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Identification of Known and Novel Arundo donax L. MicroRNAs and Their Targets Using High-Throughput Sequencing and Degradome Analysis. Life (Basel) 2022; 12:life12050651. [PMID: 35629319 PMCID: PMC9142972 DOI: 10.3390/life12050651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 11/17/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of non-coding molecules involved in the regulation of a variety of biological processes. They have been identified and characterized in several plant species, but only limited data are available for Arundo donax L., one of the most promising bioenergy crops. Here we identified, for the first time, A. donax conserved and novel miRNAs together with their targets, through a combined analysis of high-throughput sequencing of small RNAs, transcriptome and degradome data. A total of 134 conserved miRNAs, belonging to 45 families, and 27 novel miRNA candidates were identified, along with the corresponding primary and precursor miRNA sequences. A total of 96 targets, 69 for known miRNAs and 27 for novel miRNA candidates, were also identified by degradome analysis and selected slice sites were validated by 5′-RACE. The identified set of conserved and novel candidate miRNAs, together with their targets, extends our knowledge about miRNAs in monocots and pave the way to further investigations on miRNAs-mediated regulatory processes in A. donax, Poaceae and other bioenergy crops.
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Faralli M, Williams K, Corke F, Li M, Doonan JH, Varotto C. Interspecific and intraspecific phenotypic diversity for drought adaptation in bioenergy Arundo species. GLOBAL CHANGE BIOLOGY. BIOENERGY 2021; 13:753-769. [PMID: 33777185 PMCID: PMC7986115 DOI: 10.1111/gcbb.12810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 01/11/2021] [Indexed: 05/29/2023]
Abstract
Biomass crops are commonly grown in low-grade land and selection of drought-tolerant accessions is of major importance to sustain productivity. In this work, we assess phenotypic variation under different environmental scenarios in a series of accessions of Arundo donax, and contrast it with two closely related species, Arundo donaciformis and Arundo plinii. Gas-exchange and stomatal anatomy analysis showed an elevated photosynthetic capacity in A. plinii compared to A. donax and A. donaciformis with a significant intraspecific variation in A. donax. The three species showed significantly contrasting behaviour of transpiration under developing water stress and increasing vapour pressure deficit (VPD), with A. donax being the most conservative while A. plinii showed an elevated degree of insensitivity to environmental cues. Under optimal conditions, A. donax had the highest estimated leaf area (projected leaf area) and plant dry weight although a significant reduction under water stress was observed for A. donax and A. donaciformis accessions while no differences were recorded for A. plinii between optimal growing conditions (well-watered [WW]) and reduced soil water availability (water-stressed [WS]). A. donax displayed a markedly conservative water use behaviour but elevated sensitivity of biomass accumulation under stress conditions. By contrast, in A. plinii, biomass and transpiration were largely insensitive to WS and increasing VPD, though biomass dry weight under optimal conditions was significantly lower than A. donax. We provide evidence of interspecific phenotypic variation within the Arundo genus while the intraspecific phenotypic plasticity may be exploited for further selection of superior clones under disadvantageous environmental conditions. The extensive trade-off between water use and biomass accumulation present in the three species under stress conditions provides a series of novel traits to be exploited in the selection of superior clones adapted to different environmental scenarios. Non-destructive approaches are provided to screen large populations for water-stress-tolerant A. donax clones.
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Affiliation(s)
- Michele Faralli
- Department of Biodiversity and Molecular Ecology, Research and Innovation CentreFondazione Edmund MachSan Michele all'Adige (TN)Italy
| | - Kevin Williams
- National Plant Phenomics Centre (NPPC)IBERSAberystwyth UniversityWalesUK
| | - Fiona Corke
- National Plant Phenomics Centre (NPPC)IBERSAberystwyth UniversityWalesUK
| | - Mingai Li
- Department of Biodiversity and Molecular Ecology, Research and Innovation CentreFondazione Edmund MachSan Michele all'Adige (TN)Italy
| | - John H. Doonan
- National Plant Phenomics Centre (NPPC)IBERSAberystwyth UniversityWalesUK
| | - Claudio Varotto
- Department of Biodiversity and Molecular Ecology, Research and Innovation CentreFondazione Edmund MachSan Michele all'Adige (TN)Italy
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Li C, Wang Z, Nong Q, Lin L, Xie J, Mo Z, Huang X, Song X, Malviya MK, Solanki MK, Li Y. Physiological changes and transcriptome profiling in Saccharum spontaneum L. leaf under water stress and re-watering conditions. Sci Rep 2021; 11:5525. [PMID: 33750876 PMCID: PMC7943799 DOI: 10.1038/s41598-021-85072-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/24/2021] [Indexed: 12/13/2022] Open
Abstract
As the polyploidy progenitor of modern sugarcane, Saccharum spontaneum is considered to be a valuable resistance source to various biotic and abiotic stresses. However, little has been reported on the mechanism of drought tolerance in S. spontaneum. Herein, the physiological changes of S. spontaneum GXS87-16 at three water-deficit levels (mild, moderate, and severe) and after re-watering during the elongation stage were investigated. RNA sequencing was utilized for global transcriptome profiling of GXS87-16 under severe drought and re-watered conditions. There were significant alterations in the physiological parameters of GXS87-16 in response to drought stress and then recovered differently after re-watering. A total of 1569 differentially expressed genes (DEGs) associated with water stress and re-watering were identified. Notably, the majority of the DEGs were induced by stress. GO functional annotations and KEGG pathway analysis assigned the DEGs to 47 GO categories and 93 pathway categories. The pathway categories were involved in various processes, such as RNA transport, mRNA surveillance, plant hormone signal transduction, and plant-pathogen interaction. The reliability of the RNA-seq results was confirmed by qRT-PCR. This study shed light on the regulatory processes of drought tolerance in S. spontaneum and identifies useful genes for genetic improvement of drought tolerance in sugarcane.
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Affiliation(s)
- Changning Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007, China
| | - Zhen Wang
- College of Biology and Pharmacy, Yulin Normal University, Yulin, 537000, China
| | - Qian Nong
- Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
| | - Li Lin
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007, China
| | - Jinlan Xie
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007, China
| | - Zhanghong Mo
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007, China
| | - Xing Huang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007, China
| | - Xiupeng Song
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007, China
| | - Mukesh Kumar Malviya
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007, China
| | - Manoj Kumar Solanki
- Department of Food Quality and Safety, The Volcani Center, Institute for Post-Harvest and Food Sciences, Agricultural Research Organization, Rishon LeZion, Israel
| | - Yangrui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007, China.
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Danelli T, Laura M, Savona M, Landoni M, Adani F, Pilu R. Genetic Improvement of Arundo donax L.: Opportunities and Challenges. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1584. [PMID: 33207586 PMCID: PMC7696946 DOI: 10.3390/plants9111584] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/09/2020] [Accepted: 11/13/2020] [Indexed: 12/29/2022]
Abstract
Arundo donax L., the giant reed-being a long-duration, low-cost, non-food energy crop able to grow in marginal lands-has emerged as a potential alternative to produce biomass for both energy production, with low carbon emissions, and industrial bioproducts. In recent years, pioneering efforts have been made to genetically improve this very promising energy crop. This review analyses the recent advances and challenges encountered in using clonal selection, mutagenesis/somaclonal variation and transgenesis/genome editing. Attempts to improve crop yield, in vitro propagation efficiency, salt and heavy metal tolerance by clonal selection were carried out, although limited by the species' low genetic diversity and availability of mutants. Mutagenesis and somaclonal variation have also been attempted on this species; however, since Arundo donax is polyploid, it is very difficult to induce and select promising mutations. In more recent years, genomics and transcriptomics data are becoming available in Arundo, closing the gap to make possible the genetic manipulation of this energy crop in the near future. The challenge will regard the functional characterization of the genes/sequences generated by genomic sequencing and transcriptomic analysis in a complex polyploid genome.
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Affiliation(s)
- Tommaso Danelli
- Gruppo Ricicla Labs—Department of Agricultural and Environmental Sciences—Production, Landscape and Agroenergy, Università’ Degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy; (T.D.); (F.A.)
- Agricultural Genetics Group—Department of Agricultural and Environmental Sciences—Production, Landscape and Agroenergy, Università’ Degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy
| | - Marina Laura
- CREA, Research Centre for Vegetable and Ornamental Crops, Corso Degli Inglesi 508, 18038 Sanremo, Italy; (M.L.); (M.S.)
| | - Marco Savona
- CREA, Research Centre for Vegetable and Ornamental Crops, Corso Degli Inglesi 508, 18038 Sanremo, Italy; (M.L.); (M.S.)
| | - Michela Landoni
- Department of Biosciences, Università’ Degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy;
| | - Fabrizio Adani
- Gruppo Ricicla Labs—Department of Agricultural and Environmental Sciences—Production, Landscape and Agroenergy, Università’ Degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy; (T.D.); (F.A.)
- Agricultural Genetics Group—Department of Agricultural and Environmental Sciences—Production, Landscape and Agroenergy, Università’ Degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy
| | - Roberto Pilu
- Gruppo Ricicla Labs—Department of Agricultural and Environmental Sciences—Production, Landscape and Agroenergy, Università’ Degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy; (T.D.); (F.A.)
- Agricultural Genetics Group—Department of Agricultural and Environmental Sciences—Production, Landscape and Agroenergy, Università’ Degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy
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Sicilia A, Santoro DF, Testa G, Cosentino SL, Lo Piero AR. Transcriptional response of giant reed (Arundo donax L.) low ecotype to long-term salt stress by unigene-based RNAseq. PHYTOCHEMISTRY 2020; 177:112436. [PMID: 32563719 DOI: 10.1016/j.phytochem.2020.112436] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/03/2020] [Accepted: 06/07/2020] [Indexed: 06/11/2023]
Abstract
The giant reed is a fast growing herbaceous non-food crop considered as eligible alternative energy source to reduce the usage of fossil fuels. Tolerance of this plant to abiotic stress has been demonstrated across a range of stressful conditions, thus allowing cultivation in marginal or poorly cultivated land in order not to compromise food security and to overcome land use controversies. In this work, we de novo sequenced, assembled and analyzed the A. donax low G34 ecotype leaf transcriptome (RNAseq analysis) subjected to severe long-term salt stress (256.67 mM NaCl corresponding to 32 dS m-1 electric conductibility). In order to shed light upon the response to high salinity of this non model plant, we analyzed clusters related to salt sensory and signaling transduction, transcription factors, hormone regulation, Reactive Oxygen Species (ROS) scavenging and osmolyte biosynthesis, all of them showing different regulation compared to untreated plants. The analysis of clusters related to ethylene biosynthesis and signaling indicated that gene transcription is modulated towards the minimization of ethylene negative effects upon plant growth. Certainly, the photosynthesis is strongly affected since genes involved in Rubisco biosynthesis and assembly are down-regulated. However, a shift towards C4 photosynthesis is likely to occur as gene regulation is aimed to activate the primary CO2 fixation to PEP (phosphoenolpyruvate). The analysis of "carbon metabolism" category revealed that G34 ecotype under salt stress induces the expression of glycolysis and Krebs cycle related genes, this being consistent with the hypothesis that some sort of salt avoidance might be occurred in A. donax G34 low ecotype. By comparing our results with findings obtained with other giant reed ecotype, we identified several differences in the response to salt that are in accordance with the possibility that heritable phenotypic differences among clones of A. donax might be accumulated especially in ecotypes originating from distant geographical areas, despite their asexual reproduction modality. Additionally, 26,838 simple sequence repeat (SSR) markers were identified and validated. This SSR dataset definitely expands the marker catalogue of A. donax facilitating the genotypic characterization of this species.
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Affiliation(s)
- Angelo Sicilia
- Department of Agriculture, Food and Environment, University of Catania, Via Santa Sofia 98, 95123, Catania, Italy
| | - Danilo Fabrizio Santoro
- Department of Agriculture, Food and Environment, University of Catania, Via Santa Sofia 98, 95123, Catania, Italy
| | - Giorgio Testa
- Department of Agriculture, Food and Environment, University of Catania, Via Santa Sofia 98, 95123, Catania, Italy
| | - Salvatore Luciano Cosentino
- Department of Agriculture, Food and Environment, University of Catania, Via Santa Sofia 98, 95123, Catania, Italy
| | - Angela Roberta Lo Piero
- Department of Agriculture, Food and Environment, University of Catania, Via Santa Sofia 98, 95123, Catania, Italy.
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Jike W, Li M, Zadra N, Barbaro E, Sablok G, Bertorelle G, Rota-Stabelli O, Varotto C. Phylogenomic proof of Recurrent Demipolyploidization and Evolutionary Stalling of the "Triploid Bridge" in Arundo (Poaceae). Int J Mol Sci 2020; 21:E5247. [PMID: 32722033 PMCID: PMC7432733 DOI: 10.3390/ijms21155247] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/20/2020] [Accepted: 07/22/2020] [Indexed: 01/09/2023] Open
Abstract
Polyploidization is a frequent phenomenon in plants, which entails the increase from one generation to the next by multiples of the haploid number of chromosomes. While tetraploidization is arguably the most common and stable outcome of polyploidization, over evolutionary time triploids often constitute only a transient phase, or a "triploid bridge", between diploid and tetraploid levels. In this study, we reconstructed in a robust phylogenomic and statistical framework the evolutionary history of polyploidization in Arundo, a small genus from the Poaceae family with promising biomass, bioenergy and phytoremediation species. Through the obtainment of 10 novel leaf transcriptomes for Arundo and outgroup species, our results prove that recurrent demiduplication has likely been a major driver of evolution in this species-poor genus. Molecular dating further demonstrates that the species originating by demiduplication stalled in the "triploid bridge" for evolutionary times in the order of millions of years without undergoing tetratploidization. Nevertheless, we found signatures of molecular evolution highlighting some of the processes that accompanied the genus radiation. Our results clarify the complex nature of Arundo evolution and are valuable for future gene functional validation as well as reverse and comparative genomics efforts in the Arundo genus and other Arundinoideae.
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Affiliation(s)
- Wuhe Jike
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige (TN), Italy; (W.J.); (M.L.); (E.B.)
- Dipartimento di Scienze della Vita e Biotecnologie, Università degli Studi di Ferrara, 44121 Ferrara, Italy;
| | - Mingai Li
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige (TN), Italy; (W.J.); (M.L.); (E.B.)
| | - Nicola Zadra
- Department of Sustainable Ecosystems & Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige (TN), Italy; (N.Z.); (O.R.-S.)
| | - Enrico Barbaro
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige (TN), Italy; (W.J.); (M.L.); (E.B.)
| | - Gaurav Sablok
- Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland;
| | - Giorgio Bertorelle
- Dipartimento di Scienze della Vita e Biotecnologie, Università degli Studi di Ferrara, 44121 Ferrara, Italy;
| | - Omar Rota-Stabelli
- Department of Sustainable Ecosystems & Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige (TN), Italy; (N.Z.); (O.R.-S.)
| | - Claudio Varotto
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige (TN), Italy; (W.J.); (M.L.); (E.B.)
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Xu J, Trainotti L, Li M, Varotto C. Overexpression of Isoprene Synthase Affects ABA- and Drought-Related Gene Expression and Enhances Tolerance to Abiotic Stress. Int J Mol Sci 2020; 21:E4276. [PMID: 32560078 PMCID: PMC7352718 DOI: 10.3390/ijms21124276] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/10/2020] [Accepted: 06/13/2020] [Indexed: 01/08/2023] Open
Abstract
Isoprene is the most abundant single biogenic volatile compound emitted by plants. Despite the relevance of this molecule to plant abiotic resistance and its impact on global atmospheric chemistry, little is known about the details of its mechanism of action. Here, we characterized through both physiological and molecular methods the mechanisms of action of isoprene using model transgenic arabidopsis lines overexpressing a monocot isoprene synthase gene. Our results demonstrated the effect that isoprene had on ABA signaling at different tissue-specific, spatial, and temporal scales. In particular, we found that isoprene enhanced stomatal sensitivity to ABA through upregulation of RD29B signaling gene. By contrast, isoprene decreased sensitivity to ABA in germinating seeds and roots, suggesting tissue-specific mechanisms of action. In leaves, isoprene caused the downregulation of COR15A and P5CS genes, suggesting that the enhanced tolerance to water-deprivation stress observed in isoprene-emitting plants may be mediated chiefly by an enhanced membrane integrity and tolerance to osmotic stress.
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Affiliation(s)
- Jia Xu
- Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, Research and Innovation Centre, via Mach 1, 38010 San Michele all’Adige (TN), Italy;
- Dipartimento di Biologia, Università degli Studi di Padova, viale Giuseppe Colombo, 3, 35131 Padova, Italy;
| | - Livio Trainotti
- Dipartimento di Biologia, Università degli Studi di Padova, viale Giuseppe Colombo, 3, 35131 Padova, Italy;
| | - Mingai Li
- Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, Research and Innovation Centre, via Mach 1, 38010 San Michele all’Adige (TN), Italy;
| | - Claudio Varotto
- Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, Research and Innovation Centre, via Mach 1, 38010 San Michele all’Adige (TN), Italy;
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Min X, Lin X, Ndayambaza B, Wang Y, Liu W. Coordinated mechanisms of leaves and roots in response to drought stress underlying full-length transcriptome profiling in Vicia sativa L. BMC PLANT BIOLOGY 2020; 20:165. [PMID: 32293274 PMCID: PMC7161134 DOI: 10.1186/s12870-020-02358-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 03/24/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Common vetch (Vicia sativa L.) is an important self-pollinating annual forage legume and is of interest for drought prone regions as a protein source to feed livestock and human consumption. However, the development and production of common vetch are negatively affected by drought stress. Plants have evolved common or distinct metabolic pathways between the aboveground and underground in response to drought stress. Little is known regarding the coordinated response of aboveground and underground tissues of common vetch to drought stress. RESULTS Our results showed that a total of 30,427 full-length transcripts were identified in 12 samples, with an average length of 2278.89 bp. Global transcriptional profiles of the above 12 samples were then analysed via Illumina-Seq. A total of 3464 and 3062 differentially expressed genes (DEGs) were identified in the leaves and roots, respectively. Gene Ontology (GO) enrichment analyses identified that the dehydrin genes and Δ1-pyrroline-5-carboxylate synthase were induced for the biosynthesis of proline and water conservation. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis results indicated that the DEGs were significantly enriched in hormone signal transduction, starch and sucrose metabolism, and arginine and proline metabolism, and various drought response candidate genes were also identified. Abscisic acid (ABA; the AREB/ABF-SnRK2 pathway) regulates the activity of AMY3 and BAM1 to induce starch degradation in leaves and increase carbon export to roots, which may be associated with the drought stress responses in common vetch. Among the co-induced transcription factors (TFs), AREB/ABF, bHLH, MYB, WRKY, and AP2/ERF had divergent expression patterns and may be key in the crosstalk between leaves and roots during adaption to drought stress. In transgenic yeast, the overexpression of four TFs increased yeast tolerance to osmotic stresses. CONCLUSION The multipronged approach identified in the leaves and roots broadens our understanding of the coordinated mechanisms of drought response in common vetch, and further provides targets to improve drought resistance through genetic engineering.
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Affiliation(s)
- Xueyang Min
- State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, China; Western China Technology Innovation Centre for Grassland Industry, Gansu Province, China; Engineering Research Center of Grassland Industry, Ministry of Education, China; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Xiaoshan Lin
- State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, China; Western China Technology Innovation Centre for Grassland Industry, Gansu Province, China; Engineering Research Center of Grassland Industry, Ministry of Education, China; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Boniface Ndayambaza
- State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, China; Western China Technology Innovation Centre for Grassland Industry, Gansu Province, China; Engineering Research Center of Grassland Industry, Ministry of Education, China; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Yanrong Wang
- State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, China; Western China Technology Innovation Centre for Grassland Industry, Gansu Province, China; Engineering Research Center of Grassland Industry, Ministry of Education, China; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China.
| | - Wenxian Liu
- State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, China; Western China Technology Innovation Centre for Grassland Industry, Gansu Province, China; Engineering Research Center of Grassland Industry, Ministry of Education, China; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China.
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Ma L, Yi D, Gong W, Gong P, Wang Z. De novo transcriptome characterisation of two auxin-related genes associated with plant growth habit in Astragalus adsurgens Pall. PLANT BIOLOGY (STUTTGART, GERMANY) 2020; 22:3-12. [PMID: 31571396 DOI: 10.1111/plb.13052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 09/25/2019] [Indexed: 06/10/2023]
Abstract
Astragalus adsurgens Pall., a perennial legume native to China, is commonly used as a forage crop. And it has great value for sustainable development of grasslands in arid and semi arid regions. However, to date, little is known regarding the A. adsurgens genome, and no studies have determined whether it would be possible to improve the germplasm of A. adsurgens through genetic modification. In this study, we used an RNA-seq protocol to generate a de novo transcriptome including 151,516 unigenes of A. adsurgens. We compared the transcriptomes of A. adsurgens having different growth habits (prostrate/erect) and identified 14,133 single nucleotide polymorphism sites (SNP) in 8,139 unigenes. Differential expression gene (DEG) analysis suggested that 10,982 unigenes were up-regulated in the prostrate plant relative to the erect plant, while 10,607 unigenes were down-regulated. Of the 21,589 DEG, Unigene72782_All (LAX4) and CL12494.Contig3_All (TIR1), an auxin transporter gene and an auxin transport inhibitor gene, respectively, were predicted to influence the growth habit of A. adsurgens, which were verified by qRT-PCR in these phenotypes. These results suggest that auxin transport was more active in the prostrate plant than in the erect plant, resulting in asymmetric distribution of auxin that affects the growth habit of A. adsurgens. Overall, this study may provide a basis for future research on key genes in A. adsurgens and may deepen our understanding of the molecular mechanisms regulating plant growth habit.
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Affiliation(s)
- L Ma
- Institute of Animal Sciences, Chinese Academy of Agriculture Sciences, Beijing, China
| | - D Yi
- Institute of Animal Sciences, Chinese Academy of Agriculture Sciences, Beijing, China
| | - W Gong
- Institute of Animal Sciences, Chinese Academy of Agriculture Sciences, Beijing, China
- College of Pratacultural Science, Gansu Agricultural University, Lanzhou, China
| | - P Gong
- Institute of Animal Sciences, Chinese Academy of Agriculture Sciences, Beijing, China
- Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Z Wang
- Institute of Animal Sciences, Chinese Academy of Agriculture Sciences, Beijing, China
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10
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Li M, Cappellin L, Xu J, Biasioli F, Varotto C. High-throughput screening for in planta characterization of VOC biosynthetic genes by PTR-ToF-MS. JOURNAL OF PLANT RESEARCH 2020; 133:123-131. [PMID: 31701286 PMCID: PMC6946754 DOI: 10.1007/s10265-019-01149-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 10/28/2019] [Indexed: 06/10/2023]
Abstract
Functional characterization of plant volatile organic compound (VOC) biosynthetic genes and elucidation of the biological function of their products often involve the screening of large numbers of plants from either independent transformation events or mapping populations. The low time resolution of standard gas chromatographic methods, however, represents a major bottleneck for in planta genetic characterization of VOC biosynthetic genes. Here we present a fast and highly-sensitive method for the high-throughput characterization of VOC emission levels/patterns by coupling a Proton Transfer Reaction Time-of-Flight Mass Spectrometer to an autosampler for automation of sample measurement. With this system more than 700 samples per day can be screened, detecting for each sample hundreds of spectrometric peaks in the m/z 15-300 range. As a case study, we report the characterization of VOC emissions from 116 independent Arabidopsis thaliana lines transformed with a putative isoprene synthase gene, confirming its function also when fused to a C-terminal 3×FLAG tag. We demonstrate that the method is more reliable than conventional characterization of transgene expression for the identification of the most highly isoprene-emitting lines. The throughput of this VOC screening method exceeds that of existing alternatives, potentially allowing its application to reverse and forward genetic screenings of genes contributing to VOC emission, constituting a powerful tool for the functional characterization of VOC biosynthetic genes and elucidation of the biological functions of their products directly in planta.
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Affiliation(s)
- Mingai Li
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, 38010, San Michele all' Adige, TN, Italy
| | - Luca Cappellin
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, 38010, San Michele all' Adige, TN, Italy
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35121, Padua, Italy
| | - Jia Xu
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, 38010, San Michele all' Adige, TN, Italy
- Dipartimento di Biologia, Università di Padova, Viale G. Colombo 3, 35121, Padua, Italy
| | - Franco Biasioli
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, 38010, San Michele all' Adige, TN, Italy
| | - Claudio Varotto
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, 38010, San Michele all' Adige, TN, Italy.
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11
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Docimo T, De Stefano R, De Palma M, Cappetta E, Villano C, Aversano R, Tucci M. Transcriptional, metabolic and DNA methylation changes underpinning the response of Arundo donax ecotypes to NaCl excess. PLANTA 2019; 251:34. [PMID: 31848729 DOI: 10.1007/s00425-019-03325-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 12/06/2019] [Indexed: 06/10/2023]
Abstract
Arundo donax ecotypes react differently to salinity, partly due to differences in constitutive defences and methylome plasticity. Arundo donax L. is a C3 fast-growing grass that yields high biomass under stress. To elucidate its ability to produce biomass under high salinity, we investigated short/long-term NaCl responses of three ecotypes through transcriptional, metabolic and DNA methylation profiling of leaves and roots. Prolonged salt treatment discriminated the sensitive ecotype 'Cercola' from the tolerant 'Domitiana' and 'Canneto' in terms of biomass. Transcriptional and metabolic responses to NaCl differed between the ecotypes. In roots, constitutive expression of ion transporter and stress-related transcription factors' genes was higher in 'Canneto' and 'Domitiana' than 'Cercola' and 21-day NaCl drove strong up-regulation in all ecotypes. In leaves, unstressed 'Domitiana' confirmed higher expression of the above genes, whose transcription was repressed in 'Domitiana' but induced in 'Cercola' following NaCl treatment. In all ecotypes, salinity increased proline, ABA and leaf antioxidants, paralleled by up-regulation of antioxidant genes in 'Canneto' and 'Cercola' but not in 'Domitiana', which tolerated a higher level of oxidative damage. Changes in DNA methylation patterns highlighted a marked capacity of the tolerant 'Domitiana' ecotype to adjust DNA methylation to salt stress. The reduced salt sensitivity of 'Domitiana' and, to a lesser extent, 'Canneto' appears to rely on a complex set of constitutively activated defences, possibly due to the environmental conditions of the site of origin, and on higher plasticity of the methylome. Our findings provide insights into the mechanisms of adaptability of A. donax ecotypes to salinity, offering new perspectives for the improvement of this species for cultivation in limiting environments.
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Affiliation(s)
- Teresa Docimo
- Institute of Biosciences and BioResources, Research Division Portici, National Research Council, via Università 133, 80055, Portici, Italy
| | - Rosalba De Stefano
- Institute of Biosciences and BioResources, Research Division Portici, National Research Council, via Università 133, 80055, Portici, Italy
| | - Monica De Palma
- Institute of Biosciences and BioResources, Research Division Portici, National Research Council, via Università 133, 80055, Portici, Italy
| | - Elisa Cappetta
- Institute of Biosciences and BioResources, Research Division Portici, National Research Council, via Università 133, 80055, Portici, Italy
| | - Clizia Villano
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055, Portici, Italy
| | - Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055, Portici, Italy
| | - Marina Tucci
- Institute of Biosciences and BioResources, Research Division Portici, National Research Council, via Università 133, 80055, Portici, Italy.
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12
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Cocozza C, Brilli F, Miozzi L, Pignattelli S, Rotunno S, Brunetti C, Giordano C, Pollastri S, Centritto M, Accotto GP, Tognetti R, Loreto F. Impact of high or low levels of phosphorus and high sodium in soils on productivity and stress tolerance of Arundo donax plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 289:110260. [PMID: 31623790 DOI: 10.1016/j.plantsci.2019.110260] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 09/06/2019] [Accepted: 09/08/2019] [Indexed: 06/10/2023]
Abstract
The potential of Arundo donax to grow in degraded soils, characterized by excess of salinity (Na+), and phosphorus deficiency (-P) or excess (+P) also coupled with salinity (+NaP), was investigated by combining in vivo plant phenotyping, quantification of metabolites and ultrastructural imaging of leaves with a transcriptome-wide screening. Photosynthesis and growth were impaired by + Na, -P and + NaP. While + Na caused stomatal closure, enhanced biosynthesis of carotenoids, sucrose and isoprene and impaired anatomy of cell walls, +P negatively affected starch production and isoprene emission, and damaged chloroplasts. Finally, +NaP largely inhibited photosynthesis due to stomatal limitations, increased sugar content, induced/repressed a number of genes 10 time higher with respect to + P and + Na, and caused appearance of numerous and large plastoglobules and starch granules in chloroplasts. Our results show that A. donax is sensitive to unbalances of soil ion content, despite activation of defensive mechanisms that enhance plant resilience, growth and biomass production of A. donax under these conditions.
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Affiliation(s)
- Claudia Cocozza
- National Research Council of Italy, Institute for the Sustainable Plant Protection (CNR - IPSP), Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy; Department of Agriculture, Food, Environment and Forestry, Via San Bonaventura 13, 50145 Florence, Italy.
| | - Federico Brilli
- National Research Council of Italy, Institute for the Sustainable Plant Protection (CNR - IPSP), Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
| | - Laura Miozzi
- National Research Council of Italy, Institute for the Sustainable Plant Protection (CNR - IPSP), Strada delle Cacce 73, 10135 Torino, Italy
| | - Sara Pignattelli
- National Research Council of Italy, Institute for the Sustainable Plant Protection (CNR - IPSP), Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
| | - Silvia Rotunno
- National Research Council of Italy, Institute for the Sustainable Plant Protection (CNR - IPSP), Strada delle Cacce 73, 10135 Torino, Italy; Department of Biosciences and Territory, University of Molise, contrada Fonte Lappone, 86090 Pesche, Italy
| | - Cecilia Brunetti
- National Research Council of Italy, Institute for BioEconomy (IBE), Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
| | - Cristiana Giordano
- National Research Council of Italy, Institute for BioEconomy (IBE), Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
| | - Susanna Pollastri
- National Research Council of Italy, Institute for the Sustainable Plant Protection (CNR - IPSP), Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
| | - Mauro Centritto
- National Research Council of Italy, Institute for the Sustainable Plant Protection (CNR - IPSP), Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
| | - Gian Paolo Accotto
- National Research Council of Italy, Institute for the Sustainable Plant Protection (CNR - IPSP), Strada delle Cacce 73, 10135 Torino, Italy
| | - Roberto Tognetti
- Department of Agriculture, Environment and Food Sciences, University of Molise, Via Francesco De Sanctis, 86100 Campobasso, Italy; The EFI Project Centre on Mountain Forests (MOUNTFOR), Edmund Mach Foundation, 38010 San Michele all'Adige, Italy
| | - Francesco Loreto
- National Research Council of Italy, Department of Biology, Agriculture, and Food Sciences, Piazzale Aldo Moro 7, Roma, Italy; Department of Biology, University of Naples Federico II, Via Cinthia, 80126 Napoli, Italy
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13
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Haworth M, Marino G, Riggi E, Avola G, Brunetti C, Scordia D, Testa G, Thiago Gaudio Gomes M, Loreto F, Luciano Cosentino S, Centritto M. The effect of summer drought on the yield of Arundo donax is reduced by the retention of photosynthetic capacity and leaf growth later in the growing season. ANNALS OF BOTANY 2019; 124:567-580. [PMID: 30566593 PMCID: PMC6821176 DOI: 10.1093/aob/mcy223] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 11/22/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS The development of Arundo donax as a biomass crop for use on drought-prone marginal lands in areas with warm to hot climates is constrained by the lack of variation within this species. We investigated the effect of morphological and physiological variation on growth and tolerance to drought under field conditions in three ecotypes of A. donax collected from habitats representing a climate gradient: a pre-desert in Morocco, a semi-arid Mediterranean climate in southern Italy and a warm sub-humid region of central Italy. METHODS The three A. donax ecotypes were grown under irrigated and rain-fed conditions in a common garden field trial in a region with a semi-arid Mediterranean climate. Physiological and morphological characteristics, and carbohydrate metabolism of the ecotypes were recorded to establish which traits were associated with yield and/or drought tolerance. KEY RESULTS Variation was observed between the A. donax ecotypes. The ecotype from the most arid habitat produced the highest biomass yield. Stem height and the retention of photosynthetic capacity later in the year were key traits associated with differences in biomass yield. The downregulation of photosynthetic capacity was not associated with changes in foliar concentrations of sugars or starch. Rain-fed plants maintained photosynthesis and growth later in the year compared with irrigated plants that began to senescence earlier, thus minimizing the difference in yield. Effective stomatal control prevented excessive water loss, and the emission of isoprene stabilized photosynthetic membranes under drought and heat stress in A. donax plants grown under rain-fed conditions without supplementary irrigation. CONCLUSIONS Arundo donax is well adapted to cultivation in drought-prone areas with warm to hot climates. None of the A. donax ecotypes exhibited all of the desired traits consistent with an 'ideotype'. Breeding or genetic (identification of quantitative trait loci) improvement of A. donax should select ecotypes on the basis of stem morphology and the retention of photosynthetic capacity.
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Affiliation(s)
- Matthew Haworth
- Tree and Timber Institute, National Research Council of Italy (CNR-IVALSA), Via Madonna del Piano, Sesto Fiorentino, Firenze, Italy
| | - Giovanni Marino
- Tree and Timber Institute, National Research Council of Italy (CNR-IVALSA), Via Madonna del Piano, Sesto Fiorentino, Firenze, Italy
| | - Ezio Riggi
- Tree and Timber Institute, National Research Council of Italy (CNR-IVALSA), Via Madonna del Piano, Sesto Fiorentino, Firenze, Italy
| | - Giovanni Avola
- Tree and Timber Institute, National Research Council of Italy (CNR-IVALSA), Via Madonna del Piano, Sesto Fiorentino, Firenze, Italy
| | - Cecilia Brunetti
- Tree and Timber Institute, National Research Council of Italy (CNR-IVALSA), Via Madonna del Piano, Sesto Fiorentino, Firenze, Italy
- Department of Agrifood Production and Environmental Sciences (DiSPAA), University of Florence, Viale delle Idee, Sesto Fiorentino, Firenze, Italy
| | - Danilo Scordia
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), Università degli Studi di Catania, via Valdisavoia, Catania, Italy
| | - Giorgio Testa
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), Università degli Studi di Catania, via Valdisavoia, Catania, Italy
| | - Marcos Thiago Gaudio Gomes
- Tree and Timber Institute, National Research Council of Italy (CNR-IVALSA), Via Madonna del Piano, Sesto Fiorentino, Firenze, Italy
- Department of Biological Sciences, Center for Human and Natural Sciences, Federal University of Espírito Santo, Avenida Fernando Ferrari, Goiabeiras, CEP, Vitória, Espírito Santo, Brazil
| | - Francesco Loreto
- Department of Biology, Agriculture and Food Sciences, National Research Council of Italy (CNR-DiSBA), Rome, Italy
| | - Salvatore Luciano Cosentino
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), Università degli Studi di Catania, via Valdisavoia, Catania, Italy
| | - Mauro Centritto
- Tree and Timber Institute, National Research Council of Italy (CNR-IVALSA), Via Madonna del Piano, Sesto Fiorentino, Firenze, Italy
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Li M, Stragliati L, Bellini E, Ricci A, Saba A, Sanità di Toppi L, Varotto C. Evolution and functional differentiation of recently diverged phytochelatin synthase genes from Arundo donax L. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5391-5405. [PMID: 31145784 PMCID: PMC6793451 DOI: 10.1093/jxb/erz266] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 05/24/2019] [Indexed: 05/15/2023]
Abstract
Phytochelatin synthases (PCSs) play pivotal roles in the detoxification of heavy metals and metalloids in plants; however, little information on the evolution of recently duplicated PCS genes in plant species is available. Here we characterize the evolution and functional differentiation of three PCS genes from the giant reed (Arundo donax L.), a biomass/bioenergy crop with remarkable resistance to cadmium and other heavy metals. Phylogenetic reconstruction with PCS genes from fully sequenced monocotyledonous genomes indicated that the three A. donax PCSs, namely AdPCS1-3, form a monophyletic clade. The AdPCS1-3 genes were expressed at low levels in many A. donax organs and displayed different levels of cadmium-responsive expression in roots. Overexpression of AdPCS1-3 in Arabidopsis thaliana and yeast reproduced the phenotype of functional PCS genes. Mass spectrometry analyses confirmed that AdPCS1-3 are all functional enzymes, but with significant differences in the amount of the phytochelatins synthesized. Moreover, heterogeneous evolutionary rates characterized the AdPCS1-3 genes, indicative of relaxed natural selection. These results highlight the elevated functional differentiation of A. donax PCS genes from both a transcriptional and an enzymatic point of view, providing evidence of the high evolvability of PCS genes and of plant responsiveness to heavy metal stress.
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Affiliation(s)
- Mingai Li
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige (TN) , Italy
| | - Luca Stragliati
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli studi di Parma, Parco Area delle Scienze, Parma, Italy
| | - Erika Bellini
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| | - Ada Ricci
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli studi di Parma, Parco Area delle Scienze, Parma, Italy
| | - Alessandro Saba
- Dipartimento di Patologia Chirurgica, Medica, Molecolare e dell’Area Critica, Università di Pisa, Pisa, Italy
| | | | - Claudio Varotto
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige (TN) , Italy
- Correspondence: or
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15
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Sicilia A, Testa G, Santoro DF, Cosentino SL, Lo Piero AR. RNASeq analysis of giant cane reveals the leaf transcriptome dynamics under long-term salt stress. BMC PLANT BIOLOGY 2019; 19:355. [PMID: 31416418 PMCID: PMC6694640 DOI: 10.1186/s12870-019-1964-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 08/07/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND To compensate for the lack of information about the molecular mechanism involved in Arundo donax L. response to salt stress, we de novo sequenced, assembled and analyzed the A. donax leaf transcriptome subjected to two levels of long-term salt stress (namely, S3 severe and S4 extreme). RESULTS The picture that emerges from the identification of differentially expressed genes is consistent with a salt dose-dependent response. Hence, a deeper re-programming of the gene expression occurs in those plants grew at extreme salt level than in those subjected to severe salt stress, probably representing for them an "emergency" state. In particular, we analyzed clusters related to salt sensory and signaling, transcription factors, hormone regulation, Reactive Oxygen Species (ROS) scavenging, osmolyte biosynthesis and biomass production, all of them showing different regulation either versus untreated plants or between the two treatments. Importantly, the photosynthesis is strongly impaired in samples treated with both levels of salinity stress. However, in extreme salt conditions, a dramatic switch from C3 Calvin cycle to C4 photosynthesis is likely to occur, this probably being the more impressive finding of our work. CONCLUSIONS Considered the distinct response to salt doses, genes either involved in severe or in extreme salt response could constitute useful markers of the physiological status of A. donax to deepen our understanding of its biology and productivity in salinized soil. Finally, many of the unigenes identified in the present study have the potential to be used for the development of A. donax varieties with improved productivity and stress tolerance, in particular the knock out of the GTL1 gene acting as negative regulator of water use efficiency has been proposed as good target for genome editing.
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Affiliation(s)
- Angelo Sicilia
- Department of Agriculture, Food and Environment, University of Catania, Via Santa Sofia 98, 95123, Catania, Italy
| | - Giorgio Testa
- Department of Agriculture, Food and Environment, University of Catania, Via Santa Sofia 98, 95123, Catania, Italy
| | - Danilo Fabrizio Santoro
- Department of Agriculture, Food and Environment, University of Catania, Via Santa Sofia 98, 95123, Catania, Italy
| | - Salvatore Luciano Cosentino
- Department of Agriculture, Food and Environment, University of Catania, Via Santa Sofia 98, 95123, Catania, Italy
| | - Angela Roberta Lo Piero
- Department of Agriculture, Food and Environment, University of Catania, Via Santa Sofia 98, 95123, Catania, Italy.
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Meng HL, Zhang W, Zhang GH, Wang JJ, Meng ZG, Long GQ, Yang SC. Unigene-based RNA-seq provides insights on drought stress responses in Marsdenia tenacissima. PLoS One 2018; 13:e0202848. [PMID: 30500823 PMCID: PMC6268015 DOI: 10.1371/journal.pone.0202848] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/02/2018] [Indexed: 12/28/2022] Open
Abstract
Marsdenia tenacissima is a well-known anti-cancer medicinal plant used in traditional Chinese medicine, which often grows on the karst landform and the water conservation capacity of land is very poorly and drought occurrences frequently. We found M. tenacissima has strong drought resistance because of continuousdrought16 d, the leaves of M. tenacissima were fully curly and dying. But the leaves were fully almost recovering after re-watering 24h. The activity of SOD and POD were almost doubled under drought stress. The content of osmotic regulating substance proline and soluble sugar were three times than control group. But after re-watering, these indexes were declined rapidly. Three cDNA libraries of control, drought stress, and re-watering treatments were constructed. There were 43,129,228, 47,116,844, and 42,815,454 clean reads with Q20 values of 98.06, 98.04, and 97.88respectively.SRA accession number of raw data was PRJNA498187 on NCBI. A total of 8672, 6043, and 6537 differentially expressed genes (DEGs) were identified in control vs drought stress, control vs re-watering, and drought stress vs re-watering, respectively. In addition, 1039, 1016, and 980 transcription factors (TFs) were identified, respectively. Among them, 363, 267, and 299 TFs were identified as DEGs in drought stress, re-watering, and drought stress and re-watering, respectively. These differentially expressed TFs mainly belonged to the bHLH, bZIP, C2H2, ERF, MYB, MYB-related, and NAC families. A comparative analysis found that 1174 genes were up-regulated and 2344 were down-regulated under drought stress and this pattern was the opposite to that found after re-watering. Among the up-regulated genes, 64 genes were homologous to known functional genes that directly protect plants against drought stress. Furthermore, 44 protein kinases and 38 TFs with opposite expression patterns under drought stress and re-watering were identified, which are possibly candidate regulators for drought stress resistance in M. tenacissima. Our study is the first to characterize the M. tenacissima transcriptome in response to drought stress, and will serve as a useful resource for future studies on the functions of candidate protein kinases and TFs involved in M. tenacissima drought stress resistance.
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Affiliation(s)
- Heng-Ling Meng
- The Life Science and Technology College, Honghe University, Mengzi, Yunnan, People’s Republic of China
| | - Wei Zhang
- The Life Science and Technology College, Honghe University, Mengzi, Yunnan, People’s Republic of China
| | - Guang-Hui Zhang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming,Yunnan, People’s Republic of China
| | - Jian-Jun Wang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming,Yunnan, People’s Republic of China
| | - Zhen-Gui Meng
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming,Yunnan, People’s Republic of China
| | - Guang-Qiang Long
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming,Yunnan, People’s Republic of China
- * E-mail: (GQL); (SCY)
| | - Sheng-Chao Yang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming,Yunnan, People’s Republic of China
- * E-mail: (GQL); (SCY)
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17
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Jike W, Sablok G, Bertorelle G, Li M, Varotto C. In silico identification and characterization of a diverse subset of conserved microRNAs in bioenergy crop Arundo donax L. Sci Rep 2018; 8:16667. [PMID: 30420632 PMCID: PMC6232160 DOI: 10.1038/s41598-018-34982-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 10/15/2018] [Indexed: 01/08/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules involved in the post-transcriptional regulation of gene expression in plants. Arundo donax L. is a perennial C3 grass considered one of the most promising bioenergy crops. Despite its relevance, many fundamental aspects of its biology still remain to be elucidated. In the present study we carried out the first in silico mining and tissue-specific characterization of microRNAs and their putative targets in A. donax. We identified a total of 141 miRNAs belonging to 14 families along with the corresponding primary miRNAs, precursor miRNAs and a total of 462 high-confidence predicted targets and novel target sites were validated by 5′-race. Gene Ontology functional annotation showed that miRNA targets are constituted mainly by transcription factors, but three of the newly validated targets are enzymes involved in novel functions like RNA editing, acyl lipid metabolism and post-Golgi trafficking. Folding variability of pre-miRNA loops and phylogenetic analyses indicate variable selective pressure acting on the different miRNA families. The set of miRNAs identified in this study will pave the road to further miRNA research in Arundo donax and contribute towards a better understanding of miRNA-mediated gene regulatory processes in other bioenergy crops.
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Affiliation(s)
- Wuhe Jike
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy.,Università degli Studi di Ferrara, Dipartimento di Scienze della Vita e Biotecnologie, Ferrara, Italy
| | - Gaurav Sablok
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy.,Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Giorgio Bertorelle
- Università degli Studi di Ferrara, Dipartimento di Scienze della Vita e Biotecnologie, Ferrara, Italy
| | - Mingai Li
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy.
| | - Claudio Varotto
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy.
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18
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Li M, Xu J, Algarra Alarcon A, Carlin S, Barbaro E, Cappellin L, Velikova V, Vrhovsek U, Loreto F, Varotto C. In Planta Recapitulation of Isoprene Synthase Evolution from Ocimene Synthases. Mol Biol Evol 2017; 34:2583-2599. [PMID: 28637270 PMCID: PMC5850473 DOI: 10.1093/molbev/msx178] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Isoprene is the most abundant biogenic volatile hydrocarbon compound naturally emitted by plants and plays a major role in atmospheric chemistry. It has been proposed that isoprene synthases (IspS) may readily evolve from other terpene synthases, but this hypothesis has not been experimentally investigated. We isolated and functionally validated in Arabidopsis the first isoprene synthase gene, AdoIspS, from a monocotyledonous species (Arundo donax L., Poaceae). Phylogenetic reconstruction indicates that AdoIspS and dicots isoprene synthases most likely originated by parallel evolution from TPS-b monoterpene synthases. Site-directed mutagenesis demonstrated invivo the functional and evolutionary relevance of the residues considered diagnostic for IspS function. One of these positions was identified by saturating mutagenesis as a major determinant of substrate specificity in AdoIspS able to cause invivo a dramatic change in total volatile emission from hemi- to monoterpenes and supporting evolution of isoprene synthases from ocimene synthases. The mechanism responsible for IspS neofunctionalization by active site size modulation by a single amino acid mutation demonstrated in this study might be general, as the very same amino acidic position is implicated in the parallel evolution of different short-chain terpene synthases from both angiosperms and gymnosperms. Based on these results, we present a model reconciling in a unified conceptual framework the apparently contrasting patterns previously observed for isoprene synthase evolution in plants. These results indicate that parallel evolution may be driven by relatively simple biophysical constraints, and illustrate the intimate molecular evolutionary links between the structural and functional bases of traits with global relevance.
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Affiliation(s)
- Mingai Li
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige (TN), Italy
| | - Jia Xu
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige (TN), Italy
- Dipartimento di Biologia, Università di Padova, Padova, Italy
| | - Alberto Algarra Alarcon
- Department of Food Quality and Nutrition, Research and Innovation Centre, San Michele all’Adige (TN), Italy
- Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Silvia Carlin
- Department of Food Quality and Nutrition, Research and Innovation Centre, San Michele all’Adige (TN), Italy
| | - Enrico Barbaro
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige (TN), Italy
| | - Luca Cappellin
- Department of Food Quality and Nutrition, Research and Innovation Centre, San Michele all’Adige (TN), Italy
| | - Violeta Velikova
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige (TN), Italy
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Urska Vrhovsek
- Department of Food Quality and Nutrition, Research and Innovation Centre, San Michele all’Adige (TN), Italy
| | - Francesco Loreto
- Department of Biology, Agriculture and Food Sciences, The National Research Council of Italy (CNR), Rome, Italy
| | - Claudio Varotto
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige (TN), Italy
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Ahmad J, Bashir H, Bagheri R, Baig A, Al-Huqail A, Ibrahim MM, Qureshi MI. Drought and salinity induced changes in ecophysiology and proteomic profile of Parthenium hysterophorus. PLoS One 2017; 12:e0185118. [PMID: 28953916 PMCID: PMC5617186 DOI: 10.1371/journal.pone.0185118] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 09/05/2017] [Indexed: 12/27/2022] Open
Abstract
Parthenium hysterophorus is a plant that tolerates drought and salinity to an extremely high degree. Higher expression of stress-responsive proteome contributes for greater defence against abiotic stresses. Thus, P. hysterophorus could be a rich source of genes that encode stress-imparting mechanisms and systems. The present study utilizes comparative physiological and proteomic approaches for identification of key proteins involved in stress-defence of P. hysterophorus. Thirty-days-old plants were exposed to drought (10% PEG 6000) and salinity (160 mM NaCl) for 10 days duration. Both stresses induced oxidative stress estimated in terms of TBARS and H2O2. Levels of both enzymatic and non-enzymatic antioxidants were elevated, more by drought than salinity. Particularly, SOD, GR, CAT and GST proved to be assisting as very commendable defence under drought, as well as salinity. Levels of ascorbate, glutathione and proline were also increased by both stresses, more in response to drought. Comparative proteomics analysis revealed a significant change in relative abundance of 72 proteins under drought and salinity. Drought and salinity increased abundance of 45 and 41 proteins and decreased abundance of 24 and 26 proteins, respectively. Drought and salinity increased and decreased abundance of 31 and 18 proteins, respectively. The functions of identified proteins included those related to defence response (26%), signal transduction (13%), transcription and translation (10%), growth and development (8.5%), photosynthesis (8.5%), metabolism (7%), terpenoid biosynthesis (5.5%), protein modification and transport (7%), oxido-reductase (4%) and Miscellaneous (11%). Among the defence related proteins, antioxidants and HSPs constituted 26% and 21%, respectively. Present study suggests a potential role of defence proteins. Proteins involved in molecular stabilization, formation of osmolytes and wax and contributing to stress-avoiding anatomical features emerged as key and complex mechanisms for imparting stress tolerance to P. hysterophorus.
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Affiliation(s)
- Javed Ahmad
- Department of Biotechnology, Jamia Millia Islamia (Central University), New Delhi, India
| | - Humayra Bashir
- Department of Biotechnology, Jamia Millia Islamia (Central University), New Delhi, India
| | - Rita Bagheri
- Department of Biotechnology, Jamia Millia Islamia (Central University), New Delhi, India
| | - Affan Baig
- Department of Biotechnology, Jamia Millia Islamia (Central University), New Delhi, India
| | - Asma Al-Huqail
- Department of Botany and Microbiology, Science College, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed M. Ibrahim
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Egypt
- Department of Biology and Horticulture, Bergen Community College, Paramus, New Jersey, United States of America
| | - M. Irfan Qureshi
- Department of Biotechnology, Jamia Millia Islamia (Central University), New Delhi, India
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20
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Poli M, Salvi S, Li M, Varotto C. Selection of reference genes suitable for normalization of qPCR data under abiotic stresses in bioenergy crop Arundo donax L. Sci Rep 2017; 7:10719. [PMID: 28878356 PMCID: PMC5587670 DOI: 10.1038/s41598-017-11019-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/16/2017] [Indexed: 02/08/2023] Open
Abstract
Suitable reference gene selection in qRT-PCR is a key pre-requisite to produce reliable data in gene expression analyses. In this study, novel primers for six commonly used reference genes (AC1, TLF, Act2, TUB α, EF-1α and GAPDH) plus two new candidates (pDUF221 and RPN6) were designed and comparatively tested for expression stability under abiotic stresses (osmotic, heavy metal and heat shock) in shoot, root and their combination of Arundo donax L., a raising non-food energy crop. Expression stability rankings from the most to the least stable gene in each condition and in two tissues (young shoots and roots) were generated with geNorm, NormFinder and BestKeeper programs. All programs provided similar rankings and, strikingly, in most cases identified one of the new candidates, RPN6, as the most suitable reference gene. This novel set of reliable references allows to choose either the best combination of reference genes across multiple stress/organ conditions or to select condition-specific genes that can improve the quality of qRT-PCR analysis. This work provides a solid basis for the functional characterization of A. donax, by enabling accurate quantification of the transcriptional responsiveness under a series of common stress conditions of any gene of interest in this promising biomass/bioenergy species.
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Affiliation(s)
- Michele Poli
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, S. Michele all'Adige (TN), Italy.,Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Silvio Salvi
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Mingai Li
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, S. Michele all'Adige (TN), Italy.
| | - Claudio Varotto
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, S. Michele all'Adige (TN), Italy.
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21
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Whole-transcriptome sequence analysis of differentially expressed genes in Phormium tenax under drought stress. Sci Rep 2017; 7:41700. [PMID: 28134322 PMCID: PMC5278365 DOI: 10.1038/srep41700] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 12/23/2016] [Indexed: 12/31/2022] Open
Abstract
Phormium tenax is a kind of drought resistant garden plant with its rich and colorful leaves. To clarify the molecular mechanism of drought resistance in Phormium tenax, transcriptome was sequenced by the Illumina sequencing technology under normal and drought stress, respectively. A large number of contigs, transcripts and unigenes were obtained. Among them, only 30,814 unigenes were annotated by comparing with the protein databases. A total of 4,380 genes were differentially expressed, 2,698 of which were finally annotated under drought stress. Differentially expression analysis was also performed upon drought treatment. In KEGG pathway, the mechanism of drought resistance in Phormium tenax was explained from three aspects of metabolism and signaling of hormones, osmotic adjustment and reactive oxygen species metabolism. These results are helpful to understand the drought tolerance mechanism of Phormium tenax and will provide a precious genetic resource for drought-resistant vegetation breeding and research.
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Sablok G, Powell JJ, Kazan K. Emerging Roles and Landscape of Translating mRNAs in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:1443. [PMID: 28919899 PMCID: PMC5585741 DOI: 10.3389/fpls.2017.01443] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 08/03/2017] [Indexed: 05/03/2023]
Abstract
Plants use a wide range of mechanisms to adapt to different environmental stresses. One of the earliest responses displayed under stress is rapid alterations in stress responsive gene expression that has been extensively analyzed through expression profiling such as microarrays and RNA-sequencing. Recently, expression profiling has been complemented with proteome analyses to establish a link between transcriptional and the corresponding translational changes. However, proteome profiling approaches have their own technical limitations. More recently, ribosome-associated mRNA profiling has emerged as an alternative and a robust way of identifying translating mRNAs, which are a set of mRNAs associated with ribosomes and more likely to contribute to proteome abundance. In this article, we briefly review recent studies that examined the processes affecting the abundance of translating mRNAs, their regulation during plant development and tolerance to stress conditions and plant factors affecting the selection of translating mRNA pools. This review also highlights recent findings revealing differential roles of alternatively spliced mRNAs and their translational control during stress adaptation. Overall, better understanding of processes involved in the regulation of translating mRNAs has obvious implications for improvement of stress tolerance in plants.
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Affiliation(s)
- Gaurav Sablok
- Finnish Museum of Natural HistoryHelsinki, Finland
- Department of Biosciences, Viikki Plant Science Center, University of HelsinkiHelsinki, Finland
- *Correspondence: Gaurav Sablok, Kemal Kazan,
| | - Jonathan J. Powell
- Commonwealth Scientific and Industrial Research Organization Agriculture, St. LuciaQLD, Australia
| | - Kemal Kazan
- Commonwealth Scientific and Industrial Research Organization Agriculture, St. LuciaQLD, Australia
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. LuciaQLD, Australia
- *Correspondence: Gaurav Sablok, Kemal Kazan,
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23
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Evangelistella C, Valentini A, Ludovisi R, Firrincieli A, Fabbrini F, Scalabrin S, Cattonaro F, Morgante M, Mugnozza GS, Keurentjes JJB, Harfouche A. De novo assembly, functional annotation, and analysis of the giant reed ( Arundo donax L.) leaf transcriptome provide tools for the development of a biofuel feedstock. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:138. [PMID: 28572841 PMCID: PMC5450047 DOI: 10.1186/s13068-017-0828-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 05/23/2017] [Indexed: 05/07/2023]
Abstract
BACKGROUND Arundo donax has attracted renewed interest as a potential candidate energy crop for use in biomass-to-liquid fuel conversion processes and biorefineries. This is due to its high productivity, adaptability to marginal land conditions, and suitability for biofuel and biomaterial production. Despite its importance, the genomic resources currently available for supporting the improvement of this species are still limited. RESULTS We used RNA sequencing (RNA-Seq) to de novo assemble and characterize the A. donax leaf transcriptome. The sequencing generated 1249 million clean reads that were assembled using single-k-mer and multi-k-mer approaches into 62,596 unique sequences (unitranscripts) with an N50 of 1134 bp. TransDecoder and Trinotate software suites were used to obtain putative coding sequences and annotate them by mapping to UniProtKB/Swiss-Prot and UniRef90 databases, searching for known transcripts, proteins, protein domains, and signal peptides. Furthermore, the unitranscripts were annotated by mapping them to the NCBI non-redundant, GO and KEGG pathway databases using Blast2GO. The transcriptome was also characterized by BLAST searches to investigate homologous transcripts of key genes involved in important metabolic pathways, such as lignin, cellulose, purine, and thiamine biosynthesis and carbon fixation. Moreover, a set of homologous transcripts of key genes involved in stomatal development and of genes coding for stress-associated proteins (SAPs) were identified. Additionally, 8364 simple sequence repeat (SSR) markers were identified and surveyed. SSRs appeared more abundant in non-coding regions (63.18%) than in coding regions (36.82%). This SSR dataset represents the first marker catalogue of A. donax. 53 SSRs (PolySSRs) were then predicted to be polymorphic between ecotype-specific assemblies, suggesting genetic variability in the studied ecotypes. CONCLUSIONS This study provides the first publicly available leaf transcriptome for the A. donax bioenergy crop. The functional annotation and characterization of the transcriptome will be highly useful for providing insight into the molecular mechanisms underlying its extreme adaptability. The identification of homologous transcripts involved in key metabolic pathways offers a platform for directing future efforts in genetic improvement of this species. Finally, the identified SSRs will facilitate the harnessing of untapped genetic diversity. This transcriptome should be of value to ongoing functional genomics and genetic studies in this crop of paramount economic importance.
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Affiliation(s)
- Chiara Evangelistella
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy
| | - Alessio Valentini
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy
| | - Riccardo Ludovisi
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy
| | - Andrea Firrincieli
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy
| | - Francesco Fabbrini
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy
- Alasia Franco Vivai s.s., Strada Solerette, 5/A, 12038 Savigliano, Italy
| | - Simone Scalabrin
- IGA Technology Services, Via J. Linussio, 51-Z.I.U, 33100 Udine, Italy
| | | | - Michele Morgante
- Department of Agricultural and Environmental Sciences, University of Udine, Via delle Scienze, 206, 33100 Udine, Italy
- Institute of Applied Genomics, Via J. Linussio, 51-Z.I.U, 33100 Udine, Italy
| | - Giuseppe Scarascia Mugnozza
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy
| | - Joost J. B. Keurentjes
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Antoine Harfouche
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy
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24
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Pigna G, Dhillon T, Dlugosz EM, Yuan JS, Gorman C, Morandini P, Lenaghan SC, Stewart CN. Methods for suspension culture, protoplast extraction, and transformation of high-biomass yielding perennial grass Arundo donax. Biotechnol J 2016; 11:1657-1666. [PMID: 27762502 DOI: 10.1002/biot.201600486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/13/2016] [Accepted: 10/19/2016] [Indexed: 11/11/2022]
Abstract
Arundo donax L. is a promising biofuel feedstock in the Mediterranean region. Despite considerable interest in its genetic improvement, Arundo tissue culture and transformation remains arduous. The authors developed methodologies for cell- and tissue culture and genetic engineering in Arundo. A media screen was conducted, and a suspension culture was established using callus induced from stem axillary bud explants. DBAP medium, containing 9 µM 2,4-D and 4.4 µM BAP, was found to be the most effective medium among those tested for inducing cell suspension cultures, which resulted in a five-fold increase in tissue mass over 14 days. In contrast, CIM medium containing 13 µM 2,4-D, resulted in just a 1.4-fold increase in mass over the same period. Optimized suspension cultures were superior to previously-described solidified medium-based callus culture methods for tissue mass increase. Suspension cultures proved to be very effective for subsequent protoplast isolation. Protoplast electroporation resulted in a 3.3 ± 1.5% transformation efficiency. A dual fluorescent reporter gene vector enabled the direct comparison of the CAMV 35S promoter with the switchgrass ubi2 promoter in single cells of Arundo. The switchgrass ubi2 promoter resulted in noticeably higher reporter gene expression compared with that conferred by the 35S promoter in Arundo.
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Affiliation(s)
- Gaia Pigna
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, USA.,Department of Biosciences, University of Milan, Milano, Italy
| | - Taniya Dhillon
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, USA
| | - Elizabeth M Dlugosz
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, USA
| | - Joshua S Yuan
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, USA
| | - Connor Gorman
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, USA
| | - Piero Morandini
- Department of Biosciences, University of Milan, Milano, Italy.,National Research Council, Institute of Biophysics, Milano, Italy
| | - Scott C Lenaghan
- Department of Food Science, University of Tennessee, Knoxville, Tennessee, USA.,Department of Mechanical, Aerospace, and Biomedical Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, USA
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25
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Quantitative proteomic analysis of two different rice varieties reveals that drought tolerance is correlated with reduced abundance of photosynthetic machinery and increased abundance of ClpD1 protease. J Proteomics 2016; 143:73-82. [DOI: 10.1016/j.jprot.2016.05.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 05/06/2016] [Accepted: 05/10/2016] [Indexed: 11/22/2022]
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