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Jariani P, Shahnejat-Bushehri AA, Naderi R, Zargar M, Naghavi MR. Molecular and Phytochemical Characteristics of Flower Color and Scent Compounds in Dog Rose ( Rosa canina L.). Molecules 2024; 29:3145. [PMID: 38999097 PMCID: PMC11242971 DOI: 10.3390/molecules29133145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/12/2024] [Accepted: 03/16/2024] [Indexed: 07/14/2024] Open
Abstract
This study delves into the chemical and genetic determinants of petal color and fragrance in Rosa canina L., a wild rose species prized for its pharmacological and cosmetic uses. Comparative analysis of white and dark pink R. canina flowers revealed that the former harbors significantly higher levels of total phenolics (TPC) and flavonoids (TFC), while the latter is distinguished by elevated total anthocyanins (TAC). Essential oils in the petals were predominantly composed of aliphatic hydrocarbons, with phenolic content chiefly constituted by flavonols and anthocyanins. Notably, gene expression analysis showed an upregulation in most genes associated with petal color and scent biosynthesis in white buds compared to dark pink open flowers. However, anthocyanin synthase (ANS) and its regulatory gene RhMYB1 exhibited comparable expression levels across both flower hues. LC-MS profiling identified Rutin, kaempferol, quercetin, and their derivatives as key flavonoid constituents, alongside cyanidin and delphinidin as the primary anthocyanin compounds. The findings suggest a potential feedback inhibition of anthocyanin biosynthesis in white flowers. These insights pave the way for the targeted enhancement of R. canina floral traits through metabolic and genetic engineering strategies.
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Affiliation(s)
- Parisa Jariani
- Division of Biotechnology, Department of Agronomy and Plant Breeding, College of Agricultural and Natural Resources, University of Tehran, Karaj 31587-77871, Iran
| | - Ali-Akbar Shahnejat-Bushehri
- Division of Biotechnology, Department of Agronomy and Plant Breeding, College of Agricultural and Natural Resources, University of Tehran, Karaj 31587-77871, Iran
| | - Roohangiz Naderi
- Department of Horticulture Science, College of Agriculture and Natural Resources, University of Tehran, Karaj 31587-77871, Iran
| | - Meisam Zargar
- Department of Agrobiotechnology, Institute of Agriculture, RUDN University, 117198 Moscow, Russia
| | - Mohammad Reza Naghavi
- Division of Biotechnology, Department of Agronomy and Plant Breeding, College of Agricultural and Natural Resources, University of Tehran, Karaj 31587-77871, Iran
- Department of Agrobiotechnology, Institute of Agriculture, RUDN University, 117198 Moscow, Russia
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2
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Singh VV, Naseer A, Sellamuthu G, Jakuš R. An Optimized and Cost-Effective RNA Extraction Method for Secondary Metabolite-Enriched Tissues of Norway Spruce ( Picea abies). PLANTS (BASEL, SWITZERLAND) 2024; 13:389. [PMID: 38337922 PMCID: PMC10857598 DOI: 10.3390/plants13030389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/21/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024]
Abstract
Since the development of next-generation sequencing techniques and with the growing interest in transcriptomic studies, there is a demand for high-throughput RNA extraction techniques. General RNA extraction protocols are unreliable when it comes to the quality and quantity of isolated RNA obtained from different tissue types of different plant species. Despite Norway spruce (Picea abies) being one of the most significant and commercially valuable tree species in European forests, only limited genetic research is available. In this study, we developed a cetyltrimethylammonium bromide (CTAB) protocol by modifying the original method. We compared this CTAB protocol with other widely used methods for extracting RNA from different tissues (needle, phloem, and root) of Norway spruce, known for its richness in polyphenols, polysaccharides, and secondary metabolites. The modified CTAB method proves to be superior to the kit-based and TRIzol-based methods for extracting RNA from the metabolite-rich tissues of Norway spruce, resulting in high RNA quality and integrity values (RIN~7-9). The modified CTAB RNA extraction method is rapid, cost-effective, and relatively simple in yielding the desired RNA quality from Norway spruce tissues. It is optimal for RNA sequencing and other downstream molecular applications.
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Affiliation(s)
- Vivek Vikram Singh
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha-Suchdol, 165 00 Prague, Czech Republic; (A.N.); (G.S.); (R.J.)
| | - Aisha Naseer
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha-Suchdol, 165 00 Prague, Czech Republic; (A.N.); (G.S.); (R.J.)
| | - Gothandapani Sellamuthu
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha-Suchdol, 165 00 Prague, Czech Republic; (A.N.); (G.S.); (R.J.)
| | - Rastislav Jakuš
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha-Suchdol, 165 00 Prague, Czech Republic; (A.N.); (G.S.); (R.J.)
- Institute of Forest Ecology, Slovak Academy of Sciences, Štúrova 2, 960 53 Zvolen, Slovakia
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Belkina D, Karpova D, Porotikova E, Lifanov I, Vinogradova S. Grapevine Virome of the Don Ampelographic Collection in Russia Has Concealed Five Novel Viruses. Viruses 2023; 15:2429. [PMID: 38140672 PMCID: PMC10747563 DOI: 10.3390/v15122429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
In this study, an analysis of the virome of 51 grapevines from the Don ampelographic collection named after Ya. I. Potapenko (Russia) was performed using high-throughput sequencing of total RNA. A total of 20 previously described grapevine viruses and 4 viroids were identified. The most detected were grapevine rupestris stem pitting-associated virus (98%), hop stunt viroid (98%), grapevine Pinot gris virus (96%), grapevine yellow speckle viroid 1 (94%), and grapevine fleck virus (GFkV, 80%). Among the economically significant viruses, the most present were grapevine leafroll-associated virus 3 (37%), grapevine virus A (24%), and grapevine leafroll-associated virus 1 (16%). For the first time in Russia, a grapevine-associated tymo-like virus (78%) was detected. After a bioinformatics analysis, 123 complete or nearly complete viral genomes and 64 complete viroid genomes were assembled. An analysis of the phylogenetic relationships with reported global isolates was performed. We discovered and characterized the genomes of five novel grapevine viruses: bipartite dsRNA grapevine alphapartitivirus (genus Alphapartitivirus, family Partitiviridae), bipartite (+) ssRNA grapevine secovirus (genus Fabavirus, family Secoviridae) and three (+) ssRNA grapevine umbra-like viruses 2, -3, -4 (which phylogenetically occupy an intermediate position between representatives of the genus Umbravirus and umbravirus-like associated RNAs).
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Affiliation(s)
- Daria Belkina
- Skryabin Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, 119071 Moscow, Russia; (D.B.)
- North Caucasian Federal Scientific Center of Horticulture, Viticulture, Wine-Making, 40 Years of Victory Street, Build. 39, 350901 Krasnodar, Russia
| | - Daria Karpova
- Skryabin Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, 119071 Moscow, Russia; (D.B.)
- North Caucasian Federal Scientific Center of Horticulture, Viticulture, Wine-Making, 40 Years of Victory Street, Build. 39, 350901 Krasnodar, Russia
| | - Elena Porotikova
- Skryabin Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, 119071 Moscow, Russia; (D.B.)
| | - Ilya Lifanov
- Skryabin Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, 119071 Moscow, Russia; (D.B.)
| | - Svetlana Vinogradova
- Skryabin Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, 119071 Moscow, Russia; (D.B.)
- North Caucasian Federal Scientific Center of Horticulture, Viticulture, Wine-Making, 40 Years of Victory Street, Build. 39, 350901 Krasnodar, Russia
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Vinogradova S, Porotikova E, Navrotskaya E, Galbacs ZN, Massart S, Varallyay E. The First Virome of a Russian Vineyard. PLANTS (BASEL, SWITZERLAND) 2023; 12:3292. [PMID: 37765456 PMCID: PMC10534617 DOI: 10.3390/plants12183292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023]
Abstract
Among other pathogens, more than 80 viruses infect grapevine. The aim of this work was to study the virome diversity of grapevine viruses and mycoviruses of a vineyard using high-throughput sequencing technologies. The grapevine virome was studied in symptomatic vines of the Rkatsiteli cultivar (V. vinifera) collected at the vineyards of the Krasnodar Krai in Russia. Ribosomal-depleted total RNA and isolated small RNAs were used for library preparation and high-throughput sequencing. Six grapevine-infecting viruses and two viroids were validated by RT-PCR and analyzed phylogenetically. We identified the presence of grapevine leafroll-associated virus 3, grapevine Pinot gris virus, grapevine virus T, grapevine rupestris stem-pitting-associated virus, grapevine fleck virus, and grapevine rupestris vein feathering virus, as well as two viroids, grapevine yellow speckle viroid 1 and hop stunt viroid. We also studied the mycovirome of the vineyard and identified nine viruses with single-stranded positive-sense RNA genomes: alternaria arborescens mitovirus 1, botrytis cinerea mitovirus 1, botrytis cinerea mitovirus 2, botrytis cinerea mitovirus 3, botrytis cinerea mitovirus 4, sclerotinia sclerotiorum mitovirus 3, botrytis cinerea hypovirus 1, grapevine-associated narnavirus 1, and botrytis virus F. In addition, we identified botrytis cinerea hypovirus 1 satellite-like RNA and two single-stranded negative-sense RNA viruses. This is the first study of grapevine mycoviruses in Russia. The obtained result will contribute to the development of biocontrol strategies in the future.
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Affiliation(s)
- Svetlana Vinogradova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Elena Porotikova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Emiliya Navrotskaya
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Zsuzsanna Nagyne Galbacs
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, H-2100 Godollo, Hungary
| | - Sébastien Massart
- Laboratory of Integrated and Urban Phytopathology, TERRA, Gembloux Agro-Bio Tech, Liège University, 5030 Gembloux, Belgium
| | - Eva Varallyay
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, H-2100 Godollo, Hungary
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Chitosan, chondroitin sulfate, and hyaluronic acid based in-situ forming scaffold for efficient cell grafting. Int J Biol Macromol 2023; 225:938-951. [PMID: 36410536 DOI: 10.1016/j.ijbiomac.2022.11.157] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/26/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022]
Abstract
Current cell grafting techniques are majorly dependent on seeding cells on a pre-formed scaffold. However, cells grow in a 2-dimensional (2D) space in such constructs, not mimicking the tissue's 3-dimensional (3D) architecture. The present study evaluated a unique poly-electrolyte complexation (PEC) based strategy for the 3D engraftment of cells in a porous polymeric scaffold. The scaffold was synthesized using a positively charged polysaccharide chitosan (CH) and negatively charged glycosaminoglycans chondroitin sulfate (CS) and hyaluronic acid (HA). Two different scaffolds were synthesized, one using CH and CS [CH-CS] and another using CH and CS + HA [CH-(CS-HA)]. The physicochemical characterization of both the PECs confirmed electrostatic interactions, leading to a porous and viscoelastic PEC formation. Fibroblast cells were grafted and seeded in both scaffolds to evaluate the effect of different scaffold compositions and the difference between seeded and grafted cells. Imaging studies confirmed that grafting of the fibroblast cells supports cellular proliferation. The qPCR studies demonstrated increased expression of functional markers TGF-β, α-SMA, collagen-I, and fibronectin in the CH-(CS-HA) grafted cells. In summary, it was demonstrated that an in-situ forming PEC of CH, CS, and HA had good physicochemical properties for cell grafting and supported grafted cells with improved function.
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Shvets D, Sandomirsky K, Porotikova E, Vinogradova S. Metagenomic Analysis of Ampelographic Collections of Dagestan Revealed the Presence of Two Novel Grapevine Viruses. Viruses 2022; 14:v14122623. [PMID: 36560627 PMCID: PMC9781968 DOI: 10.3390/v14122623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/21/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
Abstract
In this study, we analyzed the virome of 73 grape samples from two Dagestan ampelographic collections in Russia using high-throughput sequencing of total RNAs. Fourteen viruses and four viroids were identified, with one to eleven of them detected in each plant. For the first time in Russia, we identified grapevine leafroll-associated virus 7 and grapevine Kizil Sapak virus. A total of 206 genomes of viruses and viroids were obtained, and their phylogenetic analysis was carried out. The de novo assembly and tblastx analysis allowed us to obtain contigs of a novel (+) ssRNA genome of a plant virus from the genus Umbravirus, which was tentatively named grapevine umbra-like virus (GULV), as well as contigs of a novel dsDNA pararetrovirus from the genus Caulimovirus, which was tentatively named grapevine pararetrovirus (GPRV). Complete genomes of these viruses were obtained and used for Sequence Demarcation Tool (SDT) analysis and phylogeny studies. GULV and GPRV were detected in 16 and 33 germplasm samples from the Dagestan collections, respectively.
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Comparative Plant Transcriptome Profiling of Arabidopsis thaliana Col-0 and Camelina sativa var. Celine Infested with Myzus persicae Aphids Acquiring Circulative and Noncirculative Viruses Reveals Virus- and Plant-Specific Alterations Relevant to Aphid Feeding Behavior and Transmission. Microbiol Spectr 2022; 10:e0013622. [PMID: 35856906 PMCID: PMC9430646 DOI: 10.1128/spectrum.00136-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Evidence is accumulating that plant viruses alter host plant traits in ways that modify their insect vectors' behavior. These alterations often enhance virus transmission, which has led to the hypothesis that these effects are manipulations caused by viral adaptation. However, we lack a mechanistic understanding of the genetic basis of these indirect, plant-mediated effects on vectors, their dependence on the plant host, and their relation to the mode of virus transmission. Transcriptome profiling of Arabidopsis thaliana and Camelina sativa plants infected with turnip yellows virus (TuYV) or cauliflower mosaic virus (CaMV) and infested with the common aphid vector Myzus persicae revealed strong virus- and host-specific differences in gene expression patterns. CaMV infection caused more severe effects on the phenotype of both plant hosts than did TuYV infection, and the severity of symptoms correlated strongly with the proportion of differentially expressed genes, especially photosynthesis genes. Accordingly, CaMV infection modified aphid behavior and fecundity more strongly than did infection with TuYV. Overall, infection with CaMV, relying on the noncirculative transmission mode, tends to have effects on metabolic pathways, with strong potential implications for insect vector-plant host interactions (e.g., photosynthesis, jasmonic acid, ethylene, and glucosinolate biosynthetic processes), while TuYV, using the circulative transmission mode, alters these pathways only weakly. These virus-induced deregulations of genes that are related to plant physiology and defense responses might impact both aphid probing and feeding behavior on infected host plants, with potentially distinct effects on virus transmission. IMPORTANCE Plant viruses change the phenotype of their plant hosts. Some of the changes impact interactions of the plant with insects that feed on the plants and transmit these viruses. These modifications may result in better virus transmission. We examine here the transcriptomes of two plant species infected with two viruses with different transmission modes to work out whether there are plant species-specific and transmission mode-specific transcriptome changes. Our results show that both are the case.
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Shvets D, Porotikova E, Sandomirsky K, Vinogradova S. Virome of Grapevine Germplasm from the Anapa Ampelographic Collection (Russia). Viruses 2022; 14:1314. [PMID: 35746784 PMCID: PMC9230720 DOI: 10.3390/v14061314] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/07/2022] [Accepted: 06/13/2022] [Indexed: 11/16/2022] Open
Abstract
Grapevine germplasm collections are unique repositories of grape cultivars; therefore, it is necessary to minimize their infection with pathogens, including viruses, and develop various programs to maintain them in a virus-free state. In our study, we examined the virome of the largest Russian grapevine germplasm collection, the Anapa Ampelographic Collection, using high-throughput sequencing of total RNAs. As a result of bioinformatics analysis and validation of its results by reverse transcription PCR (RT-PCR) and quantitative RT-PCR (RT-qPCR), we identified 20 viruses and 3 viroids in 47 libraries. All samples were infected with 2 to 12 viruses and viroids, including those that cause economically significant diseases: leafroll, fleck, and rugose wood complex. For the first time in Russia, we detected Grapevine virus B (GVB), Grapevine virus F (GVF), Grapevine asteroid mosaic-associated virus (GAMaV), Grapevine Red Globe virus (GRGV), Grapevine satellite virus (GV-Sat), Grapevine virga-like virus (GVLV), Grapevine-associated jivivirus 1 (GaJV-1) and Vitis cryptic virus (VCV). A new putative representative of the genus Umbravirus with the provisional name Grapevine umbra-like virus (GULV) was also identified in Russian grape samples.
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Affiliation(s)
| | | | | | - Svetlana Vinogradova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky, Prospect 33, 119071 Moscow, Russia; (D.S.); (E.P.); (K.S.)
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Navrotskaya E, Porotikova E, Yurchenko E, Galbacs ZN, Varallyay E, Vinogradova S. High-Throughput Sequencing of Small RNAs for Diagnostics of Grapevine Viruses and Viroids in Russia. Viruses 2021; 13:2432. [PMID: 34960701 PMCID: PMC8709451 DOI: 10.3390/v13122432] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 11/16/2022] Open
Abstract
The use of high-throughput sequencing (HTS) technology has led to significant progress in the identification of many viruses and their genetic variants. In this study, we used the HTS platform to sequence small RNAs (sRNAs) of grapevine to study the virome. Isolation of RNA was performed using symptomatic grapevines collected from commercial vineyards in Krasnodar Krai in 2017-2018. To determine the viromes of vineyards, we used an integrated approach that included a bioinformatic analysis of the results of sRNA HTS and the molecular method RT-PCR, which made it possible to identify 13 viruses and 4 viroids. Grapevine leafroll-associated virus 4 (GLRaV-4), Grapevine Syrah Virus-1 (GSyV-1), Raspberry bushy dwarf virus (RBDV), Australian grapevine viroid (AGVd), and Grapevine yellow speckle viroid 2 (GYSVd-2) were identified for the first time in Russia. Out of 38 samples analyzed, 37 had mixed infections with 4-11 viruses, indicating a high viral load. Analysis of the obtained sequences of fragments of virus genomes made it possible to identify recombination events in GLRaV-1, GLRaV-2, GLRaV-3, GLRaV-4, GVT, GPGV, GRSPaV, GVA, and GFLV. The obtained results indicate a wide spread of the viruses and a high genetic diversity in the vineyards of Krasnodar Krai and emphasize the urgent need to develop and implement long-term strategies for the control of viral grapevine diseases.
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Affiliation(s)
- Emiliya Navrotskaya
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia; (E.N.); (E.P.)
| | - Elena Porotikova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia; (E.N.); (E.P.)
| | - Eugeniya Yurchenko
- Federal State Budgetary Scientific Institution ‘North Caucasian Federal Scientific Horticulture and Viticulture Center’, Protection and Plant Biotechnology Scientific Center, Head, 40 Years of Victory Street 39, 350072 Krasnodar, Russia;
| | - Zsuzsanna Nagyne Galbacs
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, H-2100 Godollo, Hungary; (Z.N.G.); (E.V.)
| | - Eva Varallyay
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, H-2100 Godollo, Hungary; (Z.N.G.); (E.V.)
| | - Svetlana Vinogradova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia; (E.N.); (E.P.)
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Hurtado-Gaitán E, Sellés-Marchart S, Hartwell J, Martínez-Esteso MJ, Bru-Martínez R. Down-Regulation of Phosphoenolpyruvate Carboxylase Kinase in Grapevine Cell Cultures and Leaves Is Linked to Enhanced Resveratrol Biosynthesis. Biomolecules 2021; 11:1641. [PMID: 34827639 PMCID: PMC8615455 DOI: 10.3390/biom11111641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 12/02/2022] Open
Abstract
In grapevine, trans-Resveratrol (tR) is produced as a defence mechanism against stress or infection. tR is also considered to be important for human health, which increases its interest to the scientific community. Transcriptomic analysis in grapevine cell cultures treated with the defence response elicitor methyl-β-cyclodextrin (CD) revealed that both copies of PHOSPHOENOLPYRUVATE CARBOXYLASE KINASE (PPCK) were down-regulated significantly. A role for PPCK in the defence response pathway has not been proposed previously. We therefore analysed the control of PPCK transcript levels in grapevine cell cultures and leaves elicited with CD. Moreover, phosphoenolpyruvate carboxylase (PPC), stilbene synthase (STS), and the transcription factors MYB14 and WRKY24, which are involved in the activation of STS transcription, were also analysed by RT-qPCR. The results revealed that under CD elicitation conditions PPCK down-regulation, increased stilbene production and loss of PPC activity occurs in both tissues. Moreover, STS transcripts were co-induced with MYB14 and WRKY24 in cell cultures and leaves. These genes have not previously been reported to respond to CD in grape leaves. Our findings thus support the hypothesis that PPCK is involved in diverting metabolism towards stilbene biosynthesis, both for in vitro cell culture and whole leaves. We thus provide new evidence for PEP being redirected between primary and secondary metabolism to support tR production and the stress response.
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Affiliation(s)
- Elías Hurtado-Gaitán
- Plant Proteomics and Functional Genomics Group, Agrochemistry and Biochemistry Department, Faculty of Science, University of Alicante, 03690 Alicante, Spain; (E.H.-G.); (S.S.-M.); (M.J.M.-E.)
| | - Susana Sellés-Marchart
- Plant Proteomics and Functional Genomics Group, Agrochemistry and Biochemistry Department, Faculty of Science, University of Alicante, 03690 Alicante, Spain; (E.H.-G.); (S.S.-M.); (M.J.M.-E.)
| | - James Hartwell
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK;
| | - Maria José Martínez-Esteso
- Plant Proteomics and Functional Genomics Group, Agrochemistry and Biochemistry Department, Faculty of Science, University of Alicante, 03690 Alicante, Spain; (E.H.-G.); (S.S.-M.); (M.J.M.-E.)
| | - Roque Bru-Martínez
- Plant Proteomics and Functional Genomics Group, Agrochemistry and Biochemistry Department, Faculty of Science, University of Alicante, 03690 Alicante, Spain; (E.H.-G.); (S.S.-M.); (M.J.M.-E.)
- Instituto de Investigación Sanitaria y Biomédica de Alicante ISABIAL-Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana FISABIO, 03010 Alicante, Spain
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Ricciuti E, Laboureau N, Noumbissié G, Chabannes M, Sukhikh N, Pooggin MM, Iskra-Caruana ML. Extrachromosomal viral DNA produced by transcriptionally active endogenous viral elements in non-infected banana hybrids impedes quantitative PCR diagnostics of banana streak virus infections in banana hybrids. J Gen Virol 2021; 102. [PMID: 34726592 DOI: 10.1099/jgv.0.001670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The main edible and cultivated banana varieties are intra- and interspecific hybrids of the two main Musa species, Musa acuminata and Musa balbisiana, having diploid genomes denoted A and B, respectively. The B genome naturally hosts sequences of banana streak virus (BSV) named endogenous BSV (eBSV). Upon stress, eBSVs are identified as the origin of BSV infection for at least three BSV species, causing banana streak disease. For each of the three species, BSV and eBSV share >99.9 % sequence identity, complicating PCR-based diagnosis of viral infection in the B genome-containing bananas. Here, we designed a quantitative PCR-based method to only quantify episomal BSV particles produced, overcoming the limitation of eBSV also being detected by qPCR by using it as a 'calibrator'. However, our results revealed unexpected variation of eBSV amplification in calibrator plants composed of a clonal population of 53 replicating virus-free banana hybrids with the same AAB genotype. Our in-depth molecular analyses suggest that this calibrator variation is due to the variable abundance of non-encapsidated extrachromosomal viral DNA, likely produced via the transcription of eBSVs, followed by occasional reverse transcription. We also present evidence that accumulation of viral transcripts in AAB plants is downregulated both at post-transcriptional and transcriptional levels by an RNA interference mechanism that keeps the plants free of virus infection. Finally, we recommend that such eBSV amplification variation be taken into account to establish a quantitative viral diagnostic for banana plants with the B genome.
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Affiliation(s)
- Emeline Ricciuti
- CIRAD, UMR BGPI, Univ Montpellier, INRAE, Montpellier SupAgro, Montpellier, 34984, France
| | - Nathalie Laboureau
- CIRAD, UMR BGPI, Univ Montpellier, INRAE, Montpellier SupAgro, Montpellier, 34984, France.,CIRAD, UMR PHIM, 34090 Montpellier, France.,PHIM Plant Health Institute, Univ Montpellier, INRAE, IRD, CIRAD, Institut Agro, Montpellier, France
| | - Guy Noumbissié
- CIRAD, UMR BGPI, Univ Montpellier, INRAE, Montpellier SupAgro, Montpellier, 34984, France
| | - Matthieu Chabannes
- CIRAD, UMR BGPI, Univ Montpellier, INRAE, Montpellier SupAgro, Montpellier, 34984, France.,CIRAD, UMR AGAP Intitute, F-34398 Montpellier, France.,AGAP Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Natalia Sukhikh
- PHIM Plant Health Institute, Univ Montpellier, INRAE, IRD, CIRAD, Institut Agro, Montpellier, France.,Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences. Moscow, 119071, Russia
| | - Mikhail M Pooggin
- PHIM Plant Health Institute, Univ Montpellier, INRAE, IRD, CIRAD, Institut Agro, Montpellier, France
| | - Marie-Line Iskra-Caruana
- CIRAD, UMR BGPI, Univ Montpellier, INRAE, Montpellier SupAgro, Montpellier, 34984, France.,CIRAD, DGD-RS, F-34398 Montpellier, France
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12
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Golyaev V, Candresse T, Rabenstein F, Pooggin MM. Plant virome reconstruction and antiviral RNAi characterization by deep sequencing of small RNAs from dried leaves. Sci Rep 2019; 9:19268. [PMID: 31848375 PMCID: PMC6917709 DOI: 10.1038/s41598-019-55547-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/15/2019] [Indexed: 12/23/2022] Open
Abstract
In plants, RNA interference (RNAi) generates small interfering (si)RNAs from entire genomes of viruses, satellites and viroids. Therefore, deep small (s)RNA sequencing is a universal approach for virome reconstruction and RNAi characterization. We tested this approach on dried barley leaves from field surveys. Illumina sequencing of sRNAs from 2 plant samples identified in both plants Hordeum vulgare endornavirus (HvEV) and barley yellow mosaic bymovirus (BaYMV) and, additionally in one plant, a novel strain of Japanese soil-borne wheat mosaic furovirus (JSBWMV). De novo and reference-based sRNA assembly yielded complete or near-complete genomic RNAs of these viruses. While plant sRNAs showed broad size distribution, viral sRNAs were predominantly 21 and 22 nucleotides long with 5′-terminal uridine or adenine, and were derived from both genomic strands. These bona fide siRNAs are presumably processed from double-stranded RNA precursors by Dicer-like (DCL) 4 and DCL2, respectively, and associated with Argonaute 1 and 2 proteins. For BaYMV (but not HvEV, or JSBWMV), 24-nucleotide sRNAs represented the third most abundant class, suggesting DCL3 contribution to anti-bymovirus defence. Thus, viral siRNAs are well preserved in dried leaf tissues and not contaminated by non-RNAi degradation products, enabling both complete virome reconstruction and inference of RNAi components mediating antiviral defense.
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Affiliation(s)
- Victor Golyaev
- BGPI, INRA Centre Occitanie, CIRAD, SupAgro, Université de Montpellier, Montpellier, 34984, France
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, Villenave d'Ornon cedex, 33882, France
| | - Frank Rabenstein
- Julius Kühn-Institut, Bundesforschungsinstitut für Kulturpflanzen, Erwin-Baur-Straße 27, Quedlinburg, 06484, Germany
| | - Mikhail M Pooggin
- BGPI, INRA Centre Occitanie, CIRAD, SupAgro, Université de Montpellier, Montpellier, 34984, France.
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13
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Saucedo S, González A, Gómez M, Contreras RA, Laporte D, Sáez CA, Zúñiga G, Moenne A. Oligo-carrageenan kappa increases glucose, trehalose and TOR-P and subsequently stimulates the expression of genes involved in photosynthesis, and basal and secondary metabolisms in Eucalyptus globulus. BMC PLANT BIOLOGY 2019; 19:258. [PMID: 31208344 PMCID: PMC6580502 DOI: 10.1186/s12870-019-1858-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 05/30/2019] [Indexed: 05/14/2023]
Abstract
BACKGROUND It has been previously shown that oligo-carrageenan (OC) kappa increases growth, photosynthesis and activities of enzymes involved in basal and secondary metabolisms in Eucalyptus globulus. However, it is not known whether OC kappa may induce the activation of TOR pathway and the increase in expression of genes encoding proteins involved in photosynthesis and enzymes of basal and secondary metabolisms. RESULTS E. globulus trees were sprayed on leaves with water (control) or with OC kappa 1 mg mL- 1, once a week, four times in total, and cultivated for 17 additional weeks (21 weeks in total). Treated trees showed a higher level of net photosynthesis than controls, beginning at week 3, a higher height, beginning at week 9, and those differences remained until week 21. In addition, treated trees showed an increase in the level of glucose beginning at week 1, trehalose at weeks 1-3, and in TOR-P level at week 1-2. On the other hand, transcripts encoding proteins involved in photosynthesis, and enzymes involved in glucose accumulation, C, N and S assimilation, and synthesis of secondary metabolites began at weeks 3-4 and with additional peaks at weeks 5-6, 8-11,13-14 and 17-19. Thus, OC kappa induced initial increases in glucose, trehalose and TOR-P levels that were followed by oscillatory increases in the level of transcripts coding for proteins involved in photosynthesis, and in basal and secondary metabolisms suggesting that initial increases in glucose, trehalose and TOR-P may trigger activation of gene expression. CONCLUSIONS The stimulation of growth induced by OC kappa in E. globulus trees is due, at least in part, to activation of TOR pathway and the increase in expression of genes encoding proteins involved in photosynthesis and enzymes of basal metabolism.
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Affiliation(s)
- Silvia Saucedo
- Faculty of Chemistry and Biology, University of Santiago of Chile, Santiago, Chile
- Facultad de Ciencias Agrarias, Universidad Técnica Estatal de Quevedo, 63 Quevedo, Ecuador
| | - Alberto González
- Faculty of Chemistry and Biology, University of Santiago of Chile, Santiago, Chile
| | - Melissa Gómez
- Faculty of Chemistry and Biology, University of Santiago of Chile, Santiago, Chile
| | - Rodrigo A. Contreras
- Faculty of Chemistry and Biology, University of Santiago of Chile, Santiago, Chile
| | - Daniel Laporte
- Faculty of Chemistry and Biology, University of Santiago of Chile, Santiago, Chile
| | - Claudio A. Sáez
- Laboratory of Coastal Environmental Research, Center of Advanced Studies, University of Playa Ancha, Viña del Mar, Chile
| | - Gustavo Zúñiga
- Faculty of Chemistry and Biology, University of Santiago of Chile, Santiago, Chile
| | - Alejandra Moenne
- Faculty of Chemistry and Biology, University of Santiago of Chile, Santiago, Chile
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14
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Martínez-Márquez A, Morante-Carriel JA, Palazon J, Bru-Martínez R. Rosa hybrida orcinol O-methyl transferase-mediated production of pterostilbene in metabolically engineered grapevine cell cultures. N Biotechnol 2018; 42:62-70. [PMID: 29477599 DOI: 10.1016/j.nbt.2018.02.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/19/2018] [Accepted: 02/20/2018] [Indexed: 01/11/2023]
Abstract
Stilbenes are naturally scarce high-added-value plant compounds with chemopreventive, pharmacological and cosmetic properties. Bioproduction strategies include engineering the metabolisms of bacterial, fungal and plant cell systems. Strikingly, one of the most effective strategies consists in the elicitation of wild grapevine cell cultures, which leads to vast stilbene resveratrol accumulation in the extracellular medium. The combination of both cell culture elicitation and metabolic engineering strategies to produce resveratrol analogs proved more efficient for the hydroxylated derivative piceatannol than for the dimethylated derivative pterostilbene, for which human hydroxylase HsCYP1B1- and grapevine O-methyltransferase VvROMT-transformed cell cultures were respectively used. Rose orcinol O-methyltransferase (OOMT) displays enzymatic properties, which makes it an appealing candidate to substitute VvROMT in the combined strategy to enhance the pterostilbene production level by engineered grapevine cells upon elicitation. Here we cloned a Rosa hybrida OOMT gene, and created a genetic construction suitable for Agrobacterium-mediated plant transformation. OOMT's ability to catalyze the conversion of resveratrol into pterostilbene was first assessed in vitro using protein extracts of agroinfiltrated N. benthamiana leaves and transformed grapevine callus. The grapevine cell cultures transformed with RhOOMT produced about 16 mg/L culture of pterostilbene and reached an extracellular distribution of up to 34% of total production at the best, which is by far the highest production reported to date in a plant system. A bonus large resveratrol production of ca. 1500-3000 mg/L was simultaneously obtained. Our results demonstrate a viable successful metabolic engineering strategy to produce pterostilbene, a resveratrol analog with enhanced pharmacological properties.
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Affiliation(s)
- Ascensión Martínez-Márquez
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Faculty of Science and Multidisciplinary Institut for Environment Studies "Ramon Margalef", University of Alicante, Alicante, Spain
| | - Jaime A Morante-Carriel
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Faculty of Science and Multidisciplinary Institut for Environment Studies "Ramon Margalef", University of Alicante, Alicante, Spain; Biotechnology and Molecular Biology Group, Quevedo State Technical University, Quevedo, Ecuador
| | - Javier Palazon
- Laboratory of Plant Physiology, Faculty of Pharmacy, University of Barcelona, Av.Joan XXIII sn, E-08028 Barcelona, Spain
| | - Roque Bru-Martínez
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Faculty of Science and Multidisciplinary Institut for Environment Studies "Ramon Margalef", University of Alicante, Alicante, Spain; Institute for Healthcare and Biomedical Research of Alicante ISABIAL-FISABIO, E-03010 Alicante, Spain.
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15
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Wang W, Liu R, Shen Y, Lian B. The Potential Correlation Between Bacterial Sporulation and the Characteristic Flavor of Chinese Maotai Liquor. Front Microbiol 2018; 9:1435. [PMID: 30013536 PMCID: PMC6037195 DOI: 10.3389/fmicb.2018.01435] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 06/11/2018] [Indexed: 12/05/2022] Open
Abstract
The relationship between the formation of characteristic Maotai-flavor substances (MTFS) and the dominant bacteria in Maotai Daqu (MTDQ) has long been a topic of research interest in the field of liquor brewing in China. To investigate the connection between MTFS and the Bacillus subtilis (one of dominant bacteria in MTDQ) cultured on solid plates of wheat extract medium at, temperatures of 37, 46, and up to 55°C (Group A), and at a constant 37°C (Group B), the transcriptomes of the bacteria grown in the two groups were studied. About 10 out of 84 differentially expressed genes (DEGs) were related to promoting sporulation. Furthermore, observations made with transmission electron microscopy (TEM) showed that a thicker spore cortex appeared in Group A. The content of 2, 6-pyridinedicarboxylic acid (DPA), an important component of the spore, was 49.77 (±2.50) and 38.23 (±3.96) μg/mg of dried spores from the bacteria cultured in Groups A and B, respectively. Combined with the production process of Maotai liquor, more DPA accumulates in the high-temperature fermentation stage and is then released by spore germination during the subsequent temperature-drop stage. We suggest that DPA (or its derivatives) can then be transformed into MTFS by the Maillard reaction after many rounds of microbial fermentation. The viewpoint that there is a potential correlation between bacterial sporulation and the production of MTFS is proposed.
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Affiliation(s)
- Weiying Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, China.,College of Life Sciences, Jiangxi Normal University, Nanchang, China
| | - Renlu Liu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ye Shen
- Shanghai OE Biotech. Co., Ltd., Shanghai, China
| | - Bin Lian
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, China
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16
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Zeinipour M, Azadi P, Majd A, Kermani MJ, Irian S, Hosseini SM, Mii M. Agroinfiltration: a rapid and reliable method to select suitable rose cultivars for blue flower production. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:503-511. [PMID: 29692557 PMCID: PMC5911261 DOI: 10.1007/s12298-018-0516-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 12/07/2017] [Accepted: 01/25/2018] [Indexed: 05/09/2023]
Abstract
Rose cultivars with blue flower color are among the most attractive breeding targets in floriculture. However, they are difficult to produce due to the low efficiency of transformation systems, interactive effects of hosts and vectors, and lengthy processes. In this study, agroinfiltration-mediated transient expression was investigated as a tool to assess the function of flower color genes and to determine appropriate host cultivars for stable transformation in Rosa hybrida. To induce delphinidin accumulation and consequently to produce blue hue, the petals of 30 rose cultivars were infiltrated with three different expression vectors namely pBIH-35S-CcF3'5'H, pBIH-35S-Del2 and pBIH-35S-Del8, harbouring different sets of flower color genes. The results obtained showed that the ectopic expression of the genes was only detected in three cultivars with dark pink petals (i.e. 'Purple power', 'High & Mora' and 'Marina') after 6-8 days. The high performance liquid chromatography analyses confirmed delphinidin accumulation in the infiltrated petals caused by transient expression of CcF3'5'H gene. Moreover, there were significant differences in the amounts of delphinidin among the three cultivars infiltrated with the three different expression vectors. More specifically, the highest delphinidin content was detected in the cultivar 'Purple power' (4.67 µg g-1 FW), infiltrated with the pBIH-35S-Del2 vector. The expression of CcF3'5'H gene in the infiltrated petals was also confirmed by real time PCR. In conclusion and based on the findings of the present study, the agroinfiltration could be regarded as a reliable method to identify suitable rose cultivars in blue rose flower production programs.
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Affiliation(s)
- Masoume Zeinipour
- Department of Genetic Engineering, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
- Faculty of Biology Science, Kharazmi University, Tehran, Iran
| | - Pejman Azadi
- Department of Genetic Engineering, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Ahmad Majd
- Faculty of Biology Science, Kharazmi University, Tehran, Iran
| | - Maryam Jafarkhani Kermani
- Department of Genetic Engineering, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Saeed Irian
- Faculty of Biology Science, Kharazmi University, Tehran, Iran
| | - Seyed Mohammad Hosseini
- Department of Genetic Engineering, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Masahiro Mii
- Laboratory of Plant Cell Technology, Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba 271-8510 Japan
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17
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Hidalgo D, Martínez-Márquez A, Cusidó R, Bru-Martínez R, Palazón J, Corchete P. Silybum marianum cell cultures stably transformed with Vitis vinifera stilbene synthase accumulate t-resveratrol in the extracellular medium after elicitation with methyl jasmonate or methylated β-cyclodextrins. Eng Life Sci 2017; 17:686-694. [PMID: 32624814 DOI: 10.1002/elsc.201600241] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 12/27/2016] [Accepted: 01/05/2017] [Indexed: 11/11/2022] Open
Abstract
The growing demand for t-resveratrol for industrial uses has generated considerable interest in its production. Heterologous resveratrol production in plant cell suspensions, apart from requiring the introduction of only one or two genes, has the advantage of high biomass yield and a short cultivation time, and thus could be an option for large-scale production. Silybum marianum is the source of the flavonolignan silymarin. Phenylpropanoid synthesis in cultures of this species can be activated by elicitation with methyl jasmonate and methylated β-cyclodextrins, with products of the pathway (coniferyl alcohol and some isomers of the silymarin complex) being released into the medium. Given that stilbene synthase shares the same key precursors involved in flavonoid and /or monolignol biosynthesis, we explored the potential of metabolically engineered S. marianum cultures for t-resveratrol production. Cell suspensions were stably transformed with Vitis vinifera stilbene synthase 3 and the expression of the transgene led to extracellular t-resveratrol accumulation at the level of milligrams per litre under elicitation. Resveratrol synthesis occurred at the expense of coniferyl alcohol. Production of silymarin was less affected in the transgenic cultures, since the flavonoid pathway is limiting for its synthesis, due to the preferred supply of precursors for the monolignol branch. The fact that the expressed STS gene took excessively produced precursors of non-bioactive compounds (coniferyl alcohol), while keeping the metabolic flow for target secondary compounds (i.e. silymarin) unaltered, opens a way to extend the applications of plant cell cultures for the simultaneous production of both constitutive and foreign valuable metabolites.
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Affiliation(s)
- Diego Hidalgo
- Laboratori de Fisiologia Vegetal Facultat de Farmacia Universitat de Barcelona Barcelona Spain
| | - Ascensión Martínez-Márquez
- Plant Proteomics and Functional Genomics Group Department of Agrochemistry and Biochemistry Faculty of Science University of Alicante Alicante Spain
| | - Rosa Cusidó
- Laboratori de Fisiologia Vegetal Facultat de Farmacia Universitat de Barcelona Barcelona Spain
| | - Roque Bru-Martínez
- Plant Proteomics and Functional Genomics Group Department of Agrochemistry and Biochemistry Faculty of Science University of Alicante Alicante Spain
| | - Javier Palazón
- Laboratori de Fisiologia Vegetal Facultat de Farmacia Universitat de Barcelona Barcelona Spain
| | - Purificación Corchete
- Department of Botany and Plant Physiology Campus Miguel de Unamuno University of Salamanca Salamanca Spain
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18
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Chenenaoui S, Daldoul S, Mliki A. High quality RNA from hydroponically grown grapevine roots suitable for gene expression studies. TURKISH JOURNAL OF BIOCHEMISTRY 2017. [DOI: 10.1515/tjb-2016-0301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractObjectives:Grapevine root system plays a great role in sensing and adapting to abiotic and biotic stresses. Identification of candidate genes involved in the tolerance to abiotic stress is becoming a crucial strategy to select and breed resilient genotypes. However, obtaining high quality RNA from grapevine roots under hydroponic culture is difficult. Hence, we have developed a new extraction procedure to improve RNA quality for root gene expression studies.Methods:Conventional RNA extraction methods using CTAB are not suitable for gene expression studies and need to be improved. Here we report the application of a CTAB- based method for RNA extraction using an additional clean-up purification step.Results:The RIN value of the resulting RNA indicated that our procedure allowed the purification of high RNA quality and quantity. Hence, the clean-up purification step efficiently eliminated contaminants which inhibit downstream applications. Derived RNA was successfully used for differential gene expression analysis in salt stressed grapevine by Northern Blot hybridizations.Conclusion:In this study, we developed an efficient RNA isolation protocol from hydroponic cultivated grapevine roots which yielded RNA suitable for gene expression studies. This will open large perspectives in grapevine functional genomics with the identification of pertinent genes of agronomic interest.
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19
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Martínez-Márquez A, Martínez-Esteso MJ, Vilella-Antón MT, Sellés-Marchart S, Morante-Carriel JA, Hurtado E, Palazon J, Bru-Martínez R. A Tau Class Glutathione- S-Transferase is Involved in Trans-Resveratrol Transport Out of Grapevine Cells. FRONTIERS IN PLANT SCIENCE 2017; 8:1457. [PMID: 28878794 PMCID: PMC5573539 DOI: 10.3389/fpls.2017.01457] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/04/2017] [Indexed: 05/20/2023]
Abstract
Vitis vinifera cell cultures respond to pathogens and elicitors by synthesizing and extracellularly accumulating stilbenoid phytoalexins. Large amounts of trans-resveratrol (t-R) are produced when a cell culture is elicited with methylated cyclodextrins (MBCD), either alone or combined with methyl jasmonate (MeJA). t-R transport to the extracellular medium, which represents the apoplastic space, would place this antifungal defense right in the battlefield to efficiently fight against pathogen attack. Yet despite their physiological relevance, these transport pathways are mostly unknown. A broad hypothesis-free DIGE-based proteomic experiment of a temporal series of elicited grapevine cell cultures was performed to explore the expression profiles of t-R biosynthetic proteins and other co-expressing proteins potentially involved in such a cell response. A correlation between two tau class glutathione-S-transferases (GSTs) with several stilbene synthase and phenylalanine ammonia-lyase isoforms, and with the t-R metabolite itself, was found and further assessed by a qRT-PCR gene expression analysis. The best candidate, GSTU-2, was cloned from the cDNA of the MBCD + MeJA-elicited grapevine cells and used for Agrobacterium-mediated grapevine cell transformation. The non-elicited lines that overexpressed GSTU-2 displayed an extracellular t-R accumulating phenotype, but stabilization of t-R required the addition to culture medium of adsorbent compounds, e.g., PVP or β-cyclodextrin. The wild-type cell cultures accumulated no t-R, not even in the presence of adsorbents. The transient expression of the GSTU-2-GFP fusion proteins in grapevine cells showed localisation in the plasma membrane, and the immunoprecipitation of HA-tagged GSTU-2 revealed its interaction with HIR, a plasma membrane-bound protein. These findings are consistent with a functional role in transport. This is the first report providing several pieces of experimental evidence for the involvement of a specific tau class GST in t-R transport to the extracellular medium.
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Affiliation(s)
- Ascensión Martínez-Márquez
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Faculty of Science, University of AlicanteAlicante, Spain
| | - María J. Martínez-Esteso
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Faculty of Science, University of AlicanteAlicante, Spain
| | - María T. Vilella-Antón
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Faculty of Science, University of AlicanteAlicante, Spain
| | - Susana Sellés-Marchart
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Faculty of Science, University of AlicanteAlicante, Spain
| | - Jaime A. Morante-Carriel
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Faculty of Science, University of AlicanteAlicante, Spain
- Biotechnology and Molecular Biology Group, Quevedo State Technical UniversityQuevedo, Ecuador
| | - Elias Hurtado
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Faculty of Science, University of AlicanteAlicante, Spain
| | - Javier Palazon
- Laboratory of Plant Physiology, Faculty of Pharmacy, University of BarcelonaBarcelona, Spain
| | - Roque Bru-Martínez
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Faculty of Science, University of AlicanteAlicante, Spain
- *Correspondence: Roque Bru-Martínez,
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20
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Ramírez Rivera NG, García-Salinas C, Aragão FJL, Díaz de la Garza RI. Metabolic engineering of folate and its precursors in Mexican common bean (Phaseolus vulgaris L.). PLANT BIOTECHNOLOGY JOURNAL 2016; 14:2021-32. [PMID: 26997331 PMCID: PMC5043471 DOI: 10.1111/pbi.12561] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 03/05/2016] [Accepted: 03/12/2016] [Indexed: 05/24/2023]
Abstract
Folate (vitamin B9) deficiency causes several health problems globally. However, folate biofortification of major staple crops is one alternative that can be used to improve vitamin intakes in populations at risk. We increased the folate levels in common bean by engineering the pteridine branch required for their biosynthesis. GTP cyclohydrolase I from Arabidopsis (AtGchI) was stably introduced into three common bean Pinto cultivars by particle bombardment. Seed-specific overexpression of AtGCHI caused significant increases of up to 150-fold in biosynthetic pteridines in the transformed lines. The pteridine boost enhanced folate levels in raw desiccated seeds by up to threefold (325 μg in a 100 g portion), which would represent 81% of the adult recommended daily allowance. Unexpectedly, the engineering also triggered a general increase in PABA levels, the other folate precursor. This was not observed in previous engineering studies and was probably caused by a feedforward mechanism that remains to be elucidated. Results from this work also show that common bean grains accumulate considerable amounts of oxidized pteridines that might represent products of folate degradation in desiccating seeds. Our study uncovers a probable different regulation of folate homoeostasis in these legume grains than that observed in other engineering works. Legumes are good sources of folates, and this work shows that they can be engineered to accumulate even greater amounts of folate that, when consumed, can improve folate status. Biofortification of common bean with folates and other micronutrients represents a promising strategy to improve the nutritional status of populations around the world.
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Affiliation(s)
- Naty G Ramírez Rivera
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Monterrey, Nuevo León, México
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21
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Martínez-Márquez A, Morante-Carriel JA, Ramírez-Estrada K, Cusidó RM, Palazon J, Bru-Martínez R. Production of highly bioactive resveratrol analogues pterostilbene and piceatannol in metabolically engineered grapevine cell cultures. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1813-25. [PMID: 26947765 PMCID: PMC5069453 DOI: 10.1111/pbi.12539] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/11/2016] [Accepted: 01/11/2016] [Indexed: 05/23/2023]
Abstract
Grapevine stilbenes, particularly trans-resveratrol, have a demonstrated pharmacological activity. Other natural stilbenes derived from resveratrol such as pterostilbene or piceatannol, display higher oral bioavailability and bioactivity than the parent compound, but are far less abundant in natural sources. Thus, to efficiently obtain these bioactive resveratrol derivatives, there is a need to develop new bioproduction systems. Grapevine cell cultures are able to produce large amounts of easily recoverable extracellular resveratrol when elicited with methylated cyclodextrins and methyl jasmonate. We devised this system as an interesting starting point of a metabolic engineering-based strategy to produce resveratrol derivatives using resveratrol-converting enzymes. Constitutive expression of either Vitis vinifera resveratrol O-methyltransferase (VvROMT) or human cytochrome P450 hydroxylase 1B1 (HsCYP1B1) led to pterostilbene or piceatannol, respectively, after the engineered cell cultures were treated with the aforementioned elicitors. Functionality of both gene products was first assessed in planta by Nicotiana benthamiana agroinfiltration assays, in which tobacco cells transiently expressed stilbene synthase and VvROMT or HsCYP1B1. Grapevine cell cultures transformed with VvROMT produced pterostilbene, which was detected in both intra- and extracellular compartments, at a level of micrograms per litre. Grapevine cell cultures transformed with HsCYP1B1 produced about 20 mg/L culture of piceatannol, displaying a sevenfold increase in relation to wild-type cultures, and reaching an extracellular distribution of up to 45% of total production. The results obtained demonstrate the feasibility of this novel system for the bioproduction of natural and more bioactive resveratrol derivatives and suggest new ways for the improvement of production yields.
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Affiliation(s)
- Ascensión Martínez-Márquez
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Faculty of Science, University of Alicante, Alicante, Spain
| | - Jaime A Morante-Carriel
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Faculty of Science, University of Alicante, Alicante, Spain
- Biotechnology and Molecular Biology Group, Quevedo State Technical University, Quevedo, Ecuador
| | - Karla Ramírez-Estrada
- Laboratory of Plant Physiology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Rosa M Cusidó
- Laboratory of Plant Physiology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Javier Palazon
- Laboratory of Plant Physiology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Roque Bru-Martínez
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Faculty of Science, University of Alicante, Alicante, Spain
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22
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Isolation of high-quality RNA from Platycladus orientalis and other Cupressaceae plants. ELECTRON J BIOTECHN 2016. [DOI: 10.1016/j.ejbt.2016.08.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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23
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Sahebi M, Hanafi MM, Azizi P, Hakim A, Ashkani S, Abiri R. Suppression Subtractive Hybridization Versus Next-Generation Sequencing in Plant Genetic Engineering: Challenges and Perspectives. Mol Biotechnol 2016; 57:880-903. [PMID: 26271955 DOI: 10.1007/s12033-015-9884-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Suppression subtractive hybridization (SSH) is an effective method to identify different genes with different expression levels involved in a variety of biological processes. This method has often been used to study molecular mechanisms of plants in complex relationships with different pathogens and a variety of biotic stresses. Compared to other techniques used in gene expression profiling, SSH needs relatively smaller amounts of the initial materials, with lower costs, and fewer false positives present within the results. Extraction of total RNA from plant species rich in phenolic compounds, carbohydrates, and polysaccharides that easily bind to nucleic acids through cellular mechanisms is difficult and needs to be considered. Remarkable advancement has been achieved in the next-generation sequencing (NGS) field. As a result of progress within fields related to molecular chemistry and biology as well as specialized engineering, parallelization in the sequencing reaction has exceptionally enhanced the overall read number of generated sequences per run. Currently available sequencing platforms support an earlier unparalleled view directly into complex mixes associated with RNA in addition to DNA samples. NGS technology has demonstrated the ability to sequence DNA with remarkable swiftness, therefore allowing previously unthinkable scientific accomplishments along with novel biological purposes. However, the massive amounts of data generated by NGS impose a substantial challenge with regard to data safe-keeping and analysis. This review examines some simple but vital points involved in preparing the initial material for SSH and introduces this method as well as its associated applications to detect different novel genes from different plant species. This review evaluates general concepts, basic applications, plus the probable results of NGS technology in genomics, with unique mention of feasible potential tools as well as bioinformatics.
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Affiliation(s)
- Mahbod Sahebi
- Laboratory of Plantation Crops, Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia,
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24
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Xiao H, Kim WS, Meng B. A highly effective and versatile technology for the isolation of RNAs from grapevines and other woody perennials for use in virus diagnostics. Virol J 2015; 12:171. [PMID: 26482551 PMCID: PMC4615883 DOI: 10.1186/s12985-015-0376-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/05/2015] [Indexed: 10/31/2022] Open
Abstract
BACKGROUND Isolation of pure RNA from woody perennials, especially fruit crops such as grapevine rich in complex secondary metabolites, has remained very challenging. Lack of effective RNA isolation technology has resulted in difficulties in viral diagnosis and discovery as well as studies on many biological processes of these highly important woody plants. It is imperative to develop and refine methodologies with which large amounts of pure nucleic acids can be readily isolated from woody perennials. METHODS We compared five commonly used RNA isolation kits in isolating total RNA from twelve species of woody perennials. We made modifications to select RNA isolation systems to simplify and improve their efficiency in RNA isolation. The yield and quality of isolated RNAs were assessed via gel electrophoresis and spectrophotometric measurement. We also performed RT-PCR and RT-qPCR to detect several major viruses from grapevines. RESULTS Two of the kits were shown to be the best in both the yield and quality of the isolated RNA from all twelve woody species. Using disposable extraction bags for tissue homogenization not only improved the yield without affecting quality, but also made the RNA isolation technology simpler, less costly, and suitable for adoption by many potential users with facility limitations. This system was successfully applied to a wide range of woody plants, including fruit crops, ornamentals and timber trees. Inclusion of polyvinylpyrrolidone in the extraction buffer drastically improved the performance of the system in isolating total RNA from old grapevine leaves collected later in the season. This modification made our system highly effective in isolating quality RNA from grapevine leaves throughout the entire growing season. We further demonstrated that the resulting nucleic acid preparations are suitable for detection of several major grapevine viruses with RNA or DNA genomes using PCR, RT-PCR and qPCR as well as for assays on plant microRNAs. CONCLUSIONS This improved RNA isolation system would have wide applications in viral diagnostics and discovery, studies on gene expression and regulation, transcriptomics, and small RNA biology in grapevines. We believe this system will also be useful in diverse applications pertaining to research on many other woody perennials and recalcitrant plant species.
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Affiliation(s)
- Huogen Xiao
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
| | - Won-Sik Kim
- Norgen BioTek, Thorald, ON, L2V 4Y6, Canada.
| | - Baozhong Meng
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
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25
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Ouyang K, Li J, Huang H, Que Q, Li P, Chen X. A simple method for RNA isolation from various tissues of the tree Neolamarckia cadamba. BIOTECHNOL BIOTEC EQ 2014; 28:1008-1013. [PMID: 26019587 PMCID: PMC4434054 DOI: 10.1080/13102818.2014.981086] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 07/28/2014] [Indexed: 10/31/2022] Open
Abstract
Plant tissues contain abundant polysaccharides, phenolic compounds and other metabolites, which makes it difficult to isolate high-quality RNA from them. In addition, Neolamarckia cadamba contains large quantities of other components, particularly RNA-binding alkaloids, which makes the isolation even more challenging. Here, we describe a concise and efficient RNA isolation method that combines the cetyltrimethyl ammonium bromide (CTAB) and Plant RNA Kit (Omega) protocols. Gel electrophoresis showed that RNA extracted from all tissues, using this protocol, was of good integrity and without DNA contamination. Furthermore, the isolated RNA was of high purity, with an A260/A280 ratio of 2.1 and an A260/A230 ratio of >2.0. The isolated RNA was also suitable for downstream applications, such as reverse transcription-polymerase chain reaction (RT-PCR) and quantitative RT-PCR (RT-qPCR). The RNA isolation method was also efficient for recalcitrant plant tissues.
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Affiliation(s)
- Kunxi Ouyang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University , Guangzhou , Guangdong , P.R. China
| | - Juncheng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University , Guangzhou , Guangdong , P.R. China
| | - Hao Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University , Guangzhou , Guangdong , P.R. China ; Guangxi Botanical Garden of Medicinal Plants , Nanning , Guangxi , P.R. China
| | - Qingmin Que
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University , Guangzhou , Guangdong , P.R. China
| | - Pei Li
- Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants, Ministry of Education, National Engineering Laboratory for Forest Tree Breeding, Beijing Forestry University , Beijing , P.R. China
| | - Xiaoyang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University , Guangzhou , Guangdong , P.R. China
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