormone biosynthesis and signal transduction, starch and sucrose metabolism, DNA replication and modification, and other processes crucial for switchgrass flower reversion. When four of the genes were overexpressed in Arabidopsis thaliana, vegetative growth was facilitated and reproductive growth was inhibited in transgenic plants. This study provides a basic understanding of genes regulating the floral transition in switchgrass and will promote the research of floral reversion and flower maintenance.
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Affiliation(s)
- Wang Yongfeng
- College of Agronomy, Northwest A&F University, Yangling, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, China
| | - Zheng Aiquan
- College of Agronomy, Northwest A&F University, Yangling, China
- Yangling Vocational & Technical College, Yangling, China
| | - Sun Fengli
- College of Agronomy, Northwest A&F University, Yangling, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, China
| | - Li Mao
- College of Agronomy, Northwest A&F University, Yangling, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, China
| | - Xu Kaijie
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhang Chao
- College of Agronomy, Northwest A&F University, Yangling, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, China
| | - Liu Shudong
- College of Agronomy, Northwest A&F University, Yangling, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, China
| | - Xi Yajun
- College of Agronomy, Northwest A&F University, Yangling, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, China
- *Correspondence: Xi Yajun,
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Zhang QY, Yu R, Xie LH, Rahman MM, Kilaru A, Niu LX, Zhang YL. Fatty Acid and Associated Gene Expression Analyses of Three Tree Peony Species Reveal Key Genes for α-Linolenic Acid Synthesis in Seeds. FRONTIERS IN PLANT SCIENCE 2018; 9:106. [PMID: 29459881 PMCID: PMC5807371 DOI: 10.3389/fpls.2018.00106] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/19/2018] [Indexed: 05/22/2023]
Abstract
The increasing demand for healthy edible oil has generated the need to identify promising oil crops. Tree peony (Paeonia section Moutan DC.) is a woody oil crop with α-linolenic acid (ALA) contributing for 45% of the total fatty acid (FA) content in seeds. Molecular and genetic differences that contribute to varied FA content and composition among the wild peony species are, however, poorly understood. Analyses of FA content and composition during seed development in three tree peony species (Paeonia rockii, P. potaninii, and P. lutea) showed varied FA content among them with highest in P. rockii, followed by P. potaninii, and P. lutea. Total FA content among these species increased with seed development and reached its maximum in its final stage. Seed FA composition analysis of the three species also revealed that ALA (C18:3) was the most abundant, followed by oleic (C18:1) and linoleic (C18:2) acids. Additionally, quantitative real-time RT-PCR analyses of 10 key seed oil synthesis genes in the three tree peony species revealed that FAD3, FAD2, β-PDHC, LPAAT, and Oleosin gene expression levels positively correlate with total FA content and rate of accumulation. Specifically, the abundance of FAD3 transcripts in P. rockii compared with P. potaninii, and P. lutea suggests that FAD3 might play an important role in synthesis of ALA via phosphatidylcholine-derived pathway. Overall, comparative analyses of FA content and composition in three different peony species revealed a correlation between efficient lipid accumulation and lipid gene expression during seed development. Further characterization and metabolic engineering of these key genes from peonies will allow for subsequent improvement of tree peony oil quality and production.
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Affiliation(s)
- Qing-Yu Zhang
- College of Landscape Architecture and Arts, Northwest A&F University, Xianyang, China
| | - Rui Yu
- College of Landscape Architecture and Arts, Northwest A&F University, Xianyang, China
| | - Li-Hang Xie
- College of Landscape Architecture and Arts, Northwest A&F University, Xianyang, China
| | - Md Mahbubur Rahman
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, United States
| | - Aruna Kilaru
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, United States
| | - Li-Xin Niu
- College of Landscape Architecture and Arts, Northwest A&F University, Xianyang, China
- *Correspondence: Yan-Long Zhang, ; Li-Xin Niu,
| | - Yan-Long Zhang
- College of Landscape Architecture and Arts, Northwest A&F University, Xianyang, China
- *Correspondence: Yan-Long Zhang, ; Li-Xin Niu,
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Zhang T, Song C, Song L, Shang Z, Yang S, Zhang D, Sun W, Shen Q, Zhao D. RNA Sequencing and Coexpression Analysis Reveal Key Genes Involved in α-Linolenic Acid Biosynthesis in Perilla frutescens Seed. Int J Mol Sci 2017; 18:ijms18112433. [PMID: 29144390 PMCID: PMC5713401 DOI: 10.3390/ijms18112433] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/09/2017] [Accepted: 11/15/2017] [Indexed: 12/24/2022] Open
Abstract
Perilla frutescen is used as traditional food and medicine in East Asia. Its seeds contain high levels of α-linolenic acid (ALA), which is important for health, but is scarce in our daily meals. Previous reports on RNA-seq of perilla seed had identified fatty acid (FA) and triacylglycerol (TAG) synthesis genes, but the underlying mechanism of ALA biosynthesis and its regulation still need to be further explored. So we conducted Illumina RNA-sequencing in seven temporal developmental stages of perilla seeds. Sequencing generated a total of 127 million clean reads, containing 15.88 Gb of valid data. The de novo assembly of sequence reads yielded 64,156 unigenes with an average length of 777 bp. A total of 39,760 unigenes were annotated and 11,693 unigenes were found to be differentially expressed in all samples. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, 486 unigenes were annotated in the “lipid metabolism” pathway. Of these, 150 unigenes were found to be involved in fatty acid (FA) biosynthesis and triacylglycerol (TAG) assembly in perilla seeds. A coexpression analysis showed that a total of 104 genes were highly coexpressed (r > 0.95). The coexpression network could be divided into two main subnetworks showing over expression in the medium or earlier and late phases, respectively. In order to identify the putative regulatory genes, a transcription factor (TF) analysis was performed. This led to the identification of 45 gene families, mainly including the AP2-EREBP, bHLH, MYB, and NAC families, etc. After coexpression analysis of TFs with highly expression of FAD2 and FAD3 genes, 162 TFs were found to be significantly associated with two FAD genes (r > 0.95). Those TFs were predicted to be the key regulatory factors in ALA biosynthesis in perilla seed. The qRT-PCR analysis also verified the relevance of expression pattern between two FAD genes and partial candidate TFs. Although it has been reported that some TFs are involved in seed development, more direct evidence is still needed to verify their function. However, these findings can provide clues to reveal the possible molecular mechanisms of ALA biosynthesis and its regulation in perilla seed.
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Affiliation(s)
- Tianyuan Zhang
- Rapeseed Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, China.
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang 550025, China.
| | - Chi Song
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Li Song
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang 550025, China.
| | - Zhiwei Shang
- Rapeseed Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, China.
| | - Sen Yang
- Rapeseed Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, China.
| | - Dong Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Qi Shen
- Rapeseed Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, China.
| | - Degang Zhao
- Rapeseed Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, China.
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang 550025, China.
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Sreedhar RV, Prasad P, Reddy LPA, Rajasekharan R, Srinivasan M. Unravelling a stearidonic acid-rich triacylglycerol biosynthetic pathway in the developing seeds of Buglossoides arvensis: A transcriptomic landscape. Sci Rep 2017; 7:10473. [PMID: 28874672 PMCID: PMC5585386 DOI: 10.1038/s41598-017-09882-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 07/31/2017] [Indexed: 01/07/2023] Open
Abstract
Buglossoides arvensis is an emerging oilseed crop that is rich in stearidonic acid (SDA) and has several potential applications in human health and nutrition. The molecular basis of SDA biosynthesis in this plant remains unknown due to lack of genomic information. To unravel key genes involved in SDA-rich triacylglycerol (TAG) biosynthesis, we performed transcriptome sequencing of pooled mRNA from five different developmental stages of B. arvensis seeds using Illumina NextSeq platform. De novo transcriptome assembly generated 102,888 clustered transcripts from 39.83 million high-quality reads. Of these, 62.1% and 55.54% of transcripts were functionally annotated using Uniprot-Viridiplantae and KOG databases, respectively. A total of 10,021 SSR-containing sequences were identified using the MISA tool. Deep mining of transcriptome assembly using in silico tools led to the identification of genes involved in fatty acid and TAG biosynthesis. Expression profiling of 17 key transcripts involved in fatty acid desaturation and TAG biosynthesis showed expression patterns specific to the development stage that positively correlated with polyunsaturated fatty acid accumulation in the developing seeds. This first comprehensive transcriptome analysis provides the basis for future research on understanding molecular mechanisms of SDA-rich TAG accumulation in B. arvensis and aids in biotechnological production of SDA in other oilseed crops.
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Affiliation(s)
- R V Sreedhar
- Department of Lipid Science, CSIR-Central Food Technological Research Institute (CSIR-CFTRI), Mysuru, 570020, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-Central Food Technological Research Institute Campus, Mysuru, 570020, India
| | - P Prasad
- Department of Lipid Science, CSIR-Central Food Technological Research Institute (CSIR-CFTRI), Mysuru, 570020, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-Central Food Technological Research Institute Campus, Mysuru, 570020, India
| | - L Prasanna Anjaneya Reddy
- Department of Lipid Science, CSIR-Central Food Technological Research Institute (CSIR-CFTRI), Mysuru, 570020, India
| | - Ram Rajasekharan
- Department of Lipid Science, CSIR-Central Food Technological Research Institute (CSIR-CFTRI), Mysuru, 570020, India
| | - Malathi Srinivasan
- Department of Lipid Science, CSIR-Central Food Technological Research Institute (CSIR-CFTRI), Mysuru, 570020, India.
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26
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Kim HU, Lee KR, Shim D, Lee JH, Chen GQ, Hwang S. Transcriptome analysis and identification of genes associated with ω-3 fatty acid biosynthesis in Perilla frutescens (L.) var. frutescens. BMC Genomics 2016; 17:474. [PMID: 27342315 PMCID: PMC4920993 DOI: 10.1186/s12864-016-2805-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/27/2016] [Indexed: 12/02/2022] Open
Abstract
Background Perilla (Perilla frutescens (L.) var frutescens) produces high levels of α-linolenic acid (ALA), a ω-3 fatty acid important to health and development. To uncover key genes involved in fatty acid (FA) and triacylglycerol (TAG) synthesis in perilla, we conducted deep sequencing of cDNAs from developing seeds and leaves for understanding the mechanism underlying ALA and seed TAG biosynthesis. Results Perilla cultivar Dayudeulkkae contains 66.0 and 56.2 % ALA in seeds and leaves, respectively. Using Illumina HiSeq 2000, we have generated a total of 392 megabases of raw sequences from four mRNA samples of seeds at different developmental stages and one mature leaf sample of Dayudeulkkae. De novo assembly of these sequences revealed 54,079 unique transcripts, of which 32,237 belong to previously annotated genes. Among the annotated genes, 66.5 % (21,429 out of 32,237) showed highest sequences homology with the genes from Mimulus guttatus, a species placed under the same Lamiales order as perilla. Using Arabidopsis acyl-lipid genes as queries, we searched the transcriptome and identified 540 unique perilla genes involved in all known pathways of acyl-lipid metabolism. We characterized the expression profiles of 43 genes involved in FA and TAG synthesis using quantitative PCR. Key genes were identified through sequence and gene expression analyses. Conclusions This work is the first report on building transcriptomes from perilla seeds. The work also provides the first comprehensive expression profiles for genes involved in seed oil biosynthesis. Bioinformatic analysis indicated that our sequence collection represented a major transcriptomic resource for perilla that added valuable genetic information in order Lamiales. Our results provide critical information not only for studies of the mechanisms involved in ALA synthesis, but also for biotechnological production of ALA in other oilseeds. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2805-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hyun Uk Kim
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul, 05006, Republic of Korea.
| | - Kyeong-Ryeol Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Science, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - Donghwan Shim
- Department of Forest Genetic Resources, National Institute of Forest Science, Suwon, 16631, Republic of Korea
| | | | - Grace Q Chen
- U.S. Department of Agriculture, Western Regional Research Center, Agricultural Research Service, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Seongbin Hwang
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul, 05006, Republic of Korea
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27
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Kim HU, Lee KR, Shim D, Lee JH, Chen GQ, Hwang S. Transcriptome analysis and identification of genes associated with ω-3 fatty acid biosynthesis in Perilla frutescens (L.) var. frutescens. BMC Genomics 2016; 17:474. [PMID: 27342315 DOI: 10.1186/s12864-016-2805-2800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/27/2016] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Perilla (Perilla frutescens (L.) var frutescens) produces high levels of α-linolenic acid (ALA), a ω-3 fatty acid important to health and development. To uncover key genes involved in fatty acid (FA) and triacylglycerol (TAG) synthesis in perilla, we conducted deep sequencing of cDNAs from developing seeds and leaves for understanding the mechanism underlying ALA and seed TAG biosynthesis. RESULTS Perilla cultivar Dayudeulkkae contains 66.0 and 56.2 % ALA in seeds and leaves, respectively. Using Illumina HiSeq 2000, we have generated a total of 392 megabases of raw sequences from four mRNA samples of seeds at different developmental stages and one mature leaf sample of Dayudeulkkae. De novo assembly of these sequences revealed 54,079 unique transcripts, of which 32,237 belong to previously annotated genes. Among the annotated genes, 66.5 % (21,429 out of 32,237) showed highest sequences homology with the genes from Mimulus guttatus, a species placed under the same Lamiales order as perilla. Using Arabidopsis acyl-lipid genes as queries, we searched the transcriptome and identified 540 unique perilla genes involved in all known pathways of acyl-lipid metabolism. We characterized the expression profiles of 43 genes involved in FA and TAG synthesis using quantitative PCR. Key genes were identified through sequence and gene expression analyses. CONCLUSIONS This work is the first report on building transcriptomes from perilla seeds. The work also provides the first comprehensive expression profiles for genes involved in seed oil biosynthesis. Bioinformatic analysis indicated that our sequence collection represented a major transcriptomic resource for perilla that added valuable genetic information in order Lamiales. Our results provide critical information not only for studies of the mechanisms involved in ALA synthesis, but also for biotechnological production of ALA in other oilseeds.
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Affiliation(s)
- Hyun Uk Kim
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul, 05006, Republic of Korea.
| | - Kyeong-Ryeol Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Science, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - Donghwan Shim
- Department of Forest Genetic Resources, National Institute of Forest Science, Suwon, 16631, Republic of Korea
| | | | - Grace Q Chen
- U.S. Department of Agriculture, Western Regional Research Center, Agricultural Research Service, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Seongbin Hwang
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul, 05006, Republic of Korea
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28
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Zhang Y, Mulpuri S, Liu A. High light exposure on seed coat increases lipid accumulation in seeds of castor bean (Ricinus communis L.), a nongreen oilseed crop. PHOTOSYNTHESIS RESEARCH 2016; 128:125-140. [PMID: 26589321 DOI: 10.1007/s11120-015-0206-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Accepted: 11/14/2015] [Indexed: 06/05/2023]
Abstract
Little was known on how sunlight affects the seed metabolism in nongreen seeds. Castor bean (Ricinus communis L.) is a typical nongreen oilseed crop and its seed oil is an important feedstock in industry. In this study, photosynthetic activity of seed coat tissues of castor bean in natural conditions was evaluated in comparison to shaded conditions. Our results indicate that exposure to high light enhances photosynthetic activity in seed coats and consequently increases oil accumulation. Consistent results were also reached using cultured seeds. High-throughput RNA-Seq analyses further revealed that genes involved in photosynthesis and carbon conversion in both the Calvin-Benson cycle and malate transport were differentially expressed between seeds cultured under light and dark conditions, implying several venues potentially contributing to light-enhanced lipid accumulation such as increased reducing power and CO2 refixation which underlie the overall lipid biosynthesis. This study demonstrated the effects of light exposure on oil accumulation in nongreen oilseeds and greatly expands our understanding of the physiological roles that light may play during seed development in nongreen oilseeds. Essentially, our studies suggest that potential exists to enhance castor oil yield through increasing exposure of the inflorescences to sunlight either by genetically changing the plant architecture (smart canopy) or its growing environment.
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Affiliation(s)
- Yang Zhang
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 88 Xuefu Road, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sujatha Mulpuri
- Indian Institute of Oilseeds Research, Rajendranagar, Hyderabad, 500 030, India
| | - Aizhong Liu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650204, China.
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29
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Honaas LA, Wafula EK, Wickett NJ, Der JP, Zhang Y, Edger PP, Altman NS, Pires JC, Leebens-Mack JH, dePamphilis CW. Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome. PLoS One 2016; 11:e0146062. [PMID: 26731733 PMCID: PMC4701411 DOI: 10.1371/journal.pone.0146062] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/11/2015] [Indexed: 12/29/2022] Open
Abstract
Whereas de novo assemblies of RNA-Seq data are being published for a growing number of species across the tree of life, there are currently no broadly accepted methods for evaluating such assemblies. Here we present a detailed comparison of 99 transcriptome assemblies, generated with 6 de novo assemblers including CLC, Trinity, SOAP, Oases, ABySS and NextGENe. Controlled analyses of de novo assemblies for Arabidopsis thaliana and Oryza sativa transcriptomes provide new insights into the strengths and limitations of transcriptome assembly strategies. We find that the leading assemblers generate reassuringly accurate assemblies for the majority of transcripts. At the same time, we find a propensity for assemblers to fail to fully assemble highly expressed genes. Surprisingly, the instance of true chimeric assemblies is very low for all assemblers. Normalized libraries are reduced in highly abundant transcripts, but they also lack 1000s of low abundance transcripts. We conclude that the quality of de novo transcriptome assemblies is best assessed through consideration of a combination of metrics: 1) proportion of reads mapping to an assembly 2) recovery of conserved, widely expressed genes, 3) N50 length statistics, and 4) the total number of unigenes. We provide benchmark Illumina transcriptome data and introduce SCERNA, a broadly applicable modular protocol for de novo assembly improvement. Finally, our de novo assembly of the Arabidopsis leaf transcriptome revealed ~20 putative Arabidopsis genes lacking in the current annotation.
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Affiliation(s)
- Loren A Honaas
- Biology Department, Penn State, University Park, Pennsylvania, 16802, United States of America
| | - Eric K Wafula
- Biology Department, Penn State, University Park, Pennsylvania, 16802, United States of America
| | - Norman J Wickett
- Biology Department, Penn State, University Park, Pennsylvania, 16802, United States of America
| | - Joshua P Der
- Biology Department, Penn State, University Park, Pennsylvania, 16802, United States of America
| | - Yeting Zhang
- Biology Department, Penn State, University Park, Pennsylvania, 16802, United States of America
| | - Patrick P Edger
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, 65211, United States of America
| | - Naomi S Altman
- Department of Statistics, Penn State, University Park, Pennsylvania, 16802, United States of America
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, 65211, United States of America
| | - James H Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, Georgia, 30602, United States of America
| | - Claude W dePamphilis
- Biology Department, Penn State, University Park, Pennsylvania, 16802, United States of America
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30
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Patnaik BB, Hwang HJ, Kang SW, Park SY, Wang TH, Park EB, Chung JM, Song DK, Kim C, Kim S, Lee JB, Jeong HC, Park HS, Han YS, Lee YS. Transcriptome Characterization for Non-Model Endangered Lycaenids, Protantigius superans and Spindasis takanosis, Using Illumina HiSeq 2500 Sequencing. Int J Mol Sci 2015; 16:29948-70. [PMID: 26694362 PMCID: PMC4691156 DOI: 10.3390/ijms161226213] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 11/28/2015] [Accepted: 12/09/2015] [Indexed: 11/22/2022] Open
Abstract
The Lycaenidae butterflies, Protantigius superans and Spindasis takanosis, are endangered insects in Korea known for their symbiotic association with ants. However, necessary genomic and transcriptomics data are lacking in these species, limiting conservation efforts. In this study, the P. superans and S. takanosis transcriptomes were deciphered using Illumina HiSeq 2500 sequencing. The P. superans and S. takanosis transcriptome data included a total of 254,340,693 and 245,110,582 clean reads assembled into 159,074 and 170,449 contigs and 107,950 and 121,140 unigenes, respectively. BLASTX hits (E-value of 1.0 × 10−5) against the known protein databases annotated a total of 46,754 and 51,908 transcripts for P. superans and S. takanosis. Approximately 41.25% and 38.68% of the unigenes for P. superans and S. takanosis found homologous sequences in Protostome DB (PANM-DB). BLAST2GO analysis confirmed 18,611 unigenes representing Gene Ontology (GO) terms and a total of 5259 unigenes assigned to 116 pathways for P. superans. For S. takanosis, a total of 6697 unigenes were assigned to 119 pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. Additionally, 382,164 and 390,516 Simple Sequence Repeats (SSRs) were compiled from the unigenes of P. superans and S. takanosis, respectively. This is the first report to record new genes and their utilization for conservation of lycaenid species population and as a reference information for closely related species.
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Affiliation(s)
- Bharat Bhusan Patnaik
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
- Trident School of Biotech Sciences, Trident Academy of Creative Technology (TACT), Chandaka Industrial Estate, Chandrasekharpur, Bhubaneswar, Odisha 751024, India.
| | - Hee-Ju Hwang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - Se Won Kang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - So Young Park
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - Tae Hun Wang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - Eun Bi Park
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - Jong Min Chung
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - Dae Kwon Song
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - Changmu Kim
- National Institute of Biological Resources, 42, Hwangyeong-ro, Seo-gu, Incheon 22689, Korea.
| | - Soonok Kim
- National Institute of Biological Resources, 42, Hwangyeong-ro, Seo-gu, Incheon 22689, Korea.
| | - Jae Bong Lee
- Korea Zoonosis Research Institute (KOZRI), Chonbuk National University, 820-120 Hana-ro, Iksan, Jeollabuk-do 54528, Korea.
| | - Heon Cheon Jeong
- Hampyeong County Insect Institute, Hampyeong County Agricultural Technology Center, 90, Hakgyohwasan-gil, Hakgyo-myeon, Hampyeong-gun, Jeollanan-do 57158, Korea.
| | - Hong Seog Park
- Research Institute, GnC BIO Co., LTD. 621-6 Banseok-dong, Yuseong-gu, Daejeon 34069, Korea.
| | - Yeon Soo Han
- College of Agriculture and Life Science, Chonnam National University 77 Yongbong-ro, Buk-gu, Gwangju 61186, Korea.
| | - Yong Seok Lee
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
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31
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Muriira NG, Xu W, Muchugi A, Xu J, Liu A. De novo sequencing and assembly analysis of transcriptome in the Sodom apple (Calotropis gigantea). BMC Genomics 2015; 16:723. [PMID: 26395839 PMCID: PMC4580217 DOI: 10.1186/s12864-015-1908-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/09/2015] [Indexed: 11/18/2022] Open
Abstract
Background The Sodom apple (Calotropis gigantea), a member of the Asclepiadaceae family, is a large evergreen shrub native to continental Asia and northern Africa. As an important medicinal shrub and a fiber resource plant, there is an urgent need for developing molecular markers to facilitate breeding and genetic improvement of varieties. Results In this study, using the Illumina high throughput sequencing technique we obtained about 45 million paired end sequencing reads, De novo assembled and generated a total of 133,634 transcripts with a mean of 1837.47 bp in length. Based on protein homology searches against available databases, a total of 21,851 unigenes were functionally annotated. In particular, many transcripts that encode for putative proteins involved in fiber and secondary metabolite biosynthesis were identified and analyzed. Key fiber genes identified were validated experimentally through Real-Time PCR technique. Various transcription factors involved in regulating plant response to abiotic stress were also identified. In addition, based on the unigene sequences assembled, 11,623 microsatellites loci were detected, which provide very useful resources for developing microsatellite molecular markers. Conclusion This study is the first report on transcriptome information in the Calotropis species and provides rich gene transcript resources for conducting further studies on understanding the molecular basis of fiber and secondary metabolite biosynthesis, serving the genetic improvement and resource utilization in Calotropis plants. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1908-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nkatha G Muriira
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, Heilongtan, Kunming, 650201, Yunnan, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,World Agroforestry Centre, East and Central Asia Office, 132 Lanhei Road, Kunming, 650201, China. .,World Agroforestry Centre (ICRAF), P.O. Box 30677-00100, Nairobi, Kenya.
| | - Wei Xu
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, Heilongtan, Kunming, 650201, Yunnan, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Alice Muchugi
- World Agroforestry Centre (ICRAF), P.O. Box 30677-00100, Nairobi, Kenya.
| | - Jianchu Xu
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, Heilongtan, Kunming, 650201, Yunnan, China. .,World Agroforestry Centre, East and Central Asia Office, 132 Lanhei Road, Kunming, 650201, China.
| | - Aizhong Liu
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, Heilongtan, Kunming, 650201, Yunnan, China.
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Wang X, Zhou C, Yang X, Miao D, Zhang Y. De Novo Transcriptome Analysis of Warburgia ugandensis to Identify Genes Involved in Terpenoids and Unsaturated Fatty Acids Biosynthesis. PLoS One 2015; 10:e0135724. [PMID: 26305373 PMCID: PMC4549110 DOI: 10.1371/journal.pone.0135724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Accepted: 07/24/2015] [Indexed: 12/24/2022] Open
Abstract
The bark of Warburgia ugandensis (Canellaceae family) has been used as a medicinal source for a long history in many African countries. The presence of diverse terpenoids and abundant polyunsaturated fatty acids (PUFAs) in this organ contributes to its broad range of pharmacological properties. Despite its medicinal and economic importance, the knowledge on the biosynthesis of terpenoid and unsaturated fatty acid in W. ugandensis bark remains largely unknown. Therefore, it is necessary to construct a genomic and/or transcriptomic database for the functional genomics study on W. ugandensis. The chemical profiles of terpenoids and fatty acids between the bark and leaves of W. ugandensis were compared by gas chromatography-mass spectrometry (GC-MS) analysis. Meanwhile, the transcriptome database derived from both tissues was created using Illumina sequencing technology. In total, about 17.1 G clean nucleotides were obtained, and de novo assembled into 72,591 unigenes, of which about 38.06% can be aligned to the NCBI non-redundant protein database. Many candidate genes in the biosynthetic pathways of terpenoids and unsaturated fatty acids were identified, including 14 unigenes for terpene synthases. Furthermore, 2,324 unigenes were discovered to be differentially expressed between both tissues; the functions of those differentially expressed genes (DEGs) were predicted by gene ontology enrichment and metabolic pathway enrichment analyses. In addition, the expression of 12 DEGs with putative roles in terpenoid and unsaturated fatty acid metabolic pathways was confirmed by qRT-PCRs, which was consistent with the data of the RNA-sequencing. In conclusion, we constructed a comprehensive transcriptome dataset derived from the bark and leaf of W. ugandensis, which forms the basis for functional genomics studies on this plant species. Particularly, the comparative analysis of the transcriptome data between the bark and leaf will provide critical clues to reveal the regulatory mechanisms underlying the biosynthesis of terpenoids and PUFAs in W. ugandensis.
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Affiliation(s)
- Xin Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Chen Zhou
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Xianpeng Yang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Di Miao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Yansheng Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
- * E-mail:
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Yang M, Zhu L, Pan C, Xu L, Liu Y, Ke W, Yang P. Transcriptomic Analysis of the Regulation of Rhizome Formation in Temperate and Tropical Lotus (Nelumbo nucifera). Sci Rep 2015; 5:13059. [PMID: 26279185 PMCID: PMC4538393 DOI: 10.1038/srep13059] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 07/10/2015] [Indexed: 12/21/2022] Open
Abstract
Rhizome is the storage organ of lotus derived from modified stems. The development of rhizome is a complex process and depends on the balanced expression of the genes that is controlled by environmental and endogenous factors. However, little is known about the mechanism that regulates rhizome girth enlargement. In this study, using RNA-seq, transcriptomic analyses were performed at three rhizome developmental stages-the stolon, middle swelling and later swelling stage -in the cultivars 'ZO' (temperate lotus with enlarged rhizome) and 'RL' (tropical lotus with stolon). About 348 million high-quality reads were generated, and 88.5% of the data were mapped to the reference genome. Of 26783 genes identified, 24069 genes were previously predicted in the reference, and 2714 genes were novel transcripts. Moreover, 8821 genes were differentially expressed between the cultivars at the three stages. Functional analysis identified that these genes were significantly enriched in pathways carbohydrate metabolism and plant hormone signal transduction. Twenty-two genes involved in photoperiod pathway, starch metabolism and hormone signal transduction were candidate genes inducing rhizome girth enlargement. Comparative transcriptomic analysis detected several differentially expressed genes and potential candidate genes required for rhizome girth enlargement, which lay a foundation for future studies on molecular mechanisms underlying rhizome formation.
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Affiliation(s)
- Mei Yang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, Hubei, China
| | - Lingping Zhu
- 1] Key Laboratory of Aquatic Plant and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, Hubei, China [2] University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng Pan
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, Hubei, China
| | - Liming Xu
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, Hubei, China
| | - Yanling Liu
- Key Laboratory of Aquatic Plant and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, Hubei, China
| | - Weidong Ke
- National Garden of Aquatic Vegetable, Wuhan Institute of Vegetable Science, Wuhan 430065, Hubei, China
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, Hubei, China
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Niu L, Tao YB, Chen MS, Fu Q, Li C, Dong Y, Wang X, He H, Xu ZF. Selection of Reliable Reference Genes for Gene Expression Studies of a Promising Oilseed Crop, Plukenetia volubilis, by Real-Time Quantitative PCR. Int J Mol Sci 2015; 16:12513-30. [PMID: 26047338 PMCID: PMC4490458 DOI: 10.3390/ijms160612513] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Accepted: 05/22/2015] [Indexed: 01/08/2023] Open
Abstract
Real-time quantitative PCR (RT-qPCR) is a reliable and widely used method for gene expression analysis. The accuracy of the determination of a target gene expression level by RT-qPCR demands the use of appropriate reference genes to normalize the mRNA levels among different samples. However, suitable reference genes for RT-qPCR have not been identified in Sacha inchi (Plukenetia volubilis), a promising oilseed crop known for its polyunsaturated fatty acid (PUFA)-rich seeds. In this study, using RT-qPCR, twelve candidate reference genes were examined in seedlings and adult plants, during flower and seed development and for the entire growth cycle of Sacha inchi. Four statistical algorithms (delta cycle threshold (ΔCt), BestKeeper, geNorm, and NormFinder) were used to assess the expression stabilities of the candidate genes. The results showed that ubiquitin-conjugating enzyme (UCE), actin (ACT) and phospholipase A22 (PLA) were the most stable genes in Sacha inchi seedlings. For roots, stems, leaves, flowers, and seeds from adult plants, 30S ribosomal protein S13 (RPS13), cyclophilin (CYC) and elongation factor-1alpha (EF1α) were recommended as reference genes for RT-qPCR. During the development of reproductive organs, PLA, ACT and UCE were the optimal reference genes for flower development, whereas UCE, RPS13 and RNA polymerase II subunit (RPII) were optimal for seed development. Considering the entire growth cycle of Sacha inchi, UCE, ACT and EF1α were sufficient for the purpose of normalization. Our results provide useful guidelines for the selection of reliable reference genes for the normalization of RT-qPCR data for seedlings and adult plants, for reproductive organs, and for the entire growth cycle of Sacha inchi.
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Affiliation(s)
- Longjian Niu
- School of Life Sciences, University of Science and Technology of China, Hefei 230027, China.
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China.
| | - Yan-Bin Tao
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China.
| | - Mao-Sheng Chen
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China.
| | - Qiantang Fu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China.
| | - Chaoqiong Li
- Department of Life Sciences, College of Life Science and Agriculture, Zhoukou Normal University, Zhoukou 466001, China.
| | - Yuling Dong
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China.
| | - Xiulan Wang
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China.
| | - Huiying He
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China.
| | - Zeng-Fu Xu
- School of Life Sciences, University of Science and Technology of China, Hefei 230027, China.
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China.
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Li SS, Wang LS, Shu QY, Wu J, Chen LG, Shao S, Yin DD. Fatty acid composition of developing tree peony (Paeonia section Moutan DC.) seeds and transcriptome analysis during seed development. BMC Genomics 2015; 16:208. [PMID: 25887415 PMCID: PMC4404109 DOI: 10.1186/s12864-015-1429-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 03/02/2015] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Tree peony (Paeonia section Moutan DC.) is known for its excellent ornamental and medicinal values. In 2011, seeds from P. ostii have been identified as novel resource of α-linolenic acid (ALA) for seed oil production and development in China. However, the molecular mechanism on biosynthesis of unsaturated fatty acids in tree peony seeds remains unknown. Therefore, transcriptome data is needed to better understand the underlying mechanisms. RESULTS In this study, lipid accumulation contents were measured using GC-MS methods across developing tree peony seeds, which exhibited an extraordinary ALA content (49.3%) in P. ostii mature seeds. Transcriptome analysis was performed using Illumina sequencing platform. A total of 144 million 100-bp paired-end reads were generated from six libraries, which identified 175,874 contigs. In the KEGG Orthology enrichment of differentially expressed genes, lipid metabolism pathways were highly represented categories. Using this data we identified 388 unigenes that may be involved in de novo fatty acid and triacylglycerol biosynthesis. In particular, three unigenes (SAD, FAD2 and FAD8) encoding fatty acid desaturase with high expression levels in the fast oil accumulation stage compared with the initial stage of seed development were identified. CONCLUSIONS This study provides the first comprehensive genomic resources characterizing tree peony seeds gene expression at the transcriptional level. These data lay the foundation for further understanding of molecular mechanism responsible for lipid biosynthesis and the high unsaturated fatty acids (especially ALA) accumulation. Meanwhile, it provides theoretical base for potential oilseed application in the respect of n-6 to n-3 ratio for human diets and future regulation of target healthy components of oils.
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Affiliation(s)
- Shan-Shan Li
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Liang-Sheng Wang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Qing-Yan Shu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Jie Wu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Li-Guang Chen
- Institute of Forest Protection, Chinese Academy of Forestry, Beijing, 100091, China. van--
| | - Shuai Shao
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Dan-Dan Yin
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Li SS, Wang LS, Shu QY, Wu J, Chen LG, Shao S, Yin DD. Fatty acid composition of developing tree peony (Paeonia section Moutan DC.) seeds and transcriptome analysis during seed development. BMC Genomics 2015; 16:208. [PMID: 25887415 DOI: 10.1186/s12864-015-1429-1420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 03/02/2015] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Tree peony (Paeonia section Moutan DC.) is known for its excellent ornamental and medicinal values. In 2011, seeds from P. ostii have been identified as novel resource of α-linolenic acid (ALA) for seed oil production and development in China. However, the molecular mechanism on biosynthesis of unsaturated fatty acids in tree peony seeds remains unknown. Therefore, transcriptome data is needed to better understand the underlying mechanisms. RESULTS In this study, lipid accumulation contents were measured using GC-MS methods across developing tree peony seeds, which exhibited an extraordinary ALA content (49.3%) in P. ostii mature seeds. Transcriptome analysis was performed using Illumina sequencing platform. A total of 144 million 100-bp paired-end reads were generated from six libraries, which identified 175,874 contigs. In the KEGG Orthology enrichment of differentially expressed genes, lipid metabolism pathways were highly represented categories. Using this data we identified 388 unigenes that may be involved in de novo fatty acid and triacylglycerol biosynthesis. In particular, three unigenes (SAD, FAD2 and FAD8) encoding fatty acid desaturase with high expression levels in the fast oil accumulation stage compared with the initial stage of seed development were identified. CONCLUSIONS This study provides the first comprehensive genomic resources characterizing tree peony seeds gene expression at the transcriptional level. These data lay the foundation for further understanding of molecular mechanism responsible for lipid biosynthesis and the high unsaturated fatty acids (especially ALA) accumulation. Meanwhile, it provides theoretical base for potential oilseed application in the respect of n-6 to n-3 ratio for human diets and future regulation of target healthy components of oils.
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Affiliation(s)
- Shan-Shan Li
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Liang-Sheng Wang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Qing-Yan Shu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Jie Wu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Li-Guang Chen
- Institute of Forest Protection, Chinese Academy of Forestry, Beijing, 100091, China. van--
| | - Shuai Shao
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Dan-Dan Yin
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Transcriptome analysis of canola (Brassica napus) under salt stress at the germination stage. PLoS One 2015; 10:e0116217. [PMID: 25679513 PMCID: PMC4332669 DOI: 10.1371/journal.pone.0116217] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 12/05/2014] [Indexed: 11/19/2022] Open
Abstract
Canola (Brassica napus) is one of the most important oil crops in the world. However, its yield has been constrained by salt stress. In this study, transcriptome profiles were explored using Digital Gene Expression (DGE) at 0, 3, 12 and 24 hours after H2O (control) and NaCl treatments on B. napus roots at the germination stage. Comparisons of gene-expression between the control and the treatment were conducted after tag-mapping to the sequenced Brassica rapa genome. The differentially expressed genes during the time course of salt stress were focused on, and 163 genes were identified to be differentially expressed at all the time points. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that some of the genes were involved in proline metabolism, inositol metabolism, carbohydrate metabolic processes and oxidation-reduction processes and may play vital roles in the salt-stress response at the germination stage. Thus, this study provides new candidate salt stress responding genes, which may function in novel putative nodes in the molecular pathways of salt stress resistance.
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Ali A, Rexroad CE, Thorgaard GH, Yao J, Salem M. Characterization of the rainbow trout spleen transcriptome and identification of immune-related genes. Front Genet 2014; 5:348. [PMID: 25352861 PMCID: PMC4196580 DOI: 10.3389/fgene.2014.00348] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 09/16/2014] [Indexed: 11/13/2022] Open
Abstract
Resistance against diseases affects profitability of rainbow trout. Limited information is available about functions and mechanisms of teleost immune pathways. Immunogenomics provides powerful tools to determine disease resistance genes/gene pathways and develop genetic markers for genomic selection. RNA-Seq sequencing of the rainbow trout spleen yielded 93,532,200 reads (100 bp). High quality reads were assembled into 43,047 contigs. 26,333 (61.17%) of the contigs had hits to the NR protein database and 7024 (16.32%) had hits to the KEGG database. Gene ontology showed significant percentages of transcripts assigned to binding (51%), signaling (7%), response to stimuli (9%) and receptor activity (4%) suggesting existence of many immune-related genes. KEGG annotation revealed 2825 sequences belonging to "organismal systems" with the highest number of sequences, 842 (29.81%), assigned to immune system. A number of sequences were identified for the first time in rainbow trout belonging to Toll-like receptor signaling (35), B cell receptor signaling pathway (44), T cell receptor signaling pathway (56), chemokine signaling pathway (73), Fc gamma R-mediated phagocytosis (52), leukocyte transendothelial migration (60) and NK cell mediated cytotoxicity (42). In addition, 51 transcripts were identified as spleen-specific genes. The list includes 277 full-length cDNAs. The presence of a large number of immune-related genes and pathways similar to other vertebrates suggests that innate and adaptive immunity in fish are conserved. This study provides deep-sequence data of rainbow trout spleen transcriptome and identifies many new immune-related genes and full-length cDNAs. This data will help identify allelic variations suitable for genomic selection and genetic manipulation in aquaculture.
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Affiliation(s)
- Ali Ali
- Department of Biology, Middle Tennessee State University Murfreesboro, TN, USA ; Department of Zoology, Faculty of Science, Benha University Benha, Egypt
| | - Caird E Rexroad
- The National Center for Cool and Cold Water Aquaculture, United States Department of Agriculture Agricultural Research Service Leetown, WV USA
| | - Gary H Thorgaard
- School of Biological Sciences, Washington State University Pullman, WA, USA
| | - Jianbo Yao
- Division of Animal and Nutritional Science, West Virginia University Morgantown, WV, USA
| | - Mohamed Salem
- Department of Biology, Middle Tennessee State University Murfreesboro, TN, USA ; Division of Animal and Nutritional Science, West Virginia University Morgantown, WV, USA
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Wang X, Liu A. Expression of Genes Controlling Unsaturated Fatty Acids Biosynthesis and Oil Deposition in Developing Seeds of Sacha Inchi (Plukenetia volubilis L.). Lipids 2014; 49:1019-31. [DOI: 10.1007/s11745-014-3938-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 07/17/2014] [Indexed: 02/03/2023]
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Che R, Sun Y, Sun D, Xu T. Characterization of the miiuy croaker (Miichthys miiuy) transcriptome and development of immune-relevant genes and molecular markers. PLoS One 2014; 9:e94046. [PMID: 24714210 PMCID: PMC3979730 DOI: 10.1371/journal.pone.0094046] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 03/10/2014] [Indexed: 12/04/2022] Open
Abstract
Background The miiuy croaker (Miichthys miiuy) is an important species of marine fish that supports capture fisheries and aquaculture. At present commercial scale aquaculture of this species is limited due to diseases caused by pathogens and parasites which restrict production and limit commercial value. The lack of transcriptomic and genomic information for the miiuy croaker limits the ability of researchers to study the pathogenesis and immune system of this species. In this study we constructed a cDNA library from liver, spleen and kidney which was sequenced using Illumina paired-end sequencing to enable gene discovery and molecular marker development. Principal Findings In our study, a total of 69,071 unigenes with an average length of 572 bp were obtained. Of these, 45,676 (66.13%) were successfully annotated in public databases. The unigenes were also annotated with Gene Ontology, Clusters of Orthologous Groups and KEGG pathways. Additionally, 498 immune-relevant genes were identified and classified. Furthermore, 14,885 putative simple sequence repeats (cSSRs) and 8,510 putative single nucleotide polymorphisms (SNPs) were identified from the 69,071 unigenes. Conclusion The miiuy croaker (Miichthys miiuy) transcriptome data provides a large resource to identify new genes involved in many processes including those involved in the response to pathogens and diseases. Furthermore, the thousands of potential cSSR and SNP markers found in this study are important resources with respect to future development of molecular marker assisted breeding programs for the miiuy croaker.
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Affiliation(s)
- Rongbo Che
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
| | - Yueyan Sun
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
| | - Dianqiao Sun
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
| | - Tianjun Xu
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
- * E-mail:
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High-throughput sequencing and de novo assembly of Brassica oleracea var. Capitata L. for transcriptome analysis. PLoS One 2014; 9:e92087. [PMID: 24682075 PMCID: PMC3969326 DOI: 10.1371/journal.pone.0092087] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 02/18/2014] [Indexed: 12/28/2022] Open
Abstract
Background The cabbage, Brassica oleracea var. capitata L., has a distinguishable phenotype within the genus Brassica. Despite the economic and genetic importance of cabbage, there is little genomic data for cabbage, and most studies of Brassica are focused on other species or other B. oleracea subspecies. The lack of genomic data for cabbage, a non-model organism, hinders research on its molecular biology. Hence, the construction of reliable transcriptomic data based on high-throughput sequencing technologies is needed to enhance our understanding of cabbage and provide genomic information for future work. Methodology/Principal Findings We constructed cDNAs from total RNA isolated from the roots, leaves, flowers, seedlings, and calcium-limited seedling tissues of two cabbage genotypes: 102043 and 107140. We sequenced a total of six different samples using the Illumina HiSeq platform, producing 40.5 Gbp of sequence data comprising 401,454,986 short reads. We assembled 205,046 transcripts (≥ 200 bp) using the Velvet and Oases assembler and predicted 53,562 loci from the transcripts. We annotated 35,274 of the loci with 55,916 plant peptides in the Phytozome database. The average length of the annotated loci was 1,419 bp. We confirmed the reliability of the sequencing assembly using reverse-transcriptase PCR to identify tissue-specific gene candidates among the annotated loci. Conclusion Our study provides valuable transcriptome sequence data for B. oleracea var. capitata L., offering a new resource for studying B. oleracea and closely related species. Our transcriptomic sequences will enhance the quality of gene annotation and functional analysis of the cabbage genome and serve as a material basis for future genomic research on cabbage. The sequencing data from this study can be used to develop molecular markers and to identify the extreme differences among the phenotypes of different species in the genus Brassica.
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Che R, Sun Y, Wang R, Xu T. Transcriptomic analysis of endangered Chinese salamander: identification of immune, sex and reproduction-related genes and genetic markers. PLoS One 2014; 9:e87940. [PMID: 24498226 PMCID: PMC3909259 DOI: 10.1371/journal.pone.0087940] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 01/01/2014] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The Chinese salamander (Hynobius chinensis), an endangered amphibian species of salamander endemic to China, has attracted much attention because of its value of studying paleontology evolutionary history and decreasing population size. Despite increasing interest in the Hynobius chinensis genome, genomic resources for the species are still very limited. A comprehensive transcriptome of Hynobius chinensis, which will provide a resource for genome annotation, candidate genes identification and molecular marker development should be generated to supplement it. PRINCIPAL FINDINGS We performed a de novo assembly of Hynobius chinensis transcriptome by Illumina sequencing. A total of 148,510 nonredundant unigenes with an average length of approximately 580 bp were obtained. In all, 60,388 (40.66%) unigenes showed homologous matches in at least one database and 33,537 (22.58%) unigenes were annotated by all four databases. In total, 41,553 unigenes were categorized into 62 sub-categories by BLAST2GO search, and 19,468 transcripts were assigned to 140 KEGG pathways. A large number of unigenes involved in immune system, local adaptation, reproduction and sex determination were identified, as well as 31,982 simple sequence repeats (SSRs) and 460,923 putative single nucleotide polymorphisms (SNPs). CONCLUSION This dataset represents the first transcriptome analysis of the Chinese salamander (Hynobius chinensis), an endangered species, to be also the first time of hynobiidae. The transcriptome will provide valuable resource for further research in discovery of new genes, protection of population, adaptive evolution and survey of various pathways, as well as development of molecule markers in Chinese salamander; and reference information for closely related species.
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Affiliation(s)
- Rongbo Che
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
| | - Yuena Sun
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
| | - Rixin Wang
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
| | - Tianjun Xu
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
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Gonzales GF, Gonzales C. A randomized, double-blind placebo-controlled study on acceptability, safety and efficacy of oral administration of sacha inchi oil (Plukenetia volubilis L.) in adult human subjects. Food Chem Toxicol 2014; 65:168-76. [PMID: 24389453 DOI: 10.1016/j.fct.2013.12.039] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 12/04/2013] [Accepted: 12/22/2013] [Indexed: 12/25/2022]
Abstract
The study was designed to assess acceptability and side-effects of consumption of sacha inchi oil, rich in α-linolenic acid and sunflower oil, rich in linoleic acid, in adult human subjects. Thirty subjects received 10 or 15ml daily of sacha inchi or sunflower oil for 4months. Acceptability was assessed with daily self-report and with a Likert test at the end of the study. Safety was assessed with self- recording of side-effects and with hepatic and renal markers. Primary efficacy variables were the change in lipid profile. Subjects reported low acceptability of sacha inchi oil at week-1 (37.5%). However, since week-6, acceptability was significantly increased to 81.25-93.75%. No differences were observed in acceptability with respect to sex or oil volume (P>0.05). Most frequent adverse effects during first weeks of consuming sacha inchi oil or sunflower oil were nauseas. The side-effects were reduced with time. Biochemical markers of hepatic and kidney function were maintained unchanged. Serum total cholesterol and LDL cholesterol levels and arterial blood pressure were lowered with both oils (P<0.05). Higher HDL-cholesterol was observed with sacha inchi oil at month-4. In conclusion, sacha inchi oil consumed has good acceptability after week-1 of consumption and it is safety.
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Affiliation(s)
- Gustavo F Gonzales
- Department of Biological and Physiological Sciences, Faculty of Sciences and Philosophy Alberto Cazorla Tálleri, Universidad Peruana Cayetano Heredia, Lima, Peru; Insituto de Investigaciones de la Altura, Universidad Peruana Cayetano Heredia, Lima, Peru.
| | - Carla Gonzales
- Department of Biological and Physiological Sciences, Faculty of Sciences and Philosophy Alberto Cazorla Tálleri, Universidad Peruana Cayetano Heredia, Lima, Peru; Insituto de Investigaciones de la Altura, Universidad Peruana Cayetano Heredia, Lima, Peru.
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Qi J, Zheng N, Zhang B, Sun P, Hu S, Xu W, Ma Q, Zhao T, Zhou L, Qin M, Li X. Mining genes involved in the stratification of Paris polyphylla seeds using high-throughput embryo transcriptome sequencing. BMC Genomics 2013; 14:358. [PMID: 23718911 PMCID: PMC3679829 DOI: 10.1186/1471-2164-14-358] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 05/27/2013] [Indexed: 12/31/2022] Open
Abstract
Background Paris polyphylla var. yunnanensis is an important medicinal plant. Seed dormancy is one of the main factors restricting artificial cultivation. The molecular mechanisms of seed dormancy remain unclear, and little genomic or transcriptome data are available for this plant. Results In this study, massive parallel pyrosequencing on the Roche 454-GS FLX Titanium platform was used to generate a substantial sequence dataset for the P. polyphylla embryo. 369,496 high quality reads were obtained, ranging from 50 to 1146 bp, with a mean of 219 bp. These reads were assembled into 47,768 unigenes, which included 16,069 contigs and 31,699 singletons. Using BLASTX searches of public databases, 15,757 (32.3%) unique transcripts were identified. Gene Ontology and Cluster of Orthologous Groups of proteins annotations revealed that these transcripts were broadly representative of the P. polyphylla embryo transcriptome. The Kyoto Encyclopedia of Genes and Genomes assigned 5961 of the unique sequences to specific metabolic pathways. Relative expression levels analysis showed that eleven phytohormone-related genes and five other genes have different expression patterns in the embryo and endosperm in the seed stratification process. Conclusions Gene annotation and quantitative RT-PCR expression analysis identified 464 transcripts that may be involved in phytohormone catabolism and biosynthesis, hormone signal, seed dormancy, seed maturation, cell wall growth and circadian rhythms. In particular, the relative expression analysis of sixteen genes (CYP707A, NCED, GA20ox2, GA20ox3, ABI2, PP2C, ARP3, ARP7, IAAH, IAAS, BRRK, DRM, ELF1, ELF2, SFR6, and SUS) in embryo and endosperm and at two temperatures indicated that these related genes may be candidates for clarifying the molecular basis of seed dormancy in P. polyphlla var. yunnanensis.
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