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Khramov DE, Nedelyaeva OI, Konoshenkova AO, Volkov VS, Balnokin YV. Identification and selection of reference genes for analysis of gene expression by quantitative real-time PCR in the euhalophyte Suaeda altissima (L.) Pall. Commun Integr Biol 2024; 17:2372313. [PMID: 38988501 PMCID: PMC11236294 DOI: 10.1080/19420889.2024.2372313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 06/20/2024] [Indexed: 07/12/2024] Open
Abstract
Сoding sequences of seven housekeeping genes: actin SaACT7, ubiquitin-conjugating protein SaUBC10, glyceraldehyde-3-phosphate dehydrogenase SaGAPDH, protein of the large subunit of ribosomes SaL2, α-tubulin SaTUA, translation elongation factor SaeEF1α, and protein phosphatase SaPP2A were identified as candidate reference genes for expression analysis of target genes in the extremely salt tolerant plant Suaeda altissima (L.) Pall. The expression profiles of the genes differed. SaACT7 and SaeEF1α demonstrated the highest expression levels, while the lowest expression levels were found for SaPP2A and SaTUA. SaPP2A and SaeEF1α genes were the most stably expressed at different steady-state salinity levels and different nitrate concentrations in nutrient solutions (NSs). SaL2, SaPP2A, and SaeEF1α genes showed the greatest stability of expression when nitrate was added to nutrient solution of plants grown under conditions of nitrate deficiency. Less constant expression was demonstrated in this experiment by SaACT7 and SaTUA. SaL2, SaACT7, SaeEF1α, and SaUBC10 genes showed the smallest expression changes under salt shock. To validate the use of the most stably expressed genes for normalization of gene expression, we checked them as reference genes to study the expression of the nitrate transporter gene SaNPF6.3 in S. altissima roots under conditions of different salinity and different nitrate supply.
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Affiliation(s)
- Dmitrii E. Khramov
- Laboratory of Ion Transport and Salinity Tolerance, K.A. Timiryazev Institute of Plant Physiology of the Russian Academy of Sciences, Moscow, Russia
| | - Olga I. Nedelyaeva
- Laboratory of Ion Transport and Salinity Tolerance, K.A. Timiryazev Institute of Plant Physiology of the Russian Academy of Sciences, Moscow, Russia
| | - Alena O. Konoshenkova
- Laboratory of Ion Transport and Salinity Tolerance, K.A. Timiryazev Institute of Plant Physiology of the Russian Academy of Sciences, Moscow, Russia
| | - Vadim S. Volkov
- Laboratory of Ion Transport and Salinity Tolerance, K.A. Timiryazev Institute of Plant Physiology of the Russian Academy of Sciences, Moscow, Russia
- Department of Plant Sciences, College of Agricultural and Environmental Sciences, University of California, Davis, CA, USA
| | - Yurii V. Balnokin
- Laboratory of Ion Transport and Salinity Tolerance, K.A. Timiryazev Institute of Plant Physiology of the Russian Academy of Sciences, Moscow, Russia
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Gao Q, Yu R, Ma X, Wuriyanghan H, Yan F. Transcriptome Analysis for Salt-Responsive Genes in Two Different Alfalfa ( Medicago sativa L.) Cultivars and Functional Analysis of MsHPCA1. PLANTS (BASEL, SWITZERLAND) 2024; 13:1073. [PMID: 38674482 PMCID: PMC11054072 DOI: 10.3390/plants13081073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024]
Abstract
Alfalfa (Medicago sativa L.) is an important forage legume and soil salinization seriously affects its growth and yield. In a previous study, we identified a salt-tolerant variety 'Gongnong NO.1' and a salt-sensitive variety 'Sibeide'. To unravel the molecular mechanism involved in salt stress, we conducted transcriptomic analysis on these two cultivars grown under 0 and 250 mM NaCl treatments for 0, 12, and 24 h. Totals of 336, and 548 differentially expressed genes (DEGs) in response to NaCl were, respectively, identified in the 'Gongnong NO.1' and 'Sibeide' varieties. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) pathway enrichment analysis showed that the DEGs were classified in carbohydrate metabolism, energy production, transcription factor, and stress-associated pathway. Expression of MsHPCA1, encoding a putative H2O2 receptor, was responsive to both NaCl and H2O2 treatment. MsHPCA1 was localized in cell membrane and overexpression of MsHPCA1 in alfalfa increased salt tolerance and H2O2 content. This study will provide new gene resources for the improvement in salt tolerance in alfalfa and legume crops, which has important theoretical significance and potential application value.
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Affiliation(s)
- Qican Gao
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (Q.G.); (R.Y.); (X.M.)
| | - Ruonan Yu
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (Q.G.); (R.Y.); (X.M.)
- Crop Cultivation and Genetic Improvement Research Center, College of Agricultural, Hulunbuir University, Hulunbuir 021008, China
| | - Xuesong Ma
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (Q.G.); (R.Y.); (X.M.)
| | - Hada Wuriyanghan
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (Q.G.); (R.Y.); (X.M.)
| | - Fang Yan
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (Q.G.); (R.Y.); (X.M.)
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Mann A, Lata C, Kumar N, Kumar A, Kumar A, Sheoran P. Halophytes as new model plant species for salt tolerance strategies. FRONTIERS IN PLANT SCIENCE 2023; 14:1137211. [PMID: 37251767 PMCID: PMC10211249 DOI: 10.3389/fpls.2023.1137211] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 04/11/2023] [Indexed: 05/31/2023]
Abstract
Soil salinity is becoming a growing issue nowadays, severely affecting the world's most productive agricultural landscapes. With intersecting and competitive challenges of shrinking agricultural lands and increasing demand for food, there is an emerging need to build resilience for adaptation to anticipated climate change and land degradation. This necessitates the deep decoding of a gene pool of crop plant wild relatives which can be accomplished through salt-tolerant species, such as halophytes, in order to reveal the underlying regulatory mechanisms. Halophytes are generally defined as plants able to survive and complete their life cycle in highly saline environments of at least 200-500 mM of salt solution. The primary criterion for identifying salt-tolerant grasses (STGs) includes the presence of salt glands on the leaf surface and the Na+ exclusion mechanism since the interaction and replacement of Na+ and K+ greatly determines the survivability of STGs in saline environments. During the last decades or so, various salt-tolerant grasses/halophytes have been explored for the mining of salt-tolerant genes and testing their efficacy to improve the limit of salt tolerance in crop plants. Still, the utility of halophytes is limited due to the non-availability of any model halophytic plant system as well as the lack of complete genomic information. To date, although Arabidopsis (Arabidopsis thaliana) and salt cress (Thellungiella halophila) are being used as model plants in most salt tolerance studies, these plants are short-lived and can tolerate salinity for a shorter duration only. Thus, identifying the unique genes for salt tolerance pathways in halophytes and their introgression in a related cereal genome for better tolerance to salinity is the need of the hour. Modern technologies including RNA sequencing and genome-wide mapping along with advanced bioinformatics programs have advanced the decoding of the whole genetic information of plants and the development of probable algorithms to correlate stress tolerance limit and yield potential. Hence, this article has been compiled to explore the naturally occurring halophytes as potential model plant species for abiotic stress tolerance and to further breed crop plants to enhance salt tolerance through genomic and molecular tools.
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Affiliation(s)
- Anita Mann
- ICAR-Central Soil Salinity Research Institute, Karnl, Haryana, India
| | - Charu Lata
- ICAR-Central Soil Salinity Research Institute, Karnl, Haryana, India
- ICAR-Indian Institute of Wheat and Barley Research, Shimla, Himachal Pardesh, India
| | - Naresh Kumar
- ICAR-Central Soil Salinity Research Institute, Karnl, Haryana, India
- Department of Biochemistry, Eternal University, Baru Sahib, Himachal Pardesh, Ludhiana, India
| | - Ashwani Kumar
- ICAR-Central Soil Salinity Research Institute, Karnl, Haryana, India
| | - Arvind Kumar
- ICAR-Central Soil Salinity Research Institute, Karnl, Haryana, India
| | - Parvender Sheoran
- ICAR-Central Soil Salinity Research Institute, Karnl, Haryana, India
- ICAR-Agriculture Technology Application Research Center, Ludhiana, India
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John JE, Maheswari M, Kalaiselvi T, Prasanthrajan M, Poornachandhra C, Rakesh SS, Gopalakrishnan B, Davamani V, Kokiladevi E, Ranjith S. Biomining Sesuvium portulacastrum for halotolerant PGPR and endophytes for promotion of salt tolerance in Vigna mungo L. Front Microbiol 2023; 14:1085787. [PMID: 36865783 PMCID: PMC9971939 DOI: 10.3389/fmicb.2023.1085787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/16/2023] [Indexed: 02/16/2023] Open
Abstract
Halophytic plants can tolerate a high level of salinity through several morphological and physiological adaptations along with the presence of salt tolerant rhizo-microbiome. These microbes release phytohormones which aid in alleviating salinity stress and improve nutrient availability. The isolation and identification of such halophilic PGPRs can be useful in developing bio-inoculants for improving the salt tolerance and productivity of non-halophytic plants under saline conditions. In this study, salt-tolerant bacteria with multiple plant growth promoting characteristics were isolated from the rhizosphere of a predominant halophyte, Sesuvium portulacastrum grown in the coastal and paper mill effluent irrigated soils. Among the isolates, nine halotolerant rhizobacterial strains that were able to grow profusely at a salinity level of 5% NaCl were screened. These isolates were found to have multiple plant growth promoting (PGP) traits, especially 1-aminocyclopropane-1-carboxylic acid deaminase activity (0.32-1.18 μM of α-ketobutyrate released mg-1 of protein h-1) and indole acetic acid (9.4-22.8 μg mL-1). The halotolerant PGPR inoculation had the potential to improve salt tolerance in Vigna mungo L. which was reflected in significantly (p < 0.05) higher germination percentage (89%) compared to un-inoculated seeds (65%) under 2% NaCl. Similarly, shoot length (8.9-14.6 cm) and vigor index (792-1785) were also higher in inoculated seeds. The strains compatible with each other were used for the preparation of two bioformulations and these microbial consortia were tested for their efficacy in salt stress alleviation of Vigna mungo L. under pot study. The inoculation improved the photosynthetic rate (12%), chlorophyll content (22%), shoot length (5.7%) and grain yield (33%) in Vigna mungo L. The enzymatic activity of catalase and superoxide dismutase were found to be lower (7.0 and 1.5%, respectively) in inoculated plants. These results revealed that halotolerant PGPR isolated from S. portulacastrum can be a cost-effective and ecologically sustainable method to improve crop productivity under high saline conditions.
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Affiliation(s)
- Joseph Ezra John
- Department of Environmental Sciences, AC&RI, Tamil Nadu Agricultural University, Coimbatore, India,*Correspondence: Joseph Ezra John, ; Chidamparam Poornachandhra,
| | | | - Thangavel Kalaiselvi
- Department of Agricultural Microbiology, AC&RI, Tamil Nadu Agricultural University, Coimbatore, India
| | - Mohan Prasanthrajan
- Department of Environmental Sciences, AC&RI, Tamil Nadu Agricultural University, Coimbatore, India
| | - Chidamparam Poornachandhra
- Department of Environmental Sciences, AC&RI, Tamil Nadu Agricultural University, Coimbatore, India,*Correspondence: Joseph Ezra John, ; Chidamparam Poornachandhra,
| | | | | | - Veeraswamy Davamani
- Department of Environmental Sciences, AC&RI, Tamil Nadu Agricultural University, Coimbatore, India
| | - Eswaran Kokiladevi
- Department of Biotechnology, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Coimbatore, India
| | - Sellappan Ranjith
- Department of Agricultural Microbiology, AC&RI, Tamil Nadu Agricultural University, Coimbatore, India
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Bejerman N, Debat H. Exploring the tymovirales landscape through metatranscriptomics data. Arch Virol 2022; 167:1785-1803. [PMID: 35708766 DOI: 10.1007/s00705-022-05493-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 05/12/2022] [Indexed: 11/26/2022]
Abstract
Tymovirales is an order of viruses with positive-sense RNA genomes that mostly infect plants, but also fungi and insects. The number of genome sequences of viruses that could fit this taxon has been growing in the last few years with the extensive use of high-throughput sequencing. Here, we report the discovery of 31 novel viral genome sequences associated with 27 different host plant species, which were hidden in public databases. These viral sequences were identified through homology searches in more than 3,000 plant transcriptomes from the NCBI Sequence Read Archive (SRA) using known tymovirales sequences as queries. Identification, assembly, and curation of raw SRA reads resulted in 29 viral genome sequences with complete coding regions, and two representing partial genomes. Some of the obtained sequences highlight novel genome organizations for members of the order. Phylogenetic analysis showed that six of the novel viruses are related to alphaflexiviruses, 17 to betaflexiviruses, two to deltaflexiviruses, and six to tymovirids. These findings shed new light on the phylogenetic relationships and evolutionary landscape of this group of viruses. Furthermore, this study illustrates the complexity and genome diversity among members of the order and demonstrates that analyzing public SRA data provides an invaluable tool to accelerate virus discovery and refine virus taxonomy.
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Affiliation(s)
- Nicolás Bejerman
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5,5 (X5020ICA), Córdoba, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola, Camino 60 Cuadras Km 5,5 (X5020ICA), Córdoba, Argentina.
| | - Humberto Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5,5 (X5020ICA), Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola, Camino 60 Cuadras Km 5,5 (X5020ICA), Córdoba, Argentina
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Yu W, Wu W, Zhang N, Wang L, Wang Y, Wang B, Lan Q, Wang Y. Research Advances on Molecular Mechanism of Salt Tolerance in Suaeda. BIOLOGY 2022; 11:biology11091273. [PMID: 36138752 PMCID: PMC9495733 DOI: 10.3390/biology11091273] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 11/16/2022]
Abstract
Plant growth and development are inevitably affected by various environmental factors. High salinity is the main factor leading to the reduction of cultivated land area, which seriously affects the growth and yield of plants. The genus Suaeda is a kind of euhalophyte herb, with seedlings that grow rapidly in moderately saline environments and can even survive in conditions of extreme salinity. Its fresh branches can be used as vegetables and the seed oil is rich in unsaturated fatty acids, which has important economic value and usually grows in a saline environment. This paper reviews the progress of research in recent years into the salt tolerance of several Suaeda species (for example, S. salsa, S. japonica, S. glauca, S. corniculata), focusing on ion regulation and compartmentation, osmotic regulation of organic solutes, antioxidant regulation, plant hormones, photosynthetic systems, and omics (transcriptomics, proteomics, and metabolomics). It helps us to understand the salt tolerance mechanism of the genus Suaeda, and provides a theoretical foundation for effectively improving crop resistance to salt stress environments.
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Affiliation(s)
- Wancong Yu
- Institute of Germplasm Resources and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin 300384, China
| | - Wenwen Wu
- Department of Agronomy, Tianjin Agricultural University, Tianjin 300392, China
| | - Nan Zhang
- Department of Agronomy, Tianjin Agricultural University, Tianjin 300392, China
| | - Luping Wang
- Institute of Germplasm Resources and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin 300384, China
| | - Yiheng Wang
- Institute of Germplasm Resources and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin 300384, China
| | - Bo Wang
- Institute of Germplasm Resources and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin 300384, China
| | - Qingkuo Lan
- Institute of Germplasm Resources and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin 300384, China
- Correspondence: (Q.L.); (Y.W.)
| | - Yong Wang
- Institute of Germplasm Resources and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin 300384, China
- Correspondence: (Q.L.); (Y.W.)
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Sagervanshi A, Geilfus CM, Kaiser H, Mühling KH. Alkali salt stress causes fast leaf apoplastic alkalinization together with shifts in ion and metabolite composition and transcription of key genes during the early adaptive response of Vicia faba L. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 319:111253. [PMID: 35487662 DOI: 10.1016/j.plantsci.2022.111253] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
The mechanisms by which plants respond to alkali salt stress are still obscure, and the relevance of alkaline pH under combined alkali salt stress. Early stress responses can indicate mechanisms leading to damage and plant resistance. The apoplast contains essential determinants for plant growth, specifically early apoplastic pH fluctuations are induced by many stressors and hypothesized to be involved in stress signalling. Hence, this study aims to identify fast responses specific to alkaline pH and alkali salt stress by exposing the root of hydroponically grown Vicia faba L. plants to 150 min of either 50 mM NaHCO3 (pH 9) treatment or alkaline pH 9 alone. Apoplastic pH was monitored in real-time by ratiometric fluorescence microscopy simultaneously with SWIR transmission-based measurements of leaf water content (LWC). Moreover, we examined the effect of these stresses on apoplastic, symplastic and xylem ion and metabolite composition together with transcriptions of certain stress-responsive genes. Physiological and transcriptional changes were observed in response to NaHCO3 but not to alkaline pH alone. NaHCO3 elicited a transient reduction in LWC, followed by a transient alkalinization of the apoplast and stomatal closure. Simultaneously, organic acids and sugars accumulated. Fast upregulation of stress-responsive genes showed the significance of gene regulation for early plant adaptation to alkali salt stress.
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Affiliation(s)
- Amit Sagervanshi
- Institute of Plant Nutrition and Soil Science, Kiel University, Kiel, Germany
| | - Christoph-Martin Geilfus
- Institute of Plant Nutrition and Soil Science, Kiel University, Kiel, Germany; Department of Soil Science and Plant Nutrition, Hochschule Geisenheim University, Germany
| | - Hartmut Kaiser
- Institute of Plant Nutrition and Soil Science, Kiel University, Kiel, Germany
| | - Karl H Mühling
- Institute of Plant Nutrition and Soil Science, Kiel University, Kiel, Germany.
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Lee S, Jeon D, Choi S, Kang Y, Seo S, Kwon S, Lyu J, Ahn J, Seo J, Kim C. Expression Profile of Sorghum Genes and Cis-Regulatory Elements under Salt-Stress Conditions. PLANTS 2022; 11:plants11070869. [PMID: 35406848 PMCID: PMC9003456 DOI: 10.3390/plants11070869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/14/2022] [Accepted: 03/21/2022] [Indexed: 11/18/2022]
Abstract
Salinity stress is one of the most important abiotic stresses that causes great losses in crop production worldwide. Identifying the molecular mechanisms of salt resistance in sorghum will help develop salt-tolerant crops with high yields. Sorghum (Sorghum bicolor (L.) Moench) is one of the world’s four major grains and is known as a plant with excellent adaptability to salt stress. Among the various genotypes of sorghum, a Korean cultivar Nampungchal is also highly tolerant to salt. However, little is known about how Nampungchal responds to salt stress. In this study, we measured various physiological parameters, including Na+ and K+ contents, in leaves grown under saline conditions and investigated the expression patterns of differentially expressed genes (DEGs) using QuantSeq analysis. These DEG analyses revealed that genes up-regulated in a 150 mM NaCl treatment have various functions related to abiotic stresses, such as ERF and DREB. In addition, transcription factors such as ABA, WRKY, MYB, and bZip bind to the CREs region of sorghum and are involved in the regulation of various abiotic stress-responsive transcriptions, including salt stress. These findings may deepen our understanding of the mechanisms of salt tolerance in sorghum and other crops.
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Affiliation(s)
- Solji Lee
- Department of Crop Science, Chungnam National University, Daejeon 34134, Korea; (S.L.); (S.C.); (Y.K.)
| | - Donghyun Jeon
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Korea; (D.J.); (S.S.)
| | - Sehyun Choi
- Department of Crop Science, Chungnam National University, Daejeon 34134, Korea; (S.L.); (S.C.); (Y.K.)
| | - Yuna Kang
- Department of Crop Science, Chungnam National University, Daejeon 34134, Korea; (S.L.); (S.C.); (Y.K.)
| | - Sumin Seo
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Korea; (D.J.); (S.S.)
| | - Soonjae Kwon
- Korea Atomic Energy Research Institute (Advanced Radiation Technology Institute), Jeongeup 56212, Korea; (S.K.); (J.L.); (J.A.); (J.S.)
| | - Jaeil Lyu
- Korea Atomic Energy Research Institute (Advanced Radiation Technology Institute), Jeongeup 56212, Korea; (S.K.); (J.L.); (J.A.); (J.S.)
- Department of Horticulture, College of Industrial Sciences, Kongju National University, Yesan 32439, Korea
| | - Joonwoo Ahn
- Korea Atomic Energy Research Institute (Advanced Radiation Technology Institute), Jeongeup 56212, Korea; (S.K.); (J.L.); (J.A.); (J.S.)
| | - Jisu Seo
- Korea Atomic Energy Research Institute (Advanced Radiation Technology Institute), Jeongeup 56212, Korea; (S.K.); (J.L.); (J.A.); (J.S.)
| | - Changsoo Kim
- Department of Crop Science, Chungnam National University, Daejeon 34134, Korea; (S.L.); (S.C.); (Y.K.)
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Korea; (D.J.); (S.S.)
- Correspondence:
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Elnaggar A, Mosa KA, Ramamoorthy K, El-Keblawy A, Navarro T, Soliman SSM. De novo transcriptome sequencing, assembly, and gene expression profiling of a salt-stressed halophyte (Salsola drummondii) from a saline habitat. PHYSIOLOGIA PLANTARUM 2021; 173:1695-1714. [PMID: 34741316 DOI: 10.1111/ppl.13591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 09/30/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Salsola drummondii is a perennial habitat-indifferent halophyte growing in saline and nonsaline habitats of the Arabian hyperarid deserts. It offers an invaluable opportunity to examine the molecular mechanisms of salt tolerance. The present study was conducted to elucidate these mechanisms through transcriptome profiling of seedlings grown from seeds collected in a saline habitat. The Illumina Hiseq 2500 platform was employed to sequence cDNA libraries prepared from shoots and roots of nonsaline-treated plants (controls) and plants treated with 1200 mM NaCl. Transcriptomic comparison between salt-treated and control samples resulted in 17,363 differentially expressed genes (DEGs), including 12,000 upregulated genes (7870 in roots, 4130 in shoots) and 5363 downregulated genes (4258 in roots and 1105 in shoots). The majority of identified DEGs are known to be involved in transcription regulation (79), signal transduction (82), defense metabolism (101), transportation (410), cell wall metabolism (27), regulatory processes (392), respiration (85), chaperoning (9), and ubiquitination (98) during salt tolerance. This study identified potential genes associated with the salt tolerance of S. drummondii and demonstrated that this tolerance may depend on the induction of certain genes in shoot and root tissues. These gene expressions were validated using reverse-transcription quantitative PCR, the results of which were consistent with transcriptomics results. To the best of our knowledge, this is the first study providing genetic information on salt tolerance mechanisms in S. drummondii.
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Affiliation(s)
- Attiat Elnaggar
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, UAE
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Alexandria, Egypt
- Departmento de Botanica y Fisiologia Vegetal, Universidad de Málaga, Málaga, Spain
| | - Kareem A Mosa
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, UAE
- Department of Biotechnology, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
| | - Kalidoss Ramamoorthy
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, UAE
| | - Ali El-Keblawy
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, UAE
- Department of Biology, Faculty of Science, Al-Arish University, Egypt
| | - Teresa Navarro
- Departmento de Botanica y Fisiologia Vegetal, Universidad de Málaga, Málaga, Spain
| | - Sameh S M Soliman
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, UAE
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Zou L, Li T, Li B, He J, Liao C, Wang L, Xue S, Sun T, Ma X, Wu Q. De novo transcriptome analysis provides insights into the salt tolerance of Podocarpus macrophyllus under salinity stress. BMC PLANT BIOLOGY 2021; 21:489. [PMID: 34696735 PMCID: PMC8543971 DOI: 10.1186/s12870-021-03274-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Soil salinization is causing ecosystem degradation and crop yield reduction worldwide, and elucidation of the mechanism of salt-tolerant plants to improve crop yield is highly significant. Podocarpus macrophyllus is an ancient gymnosperm species with a unique environmental adaptation strategy that may be attributed to its lengthy evolutionary process. The present study investigated the physiological and molecular responses of P. macrophyllus plants to salt stress by analyzing its photosynthetic system and antioxidant enzyme activity. We also analyzed the differentially expressed genes (DEGs) in P. macrophyllus under salt stress using RNA sequencing and de novo transcriptome assembly. RESULTS Salt treatment significantly affected the photosynthetic system in P. macrophyllus seedlings, which decreased chlorophyll content, altered chloroplast ultrastructure, and reduced photosynthesis. The activities of antioxidant enzymes increased significantly following salt stress treatment. Transcriptome analysis showed that salt stress induced a large number of genes involved in multiple metabolic and biological regulation processes. The transcription levels of genes that mediate phytohormone transport or signaling were altered. K+ and Ca2+ transporter-encoding genes and the MYB transcription factor were upregulated under salt stress. However, the genes involved in cell wall biosynthesis and secondary metabolism were downregulated. CONCLUSION Our research identified some important pathways and putative genes involved in salt tolerance in P. macrophyllus and provided clues for elucidating the mechanism of salt tolerance and the utilization of the salt tolerance genes of P. macrophyllus for crop improvement.
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Affiliation(s)
- Lijuan Zou
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, 621000 China
| | - Taotao Li
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan, 467036 Henan China
| | - Bingbing Li
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan, 467036 Henan China
| | - Jing He
- The Environmental Monitoring Station of Chuanshan District, Suining, 629000 China
| | - Chunli Liao
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan, 467036 Henan China
| | - Lianzhe Wang
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan, 467036 Henan China
| | - Shouyu Xue
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan, 467036 Henan China
| | - Tao Sun
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan, 467036 Henan China
| | - Xuan Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Qinggui Wu
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, 621000 China
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11
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Qiu T, Du K, Jing Y, Zeng Q, Liu Z, Li Y, Ren Y, Yang J, Kang X. Integrated transcriptome and miRNA sequencing approaches provide insights into salt tolerance in allotriploid Populus cathayana. PLANTA 2021; 254:25. [PMID: 34226949 DOI: 10.1007/s00425-021-03600-9] [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: 01/05/2021] [Accepted: 03/18/2021] [Indexed: 06/13/2023]
Abstract
Some salt-stress responsive DEGs, mainly involved in ion transmembrane transport, hormone regulation, antioxidant system, osmotic regulation, and some miRNA jointly regulated the salt response process in allotriploid Populus cathayana. The molecular mechanism of plant polyploid stress resistance has been a hot topic in biological research. In this study, Populus diploids and first division restitution (FDR) and second division restitution (SDR) triploids were selected as research materials. All materials were treated with 70 mM NaCl solutions for 30 days in the same pot environment. We observed the growth state of triploids and diploids and determined the ratio of potassium and sodium ions, peroxidase (POD) activity, proline content, and ABA and jasmonic acid (JA) hormone content in leaves in the same culture environment with the same concentration of NaCl solution treatment. In addition, RNA-seq technology was used to study the differential expression of mRNA and miRNA. The results showed that triploid Populus grew well and the K+ content and the K+/Na+ ratio in the salt treatment were significantly lower than those in the control. The contents of ABA, JA, POD, and proline were increased compared with contents in diploid under salt stress. The salt-stress responsive DEGs were mainly involved in ion transport, cell homeostasis, the MAPK signaling pathway, peroxisome, citric acid cycle, and other salt response and growth pathways. The transcription factors mainly included NAC, MYB, MYB_related and AP2/ERF. Moreover, the differentially expressed miRNAs involved 32 families, including 743 miRNAs related to predicted target genes, among which 22 miRNAs were significantly correlated with salt-stress response genes and related to the regulation of hormones, ion transport, reactive oxygen species (ROS) and other biological processes. Our results provided insights into the physiological and molecular aspects for further research into the response mechanisms of allotriploid Populus cathayana to salt stress. This study provided valuable information for the salt tolerance mechanism of allopolyploids.
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Affiliation(s)
- Tong Qiu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Kang Du
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yanchun Jing
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Qingqing Zeng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Zhao Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yun Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yongyu Ren
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jun Yang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xiangyang Kang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
- National Engineering Laboratory for Tree Breeding, Ministry of Education, Beijing Forestry University, Beijing, 100083, China.
- Beijing Laboratory of Urban and Rural Ecological Environment, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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Amin I, Rasool S, Mir MA, Wani W, Masoodi KZ, Ahmad P. Ion homeostasis for salinity tolerance in plants: a molecular approach. PHYSIOLOGIA PLANTARUM 2021; 171:578-594. [PMID: 32770745 DOI: 10.1111/ppl.13185] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/23/2020] [Accepted: 08/06/2020] [Indexed: 05/07/2023]
Abstract
Soil salinity is one of the major environmental stresses faced by the plants. Sodium chloride is the most important salt responsible for inducing salt stress by disrupting the osmotic potential. Due to various innate mechanisms, plants adapt to the sodic niche around them. Genes and transcription factors regulating ion transport and exclusion such as salt overly sensitive (SOS), Na+ /H+ exchangers (NHXs), high sodium affinity transporter (HKT) and plasma membrane protein (PMP) are activated during salinity stress and help in alleviating cells of ion toxicity. For salt tolerance in plants signal transduction and gene expression is regulated via transcription factors such as NAM (no apical meristem), ATAF (Arabidopsis transcription activation factor), CUC (cup-shaped cotyledon), Apetala 2/ethylene responsive factor (AP2/ERF), W-box binding factor (WRKY) and basic leucine zipper domain (bZIP). Cross-talk between all these transcription factors and genes aid in developing the tolerance mechanisms adopted by plants against salt stress. These genes and transcription factors regulate the movement of ions out of the cells by opening various membrane ion channels. Mutants or knockouts of all these genes are known to be less salt-tolerant compared to wild-types. Using novel molecular techniques such as analysis of genome, transcriptome, ionome and metabolome of a plant, can help in expanding the understanding of salt tolerance mechanism in plants. In this review, we discuss the genes responsible for imparting salt tolerance under salinity stress through transport dynamics of ion balance and need to integrate high-throughput molecular biology techniques to delineate the issue.
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Affiliation(s)
- Insha Amin
- Molecular Biology Lab, Division of Veterinary Biochemistry, FVSc & A.H., SKUAST, Shuhama, India
| | - Saiema Rasool
- Department of School Education, Govt. of Jammu & Kashmir, Srinagar, 190001, India
| | - Mudasir A Mir
- Transcriptomics Lab, Division of Plant Biotechnology, SKUAST-Kashmir, Shalimar, 190025, India
| | - Wasia Wani
- Transcriptomics Lab, Division of Plant Biotechnology, SKUAST-Kashmir, Shalimar, 190025, India
| | - Khalid Z Masoodi
- Transcriptomics Lab, Division of Plant Biotechnology, SKUAST-Kashmir, Shalimar, 190025, India
| | - Parvaiz Ahmad
- Botany and Microbiology Department, College of Sciences, King Saud University, Riyadh, 11451, Saudi Arabia
- Department of Botany, S. P. College, Srinagar, Jammu and Kashmir, 190001, India
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Kumar A, Mann A, Kumar A, Kumar N, Meena BL. Physiological response of diverse halophytes to high salinity through ionic accumulation and ROS scavenging. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2021; 23:1041-1051. [PMID: 33528269 DOI: 10.1080/15226514.2021.1874289] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Salt stress induced modulations in different ionic ratios and ROS system were studied in ten halophytic species, namely Atriplex lentiformis, Tamarix aphylla, Sporobolus marginatus, Suaeda nudiflora, Urochondra setulosa, Arundo donax, Aeluropus lagopoides, Heliotropium ramossimum, Atriplex nummularia, Leptachloa fusca at salinity level of ECe ∼ 30 dSm-1 (≈300 mM NaCl) to explore their possible role in salt tolerance ability of these halophytes. These halophytes were categorized for their salt tolerance levels based on the ratios of Na+/K+, Na+/Ca2+, Na+/Cl- and Na + Cl/K + Ca. Variable responses were observed among all halophytes where Atriplex lentiformis had lowest leaf Na+/K+ (0.44) which is one of the best indicator of salt tolerance, Heliotropium ramossimum had lowest Na+/Ca2+ and Na+/Cl- (0.97 and 0.18), whereas Sporobolus marginatus had lowest Na + Cl/K + Ca (0.79). Specific enzymes activities of ascorbate peroxidase (APX), superoxide dismutase (SOD), catalase (CAT) and peroxidase (POX) were also assessed to get better comprehension of the ROS scavenging system under salinity in these halophytes. Urochondra setulosa showed highest APX and SOD activity followed by Atriplex lentiformis. Most efficient enzyme in degrading hydrogen peroxide i.e. CAT showed highest activity in Suaeda nudiflora followed by Atriplex nummularia and Urochondra setulosa, whereas Atriplex nummularia and Atriplex lentiformis showed higher POX activity. Significant variability in H2O2 and MDA content was also observed. These results possibly suggest higher inbuilt genetic potential of these halophytes to combat high salinity induced oxidative stress via higher antioxidant activities. Novelty statement: Halophytic plant adopt different strategies to cope up with the toxic ions and our studies show that the induction of antioxidant defense system to scavenge ROS, alongwith structural modifications in terms of lipid peroxidation and compartmentalization of toxic ions are the main strategies for tighter control of ion fluxes in the studied halophytes.
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Affiliation(s)
- Ashwani Kumar
- ICAR - Central Soil Salinity Research Institute, Karnal, India
| | - Anita Mann
- ICAR - Central Soil Salinity Research Institute, Karnal, India
| | - Arvind Kumar
- ICAR - Central Soil Salinity Research Institute, Karnal, India
| | - Naresh Kumar
- ICAR - Central Soil Salinity Research Institute, Karnal, India
| | - Babu Lal Meena
- ICAR - Central Soil Salinity Research Institute, Karnal, India
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Gaafar ARZ, Al-Qurainy F, Alshameri A, Khan S, Nadeem M, Tarroum M, Alansi S, Shaikhaldein HO, Salih AM, Arrak Alenezi N. High RNA quality extracted from the tolerant crop Cyamopsis tetragonoloba (L.) despite possession of low RNA integrity number. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1910567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
| | - Fahad Al-Qurainy
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Aref Alshameri
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Salim Khan
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Nadeem
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed Tarroum
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saleh Alansi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Hassan O. Shaikhaldein
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdalrhaman M. Salih
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Norah Arrak Alenezi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
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Tiwari P, Chakrabarty D. Dehydrin in the past four decades: From chaperones to transcription co-regulators in regulating abiotic stress response. CURRENT RESEARCH IN BIOTECHNOLOGY 2021. [DOI: 10.1016/j.crbiot.2021.07.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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16
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Transcriptomic profile analysis of the halophyte Suaeda rigida response and tolerance under NaCl stress. Sci Rep 2020; 10:15148. [PMID: 32939003 PMCID: PMC7494938 DOI: 10.1038/s41598-020-71529-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 08/17/2020] [Indexed: 11/17/2022] Open
Abstract
Suaeda rigida is a lignified, true haplotype that predominantly grows in the Tarim basin, China. It has significant economic and ecological value. Herein, with aim to determine the genes associated with salt tolerance, transcriptome sequencing was performed on its stem, leaves and root over three set NaCl gradients regimens at treatment intervals of 3 h and 5 days. From our findings, we identified 829,095 unigenes, with 331,394 being successfully matched to at least one annotation database. In roots, under 3 h treatment, no up-regulated DEGs were identified in 100 and 500 mM NaCl treated samples. Under 5 days treatment, 97, 60 and 242 up-regulated DEGs were identified in 100, 300, 500 mM NaCl treated samples, respectively. We identified 50, 22 and 255 down-regulated DEGs in 100, 300, 500 mM NaCl treated samples, respectively. GO biological process enrichment analysis established that down-regulated DEGs were associated with nitrogen compound transport, organic substance transport and intracellular protein transport while the up-regulated genes were enriched in cell wall biogenesis, such as plant-type cell wall biogenesis, cell wall assembly, extracellular matrix organization and plant-type cell wall organization. These findings provide valuable knowledge on genes associated with salt tolerance of Suaeda rigida, and can be applied in other downstream haplotype studies.
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Mangal V, DeGasparro S, Beresford DV, Guéguen C. Linking molecular and optical properties of dissolved organic matter across a soil-water interface on Akimiski Island (Nunavut, Canada). THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 704:135415. [PMID: 31791775 DOI: 10.1016/j.scitotenv.2019.135415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/25/2019] [Accepted: 11/05/2019] [Indexed: 06/10/2023]
Abstract
Dissolved organic matter (DOM) plays a crucial role in terrestrial and aquatic carbon and biogeochemical cycles; however, molecular transformations between aquatic and terrestrial systems remain poorly understood due to the complexity and heterogeneity of DOM. In this study, we investigated the molecular diversity of aquatic DOM and adjacent soil derived water extractable organic matter (WEOM) from seven locations on Akimiski Island, Nunavut using a combination of absorbance spectroscopy and Fourier transform ion cyclotron mass spectrometry (FT-ICR-MS). Assigned elemental formula and Van Krevelen compositional analysis reveal compositional similarities in river, inland ponds and coastal pool sites for aquatic DOM and WEOM. More aromatic, oxygenated polyphenolic carbon rich molecules were found in aquatic DOM whereas WEOM was abundant in highly unsaturated aliphatic material. A total of 276 phenolic, unsaturated aliphatic, and vascular plant-derived polyphenolic molecules were identified as being conserved between WEOM and aquatic DOM at one river and two inland pond locations suggesting similar CHO sources from adjacent soils. Moreover, contributions of polyphenolic compounds in aquatic DOM and WEOM were greater at inland ponds than coastal pools, congruent with a greater aromaticity at inland sites. Our results highlight the similarities and differences in WEOM to aquatic DOM composition and how they range across surrounding watersheds that provide insight into the biogeochemical dynamics across a Canadian subarctic terrestrial-aquatic-continuum.
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Affiliation(s)
- V Mangal
- Department of Chemistry, Université de Sherbrooke, 2500 Blvd de l'Université, Sherbrooke, QC J1K 2R1, Canada
| | - S DeGasparro
- Environmental and Life Sciences Graduate Program, Trent University, 1600 West Bank Drive Peterborough, ON K9J 7B8, Canada
| | - D V Beresford
- Environmental and Life Sciences Graduate Program, Trent University, 1600 West Bank Drive Peterborough, ON K9J 7B8, Canada; Biology/Trent School of the Environment Departments, Trent University, 1600 West Bank Drive Peterborough, ON K9J 7B8, Canada
| | - C Guéguen
- Department of Chemistry, Université de Sherbrooke, 2500 Blvd de l'Université, Sherbrooke, QC J1K 2R1, Canada.
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Furtado BU, Nagy I, Asp T, Tyburski J, Skorupa M, Gołębiewski M, Hulisz P, Hrynkiewicz K. Transcriptome profiling and environmental linkage to salinity across Salicornia europaea vegetation. BMC PLANT BIOLOGY 2019; 19:427. [PMID: 31619171 PMCID: PMC6794796 DOI: 10.1186/s12870-019-2032-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 09/12/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Salicornia europaea, a succulent obligatory halophyte is the most salt-tolerant plant species in the world. It survives salt concentrations of more than 1 M. Therefore, it is a suitable model plant to identify genes involved in salt tolerance mechanisms that can be used for the improvement of crops. The changes in a plant's gene expression in response to abiotic stresses may depend on factors like soil conditions at the site, seasonality, etc. To date, experiments were performed to study the gene expression of S. europaea only under controlled conditions. Conversely, the present study investigates the transcriptome and physicochemical parameters of S. europaea shoots and roots from two different types of saline ecosystems growing under natural conditions. RESULTS The level of soil salinity was higher at the naturally saline site than at the anthropogenic saline site. The parameters such as ECe, Na+, Cl-, Ca+, SO42- and HCO3- of the soils and plant organs significantly varied according to sites and seasons. We found that Na+ mainly accumulated in shoots, whereas K+ and Ca2+ levels were higher in roots throughout the growing period. Moreover, changes in S. europaea gene expression were more prominent in seasons, than sites and plant organs. The 30 differentially expressed genes included enzymes for synthesis of S-adenosyl methionine, CP47 of light-harvesting complex II, photosystem I proteins, Hsp70 gene, ATP-dependent Clp proteases, ribulose bisphosphate carboxylase/oxygenase (Rubisco), phenylalanine ammonia-lyase (PAL), cytochrome c oxidase (COX) and ATP synthase. CONCLUSION The comparisons made based on two seasons, plant organs and two different sites suggest the importance of seasonal variations in gene expression of S. europaea. We identify the genes that may play an important role in acclimation to season-dependent changes of salinity. The genes were involved in processes such as osmotic adjustment, energy metabolism and photosynthesis.
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Affiliation(s)
- Bliss Ursula Furtado
- Department of Microbiology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland
- Interdisciplinary Center for Modern Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100 Toruń, Poland
| | - Istvan Nagy
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, 4200 Slagelse, Denmark
| | - Torben Asp
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, 4200 Slagelse, Denmark
| | - Jarosław Tyburski
- Interdisciplinary Center for Modern Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100 Toruń, Poland
- Chair of Plant Physiology and Biotechnology, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland
| | - Monika Skorupa
- Interdisciplinary Center for Modern Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100 Toruń, Poland
| | - Marcin Gołębiewski
- Interdisciplinary Center for Modern Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100 Toruń, Poland
- Chair of Plant Physiology and Biotechnology, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland
| | - Piotr Hulisz
- Department of Soil Science and Landscape Management, Faculty of Earth Sciences and Spatial Management, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland
| | - Katarzyna Hrynkiewicz
- Department of Microbiology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland
- Interdisciplinary Center for Modern Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100 Toruń, Poland
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RNA-Seq analysis of Clerodendrum inerme (L.) roots in response to salt stress. BMC Genomics 2019; 20:724. [PMID: 31601194 PMCID: PMC6785863 DOI: 10.1186/s12864-019-6098-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 09/11/2019] [Indexed: 01/29/2023] Open
Abstract
Background Clerodendrum inerme (L.) Gaertn, a halophyte, usually grows on coastal beaches as an important mangrove plant. The salt-tolerant mechanisms and related genes of this species that respond to short-term salinity stress are unknown for us. The de novo transcriptome of C. inerme roots was analyzed using next-generation sequencing technology to identify genes involved in salt tolerance and to better understand the response mechanisms of C. inerme to salt stress. Results Illumina RNA-sequencing was performed on root samples treated with 400 mM NaCl for 0 h, 6 h, 24 h, and 72 h to investigate changes in C. inerme in response to salt stress. The de novo assembly identified 98,968 unigenes. Among these unigenes, 46,085 unigenes were annotated in the NCBI non-redundant protein sequences (NR) database, 34,756 sequences in the Swiss-Prot database and 43,113 unigenes in the evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) database. 52 Gene Ontology (GO) terms and 31 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were matched to those unigenes. Most differentially expressed genes (DEGs) related to the GO terms “single-organism process”, “membrane” and “catalytic activity” were significantly enriched while numerous DEGs related to the plant hormone signal transduction pathway were also significantly enriched. The detection of relative expression levels of 9 candidate DEGs by qRT-PCR were basically consistent with fold changes in RNA sequencing analysis, demonstrating that transcriptome data can accurately reflect the response of C. inerme roots to salt stress. Conclusions This work revealed that the response of C. inerme roots to saline condition included significant alteration in response of the genes related to plant hormone signaling. Besides, our findings provide numerous salt-tolerant genes for further research to improve the salt tolerance of functional plants and will enhance research on salt-tolerant mechanisms of halophytes.
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Comprehensive Stress-Based De Novo Transcriptome Assembly and Annotation of Guar ( Cyamopsis tetragonoloba (L.) Taub.): An Important Industrial and Forage Crop. Int J Genomics 2019; 2019:7295859. [PMID: 31687376 PMCID: PMC6800914 DOI: 10.1155/2019/7295859] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 08/23/2019] [Accepted: 09/05/2019] [Indexed: 11/17/2022] Open
Abstract
The forage crop Guar (Cyamopsis tetragonoloba (L.) Taub.) has the ability to endure heat, drought, and mild salinity. A complete image on its genic architecture will promote our understanding about gene expression networks and different tolerance mechanisms at the molecular level. Therefore, whole mRNA sequence approach on the Guar plant was conducted to provide a snapshot of the mRNA information in the cell under salinity, heat, and drought stresses to be integrated with previous transcriptomic studies. RNA-Seq technology was employed to perform a 2 × 100 paired-end sequencing using an Illumina HiSeq 2500 platform for the transcriptome of leaves of C. tetragonoloba under normal, heat, drought, and salinity conditions. Trinity was used to achieve a de novo assembly followed by gene annotation, functional classification, metabolic pathway analysis, and identification of SSR markers. A total of 218.2 million paired-end raw reads (~44 Gbp) were generated. Of those, 193.5M paired-end reads of high quality were used to reconstruct a total of 161,058 transcripts (~266 Mbp) with N50 of 2552 bp and 61,508 putative genes. There were 6463 proteins having >90% full-length coverage against the Swiss-Prot database and 94% complete orthologs against Embryophyta. Approximately, 62.87% of transcripts were blasted, 50.46% mapped, and 43.50% annotated. A total of 4715 InterProScan families, 3441 domains, 74 repeats, and 490 sites were detected. Biological processes, molecular functions, and cellular components comprised 64.12%, 25.42%, and 10.4%, respectively. The transcriptome was associated with 985 enzymes and 156 KEGG pathways. A total of 27,066 SSRs were gained with an average frequency of one SSR/9.825 kb in the assembled transcripts. This resulting data will be helpful for the advanced analysis of Guar to multi-stress tolerance.
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Diray-Arce J, Knowles A, Suvorov A, O’Brien J, Hansen C, Bybee SM, Gul B, Khan MA, Nielsen BL. Identification and evolutionary characterization of salt-responsive transcription factors in the succulent halophyte Suaeda fruticosa. PLoS One 2019; 14:e0222940. [PMID: 31545841 PMCID: PMC6756544 DOI: 10.1371/journal.pone.0222940] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 09/10/2019] [Indexed: 01/05/2023] Open
Abstract
Transcription factors are key regulatory elements that affect gene expression in response to specific signals, including environmental stresses such as salinity. Halophytes are specialized plants that have the ability to complete their life cycle in saline environments. In this study we have identified and characterized the evolutionary relationships of putative transcription factors (TF) in an obligate succulent halophyte, Suaeda fruticosa, that are involved in conferring salt tolerance. Using RNA-seq data we have analyzed the expression patterns of certain TF families, predicted protein-protein interactions, and analyzed evolutionary trajectories to elucidate their possible roles in salt tolerance. We have detected the top differentially expressed (DE) transcription factor families (MYB, CAMTA, MADS-box and bZIP) that show the most pronounced response to salinity. The majority of DE genes in the four aforementioned TF families cluster together on TF phylogenetic trees, which suggests common evolutionary origins and trajectories. This research represents the first comprehensive TF study of a leaf succulent halophyte including their evolutionary relationships with TFs in other halophyte and salt-senstive plants. These findings provide a foundation for understanding the function of salt-responsive transcription factors in salt tolerance and associated gene regulation in plants.
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Affiliation(s)
- Joann Diray-Arce
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States of America
| | - Alisa Knowles
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States of America
| | - Anton Suvorov
- Department of Biology, Brigham Young University, Provo, Utah, United States of America
| | - Jacob O’Brien
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States of America
| | - Collin Hansen
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States of America
| | - Seth M. Bybee
- Department of Biology, Brigham Young University, Provo, Utah, United States of America
| | - Bilquees Gul
- Institute of Sustainable Halophyte Utilization, University of Karachi, Karachi, Pakistan
| | - M. Ajmal Khan
- Institute of Sustainable Halophyte Utilization, University of Karachi, Karachi, Pakistan
| | - Brent L. Nielsen
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States of America
- * E-mail:
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Guo SM, Tan Y, Chu HJ, Sun MX, Xing JC. Transcriptome sequencing revealed molecular mechanisms underlying tolerance of Suaeda salsa to saline stress. PLoS One 2019; 14:e0219979. [PMID: 31335886 PMCID: PMC6650071 DOI: 10.1371/journal.pone.0219979] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 07/05/2019] [Indexed: 11/19/2022] Open
Abstract
The halophyte Suaeda salsa displayed strong resistance to salinity. Up to date, molecular mechanisms underlying tolerance of S. salsa to salinity have not been well understood. In the present study, S. salsa seedlings were treated with 30‰ salinity and then leaves and roots were subjected to Illumina sequencing. Compared with the control, 68,599 and 77,250 unigenes were significantly differentially expressed in leaves and roots in saline treatment, respectively. KEGG enrichment analyses indicated that photosynthesis process, carbohydrate, lipid and amino acid metabolisms were all downregulated in saline treatment, which should inhibit growth of S. salsa. Expression levels of Na+/H+ exchanger, V-H+ ATPase, choline monooxygenase, potassium and chloride channels were upregulated in saline treatment, which could relieve reduce over-accumulation of Na+ and Cl-. Fe-SOD, glutathione, L-ascorbate and flavonoids function as antioxidants in plants. Genes in relation to them were all upregulated, suggesting that S. salsa initiated various antioxidant mechanisms to tolerate high salinity. Besides, plant hormones, especially auxin, ethylene and jasmonic acid signaling transduction pathways were all upregulated in response to saline treatment, which were important to gene regulations of ion transportation and antioxidation. These changes might comprehensively contribute to tolerance of S. salsa to salinity. Overall, the present study provided new insights to understand the mechanisms underlying tolerance to salinity in halophytes.
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Affiliation(s)
- Su-Ming Guo
- College of Landscape Architecture, Nanjing Forestry University, Nanjing City, Jiangsu Province, P. R. China
| | - Ying Tan
- College of Architecture, Southeast University, Nanjing City, Jiangsu Province, P. R. China
| | - Han-Jie Chu
- College of Landscape Architecture, Nanjing Forestry University, Nanjing City, Jiangsu Province, P. R. China
| | - Mei-Xia Sun
- College of Landscape Architecture, Nanjing Forestry University, Nanjing City, Jiangsu Province, P. R. China
| | - Jin-Cheng Xing
- Jiangsu Coastal Area Institute of Agricultural Sciences, Yancheng City, Jiangsu Province, P. R. China
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Zhu Y, Yin J, Liang Y, Liu J, Jia J, Huo H, Wu Z, Yang R, Gong H. Transcriptomic dynamics provide an insight into the mechanism for silicon-mediated alleviation of salt stress in cucumber plants. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 174:245-254. [PMID: 30831473 DOI: 10.1016/j.ecoenv.2019.02.075] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/02/2019] [Accepted: 02/25/2019] [Indexed: 05/20/2023]
Abstract
Salinity decreases the yield and quality of crops. Silicon (Si) has been widely reported to have beneficial effects on plant growth and development under salt stress. However, the mechanism is still poorly understood. In an attempt to identify genes or gene networks that may be orchestrated to improve salt tolerance of cucumber plants, we sequenced the transcriptomes of both control and salt-stressed cucumber leaves in the presence or absence of added Si. Seedlings of cucumber 'JinYou 1' were subjected to salt stress (75 mM NaCl) without or with addition of 0.3 mM Si. Plant growth, photosynthetic gas exchange and transcriptomic dynamics were investigated. The results showed that Si addition improved the growth and photosynthetic performance of cucumber seedlings under salt stress. The comparative transcriptome analysis revealed that Si played an important role in shaping the transcriptome of cucumber: the expressions of 1469 genes were altered in response to Si treatment in the control conditions, and these genes were mainly involved in ion transport, hormone and signal transduction, biosynthetic and metabolic processes, and stress and defense responses. Under salt stress alone, 1482 genes with putative functions associated with metabolic processes and responses to environmental stimuli have changed their expression levels. Si treatment shifted the transcriptome of salt-stressed cucumber back to that of the control, as evidenced that among the 708 and 774 genes that were up- or down-regulated under salt stress, a large majority of them (609 and 595, respectively) were reverted to the normal expression levels. These results suggest that Si may act as an elicitor to precondition cucumber plants and induce salt tolerance. The study may help us understand the mechanism for silicon-mediated salt tolerance and provide a theoretical basis for silicon application in crop production in saline soils.
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Affiliation(s)
- Yongxing Zhu
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; College of Horticulture and Gardening, College of Agronomy, Yangtze University, Jingzhou 434025, Hubei, China
| | - Junliang Yin
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; College of Horticulture and Gardening, College of Agronomy, Yangtze University, Jingzhou 434025, Hubei, China
| | - Yufei Liang
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jiaqi Liu
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jianhua Jia
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Heqiang Huo
- Mid-Florida Research and Education Center, University of Florida, Institute of Food and Agricultural Sciences, 2725 South Binion Road, Apopka, FL 32703, USA
| | - Zefeng Wu
- College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Ruolin Yang
- College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Haijun Gong
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
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Rashmi D, Barvkar VT, Nadaf A, Mundhe S, Kadoo NY. Integrative omics analysis in Pandanus odorifer (Forssk.) Kuntze reveals the role of Asparagine synthetase in salinity tolerance. Sci Rep 2019; 9:932. [PMID: 30700750 PMCID: PMC6353967 DOI: 10.1038/s41598-018-37039-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 11/30/2018] [Indexed: 11/12/2022] Open
Abstract
Pandanus odorifer (Forssk) Kuntze grows naturally along the coastal regions and withstands salt-sprays as well as strong winds. A combination of omics approaches and enzyme activity studies was employed to comprehend the mechanistic basis of high salinity tolerance in P. odorifer. The young seedlings of P. odorifer were exposed to 1 M salt stress for up to three weeks and analyzed using RNAsequencing (RNAseq) and LC-MS. Integrative omics analysis revealed high expression of the Asparagine synthetase (AS) (EC 6.3.5.4) (8.95 fold) and remarkable levels of Asparagine (Asn) (28.5 fold). This indicated that salt stress promoted Asn accumulation in P. odorifer. To understand this further, the Asn biosynthesis pathway was traced out in P. odorifer. It was noticed that seven genes involved in Asn bisynthetic pathway namely glutamine synthetase (GS) (EC 6.3.1.2) glutamate synthase (GOGAT) (EC 1.4.1.14), aspartate kinase (EC 2.7.2.4), pyruvate kinase (EC 2.7.1.40), aspartate aminotransferase (AspAT) (EC 2.6.1.1), phosphoenolpyruvate carboxylase (PEPC) (EC 4.1.1.31) and AS were up-regulated under salt stress. AS transcripts were most abundant thereby showed its highest activity and thus were generating maximal Asn under salt stress. Also, an up-regulated Na+/H+ antiporter (NHX1) facilitated compartmentalization of Na+ into vacuoles, suggesting P. odorifer as salt accumulator species.
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Affiliation(s)
- Deo Rashmi
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India
| | - Vitthal T Barvkar
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India.
| | - Altafhusain Nadaf
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India.
| | - Swapnil Mundhe
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411008, India
| | - Narendra Y Kadoo
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411008, India
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Liu Q, Tang J, Wang W, Zhang Y, Yuan H, Huang S. Transcriptome analysis reveals complex response of the medicinal/ornamental halophyte Iris halophila Pall. to high environmental salinity. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 165:250-260. [PMID: 30199796 DOI: 10.1016/j.ecoenv.2018.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/28/2018] [Accepted: 09/01/2018] [Indexed: 05/25/2023]
Abstract
The remediation and subsequent use of saline-alkaline land are of great significance to ecological environment construction and sustainable agricultural development. Iris halophila Pall. is a salt-tolerant medicinal and ornamental plant, which has good application prospects in the ecological construction of saline-alkaline land; therefore, study of the molecular mechanisms of salt tolerance in I. halophila has important theoretical and practical value. To evaluate the molecular mechanism of the response of I. halophila to salt toxicity, I. halophila seedlings were treated with salt (300 mM NaCl) and subjected to deep RNA sequencing. The clean reads were obtained and assembled into 297,188 unigenes. Among them, 1120 and 100 salt-responsive genes were identified in I. halophila shoots and roots, respectively. Among them, the key flavonoid and lignin biosynthetic genes, hormone signaling genes, sodium/potassium ion transporter genes, and transcription factors were analyzed and summarized. Quantitative reverse-transcription PCR analysis strengthened the reliability of the RNA sequencing results. This work provides an overview of the transcriptomic responses to salt toxicity in I. halophila and identifies the responsive genes that may contribute to its reduced salt toxicity. These results lay an important foundation for further study of the molecular mechanisms of salt tolerance in I. halophila and related species.
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Affiliation(s)
- Qingquan Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Jun Tang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Weilin Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Yongxia Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Haiyan Yuan
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Suzhen Huang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China.
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Yang L, Jin Y, Huang W, Sun Q, Liu F, Huang X. Full-length transcriptome sequences of ephemeral plant Arabidopsis pumila provides insight into gene expression dynamics during continuous salt stress. BMC Genomics 2018; 19:717. [PMID: 30261913 PMCID: PMC6161380 DOI: 10.1186/s12864-018-5106-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 09/21/2018] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Arabidopsis pumila is native to the desert region of northwest China and it is extraordinarily well adapted to the local semi-desert saline soil, thus providing a candidate plant system for environmental adaptation and salt-tolerance gene mining. However, understanding of the salt-adaptation mechanism of this species is limited because of genomic sequences scarcity. In the present study, the transcriptome profiles of A. pumila leaf tissues treated with 250 mM NaCl for 0, 0.5, 3, 6, 12, 24 and 48 h were analyzed using a combination of second-generation sequencing (SGS) and third-generation single-molecule real-time (SMRT) sequencing. RESULTS Correction of SMRT long reads by SGS short reads resulted in 59,328 transcripts. We found 8075 differentially expressed genes (DEGs) between salt-stressed tissues and controls, of which 483 were transcription factors and 1157 were transport proteins. Most DEGs were activated within 6 h of salt stress and their expression stabilized after 48 h; the number of DEGs was greatest within 12 h of salt stress. Gene annotation and functional analyses revealed that expression of genes associated with the osmotic and ionic phases rapidly and coordinately changed during the continuous salt stress in this species, and salt stress-related categories were highly enriched among these DEGs, including oxidation-reduction, transmembrane transport, transcription factor activity and ion channel activity. Orphan, MYB, HB, bHLH, C3H, PHD, bZIP, ARF and NAC TFs were most enriched in DEGs; ABCB1, CLC-A, CPK30, KEA2, KUP9, NHX1, SOS1, VHA-A and VP1 TPs were extensively up-regulated in salt-stressed samples, suggesting that they play important roles in slat tolerance. Importantly, further experimental studies identified a mitogen-activated protein kinase (MAPK) gene MAPKKK18 as continuously up-regulated throughout salt stress, suggesting its crucial role in salt tolerance. The expression patterns of the salt-responsive 24 genes resulted from quantitative real-time PCR were basically consistent with their transcript abundance changes identified by RNA-Seq. CONCLUSION The full-length transcripts generated in this study provide a more accurate depiction of gene transcription of A. pumila. We identified potential genes involved in salt tolerance of A. pumila. These data present a genetic resource and facilitate better understanding of salt-adaptation mechanism for ephemeral plants.
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Affiliation(s)
- Lifei Yang
- Special Plant Genomics Laboratory, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Yuhuan Jin
- Special Plant Genomics Laboratory, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Wei Huang
- Special Plant Genomics Laboratory, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Qi Sun
- Special Plant Genomics Laboratory, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Fang Liu
- Special Plant Genomics Laboratory, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Xianzhong Huang
- Special Plant Genomics Laboratory, College of Life Sciences, Shihezi University, Shihezi, 832003, China.
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Asrar H, Hussain T, Gul B, Khan MA, Nielsen BL. Differential protein expression reveals salt tolerance mechanisms of Desmostachya bipinnata at moderate and high levels of salinity. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 45:793-812. [PMID: 32291063 DOI: 10.1071/fp17281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 01/26/2018] [Indexed: 06/11/2023]
Abstract
A proteomics approach was used to investigate salt tolerance mechanisms of Desmostachya bipinnata (L.) Stapf. Plants were subjected to 0mM (control), 100mM (moderate) and 400mM (high) NaCl. Proteins were separated by two-dimensional gel electrophoresis and identified with available databases. Optimal plant fresh weight was found at moderate salinity but declined at high salinity. Water potential, osmotic potential, Na+/K+ ratio, leaf electrolyte leakage, sugars and proline were altered at high salinity. However, water potential, proline content and electrolyte leakage were maintained at moderate salinity; Na+ and K+ concentrations increased, whereas sugars and osmotic potential decreased. Comparative proteome analysis revealed 103 salt responsive proteins. At moderate salinity, most of the proteins involved in energy metabolism, transport, antioxidative defence and cell growth were either unchanged or increased. Proteins related to amino-acid metabolism were decreased while those associated with secondary metabolism were accumulated. At high salinity, amino-acid metabolism and dehydration responses were evident; proteins of energy metabolism, transport and stress defence were downregulated. These results suggest that an efficient defence system, improved transport of water and metabolites, increased cell wall lignification and regulation of energy and carbohydrate metabolism allowed better potential for plant growth under moderately saline conditions.
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Affiliation(s)
- Hina Asrar
- Institute of Sustainable Halophyte Utilisation, University of Karachi, Karachi-75270, Pakistan
| | - Tabassum Hussain
- Institute of Sustainable Halophyte Utilisation, University of Karachi, Karachi-75270, Pakistan
| | - Bilquees Gul
- Institute of Sustainable Halophyte Utilisation, University of Karachi, Karachi-75270, Pakistan
| | - M Ajmal Khan
- Institute of Sustainable Halophyte Utilisation, University of Karachi, Karachi-75270, Pakistan
| | - Brent L Nielsen
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
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Nikalje GC, Suprasanna P. Coping With Metal Toxicity - Cues From Halophytes. FRONTIERS IN PLANT SCIENCE 2018; 9:777. [PMID: 29971073 PMCID: PMC6018462 DOI: 10.3389/fpls.2018.00777] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 05/22/2018] [Indexed: 05/18/2023]
Abstract
Being the native flora of saline soil, halophytes are well studied for their salt tolerance and adaptation mechanism at the physiological, biochemical, molecular and metabolomic levels. However, these saline habitats are getting contaminated due to various anthropogenic activities like urban waste, agricultural runoff, mining, industrial waste that are rich in toxic metals and metalloids. These toxic metals impose detrimental effects on growth and development of most plant species. Halophytes by virtue of their tolerance to salinity also show high tolerance to heavy metals which is attributed to the enhanced root to shoot metal translocation and bioavailability. Halophytes rapidly uptake toxic ions from the root and transport them toward aerial parts by using different transporters which are involved in metal tolerance and homeostasis. A number of defense related physiological and biochemical strategies are known to be crucial for metal detoxification in halophytes however; there is paucity of information on the molecular regulators. Understanding of the phenomenon of cross-tolerance of salinity with other abiotic stresses in halophytes could very well boost their potential use in phytoremediation. In this article, we present an overview of heavy metal tolerance in case of halophytes, associated mechanisms and cross-tolerance of salinity with other abiotic stresses.
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Affiliation(s)
- Ganesh C. Nikalje
- Department of Botany, R. K. Talreja College of Arts, Science and Commerce, Ulhasnagar, India
| | - Penna Suprasanna
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
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Gu C, Xu S, Wang Z, Liu L, Zhang Y, Deng Y, Huang S. De novo sequencing, assembly, and analysis of Iris lactea var. chinensis roots' transcriptome in response to salt stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 125:1-12. [PMID: 29413626 DOI: 10.1016/j.plaphy.2018.01.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 01/22/2018] [Indexed: 06/08/2023]
Abstract
As a halophyte, Iris lactea var. chinensis (I. lactea var. chinensis) is widely distributed and has good drought and heavy metal resistance. Moreover, it is an excellent ornamental plant. I. lactea var. chinensis has extensive application prospects owing to the global impacts of salinization. To better understand its molecular mechanism involved in salt resistance, the de novo sequencing, assembly, and analysis of I. lactea var. chinensis roots' transcriptome in response to salt-stress conditions was performed. On average, 74.17% of the clean reads were mapped to unigenes. A total of 121,093 unigenes were constructed and 56,398 (46.57%) were annotated. Among these, 13,522 differentially expressed genes (DEGs) were identified between salt-treated and control samples Compared to the transcriptional level of control, 7037 DEGs were up-regulated and 6539 down-regulated. In addition, 129 up-regulated and 1609 down-regulated genes were simultaneously detected in all three pairwise comparisons between control and salt-stressed libraries. At least 247 and 250 DEGs encoding transcription factors and transporter proteins were identified. Meanwhile, 130 DEGs regarding reactive oxygen species (ROS) scavenging system were also summarized. Based on real-time quantitative RT-PCR, we verified the changes in the expression patterns of 10 unigenes. Our study identified potential salt-responsive candidate genes and increased the understanding of halophyte responses to salinity stress.
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Affiliation(s)
- Chunsun Gu
- Jiangsu Key Laboratory for Bioresources of Saline Solis, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.
| | - Sheng Xu
- Jiangsu Key Laboratory for Bioresources of Saline Solis, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Zhiquan Wang
- Jiangsu Key Laboratory for Bioresources of Saline Solis, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Liangqin Liu
- Jiangsu Key Laboratory for Bioresources of Saline Solis, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Yongxia Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Solis, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Yanming Deng
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Suzhen Huang
- Jiangsu Key Laboratory for Bioresources of Saline Solis, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
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Transcriptomic Profiling and Physiological Analysis of Haloxylon ammodendron in Response to Osmotic Stress. Int J Mol Sci 2017; 19:ijms19010084. [PMID: 29286291 PMCID: PMC5796034 DOI: 10.3390/ijms19010084] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 12/23/2017] [Accepted: 12/25/2017] [Indexed: 11/17/2022] Open
Abstract
Haloxylon ammodendron, a perennial xero-halophyte, is an essential species for investigating the effects of drought on desert tree. To gain a comprehensive knowledge on the responses of H. ammodendron to drought stress, we specially performed the molecular and physiological analysis of H. ammodendron in response to -0.75 MPa osmotic stress for six and 24 h in lab condition via RNA-seq and digital gene expression (DGE). In total, 87,109 unigenes with a mean length of 680 bp and 13,486 potential simple sequence repeats (SSRs) were generated, and 3353 differentially expressed genes (DEGs) in shoots and 4564 in roots were identified under stress. These DEGs were mainly related to ion transporters, signal transduction, ROS-scavenging, photosynthesis, cell wall organization, membrane stabilization and hormones. Moreover, the physiological changes of inorganic ions and organic solute content, peroxidase (POD) activity and osmotic potential were in accordance with dynamic transcript profiles of the relevant genes. In this study, a detailed investigation of the pathways and candidate genes identified promote the research on the molecular mechanisms of abiotic stress tolerance in the xero-halophytic species. Our data provides valuable genetic resources for future improvement of forage and crop species for better adaptation to abiotic stresses.
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Wang L, Wang HL, Yin L, Tian CY. Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination. BMC Genomics 2017; 18:806. [PMID: 29052505 PMCID: PMC5649071 DOI: 10.1186/s12864-017-4209-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 10/12/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Dimorphic seeds from Suaeda aralocaspica exhibit different germination behaviors that are thought to be a bet-hedging strategy advantageous in harsh and unpredictable environments. To understand the molecular mechanisms of Suaeda aralocaspica dimorphic seed germination, we applied RNA sequencing and small RNA sequencing for samples collected at three germination stages. RESULTS A total of 79,414 transcripts were assembled using Trinity, of which 57.67% were functionally annotated. KEGG enrichment unveiled that photosynthesis and flavonol biosynthesis pathways were activated earlier in brown seed compared with black seed. Gene expression analysis revealed that nine candidate unigenes in gibberellic acid and abscisic acid signal transduction and 23 unigenes in circadian rhythm-plant pathway showed distinct expression profiles to promote dimorphic seed germination. 194 conserved miRNAs comprising 40 families and 21 novel miRNAs belonging to 20 families in Suaeda aralocaspica were identified using miRDeep-P and Mfold. The expression of miRNAs in black seed was suppressed at imbibition stage. Among the identified miRNAs, 59 conserved and 13 novel miRNAs differentially expressed during seed germination. Of which, 43 conserved and nine novel miRNAs showed distinct expression patterns between black and brown seed. Using TAPIR, 208 unigenes were predicted as putative targets of 35 conserved miRNA families and 17 novel miRNA families. Among functionally annotated targets, genes participated in transcription regulation constituted the dominant category, followed by genes involved in signaling and stress response. Seven of the predicted targets were validated using 5' rapid amplification of cDNA ends or real-time quantitative reverse transcription-PCR. CONCLUSIONS Our results indicate that specific genes and miRNAs are regulated differently between black and brown seed during germination, which may contribute to the different germination behaviors of Suaeda aralocaspica dimorphic seeds in unpredictable variable environments. Our results lay a solid foundation for further studying the roles of candidate genes and miRNAs in Suaeda aralocaspica dimorphic seed germination.
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Affiliation(s)
- Lei Wang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Hong-Ling Wang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Lan Yin
- ABLife, Inc., Optics Valley International Biomedical Park, Building 18, East Lake High-Tech Development Zone, 858 Gaoxin Boulevard, Wuhan, 430075, China.
| | - Chang-Yan Tian
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
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Comparative proteomic analysis of alfalfa revealed new salt and drought stress-related factors involved in seed germination. Mol Biol Rep 2017; 44:261-272. [PMID: 28597411 DOI: 10.1007/s11033-017-4104-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 08/16/2016] [Indexed: 10/19/2022]
Abstract
Salinity and drought are two major environmental factors that limit the growth and yield of many forage crops in semi-arid and arid regions. Alfalfa (Medicago sativa L.) is one of the most important forage crops in many countries. We aim to investigate the molecular mechanisms of alfalfa in response to salt and drought stresses in this study. Physiological and proteomic analyses were applied to examine the Zhongmu NO.3 alfalfa seed germination stage with 200 mM NaCl and 180 g·L-1 polyethylene glycol (PEG) treatments. The germination ability of the seed and the accumulation of osmotic solutes were quite different between the NaCl and PEG treatments. More than 800 protein spots were detected by proteomics technology on two-dimensional electrophoresis (2-DE) gels. The abundance of twenty-eight proteins were decreased or increased after salt and drought stress. Seventeen of these proteins were identified and classified into six functional categories through mass spectrometry (MS). The six groups involved in salt- and PEG-mediated stress included defense response, energy metabolism, protein synthesis and degradation, oxidative stress, carbohydrate metabolism-associated proteins, and unknown proteins. We discovered that some proteins related to carbohydrate metabolism and energy production increased in abundance under salt- and PEG-mediated drought stress. This demonstrates a common mechanism of energy consumption during abiotic stresses. Further study of these proteins with unknown function will provide insights into the molecular mechanisms of abiotic stress and the discovery of new candidate markers.
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Harding T, Roger AJ, Simpson AGB. Adaptations to High Salt in a Halophilic Protist: Differential Expression and Gene Acquisitions through Duplications and Gene Transfers. Front Microbiol 2017; 8:944. [PMID: 28611746 PMCID: PMC5447177 DOI: 10.3389/fmicb.2017.00944] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 05/11/2017] [Indexed: 11/13/2022] Open
Abstract
The capacity of halophiles to thrive in extreme hypersaline habitats derives partly from the tight regulation of ion homeostasis, the salt-dependent adjustment of plasma membrane fluidity, and the increased capability to manage oxidative stress. Halophilic bacteria, and archaea have been intensively studied, and substantial research has been conducted on halophilic fungi, and the green alga Dunaliella. By contrast, there have been very few investigations of halophiles that are phagotrophic protists, i.e., protozoa. To gather fundamental knowledge about salt adaptation in these organisms, we studied the transcriptome-level response of Halocafeteria seosinensis (Stramenopiles) grown under contrasting salinities. We provided further evolutionary context to our analysis by identifying genes that underwent recent duplications. Genes that were highly responsive to salinity variations were involved in stress response (e.g., chaperones), ion homeostasis (e.g., Na+/H+ transporter), metabolism and transport of lipids (e.g., sterol biosynthetic genes), carbohydrate metabolism (e.g., glycosidases), and signal transduction pathways (e.g., transcription factors). A significantly high proportion (43%) of duplicated genes were also differentially expressed, accentuating the importance of gene expansion in adaptation by H. seosinensis to high salt environments. Furthermore, we found two genes that were lateral acquisitions from bacteria, and were also highly up-regulated and highly expressed at high salt, suggesting that this evolutionary mechanism could also have facilitated adaptation to high salt. We propose that a transition toward high-salt adaptation in the ancestors of H. seosinensis required the acquisition of new genes via duplication, and some lateral gene transfers (LGTs), as well as the alteration of transcriptional programs, leading to increased stress resistance, proper establishment of ion gradients, and modification of cell structure properties like membrane fluidity.
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Affiliation(s)
- Tommy Harding
- Department of Biochemistry and Molecular Biology, Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie UniversityHalifax, NS, Canada
| | - Andrew J. Roger
- Department of Biochemistry and Molecular Biology, Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie UniversityHalifax, NS, Canada
| | - Alastair G. B. Simpson
- Department of Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie UniversityHalifax, NS, Canada
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Gong W, Xu F, Sun J, Peng Z, He S, Pan Z, Du X. iTRAQ-Based Comparative Proteomic Analysis of Seedling Leaves of Two Upland Cotton Genotypes Differing in Salt Tolerance. FRONTIERS IN PLANT SCIENCE 2017; 8:2113. [PMID: 29326733 PMCID: PMC5733471 DOI: 10.3389/fpls.2017.02113] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 11/27/2017] [Indexed: 05/21/2023]
Abstract
Cotton yields are greatly reduced under high salinity stress conditions, although cotton is considered a moderately salt-tolerant crop. Understanding at the molecular level how cotton responds to salt stress will help in developing salt tolerant varieties. Here, we combined physiological analysis with isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomics of seedling leaves of 2 genotypes differing in salinity tolerance to 200 mM (18.3 dS/m) NaCl stress. Salt stress produced significant stress symptoms in the sensitive genotype Nan Dan Ba Di Da Hua (N), including lower relative water and chlorophyll contents and higher relative electrolyte leakage and Na+/K+ ratio in leaf samples, compared with those in the tolerant genotype Earlistaple 7 (Z). A total of 58 differentially abundant salt-responsive proteins were identified. Asp-Glu-Ala-Asp (DEAD)-box ATP-dependent RNA helicase 3 and protochlorophyllide reductase were markedly suppressed after salt treatment, whereas the phosphate-related differentially abundant proteins (DAPs) phosphoethanolamine N-methyltransferase 1 and 14-3-3-like protein E were induced, and all these proteins may play significant roles in salt stress. Twenty-nine salt-responsive proteins were also genotype specific, and 62.1 and 27.6% of these were related to chloroplast and defense responses, respectively. Based on the Arabidopsis thaliana protein interaction database, orthologs of 25 proteins showed interactions in Arabidopsis, and among these, a calmodulin protein was predicted to have 212 functional partners. In addition, the Golgi apparatus and calcium may be important for salt secretion in cotton. Through integrative proteome and transcriptome analysis, 16 DAPs were matched to differentially expressed genes and verified using qRT-PCR. On the basis of these findings, we proposed that some proteins related to chloroplast, ATP, ribosomal, and phosphate metabolism as well as to the Golgi apparatus and calcium may play key roles in the short-term salt stress response of cotton seedling leaves.
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Gharat SA, Parmar S, Tambat S, Vasudevan M, Shaw BP. Transcriptome Analysis of the Response to NaCl in Suaeda maritima Provides an Insight into Salt Tolerance Mechanisms in Halophytes. PLoS One 2016; 11:e0163485. [PMID: 27682829 PMCID: PMC5040429 DOI: 10.1371/journal.pone.0163485] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 09/10/2016] [Indexed: 01/02/2023] Open
Abstract
Although salt tolerance is a feature representative of halophytes, most studies on this topic in plants have been conducted on glycophytes. Transcriptome profiles are also available for only a limited number of halophytes. Hence, the present study was conducted to understand the molecular basis of salt tolerance through the transcriptome profiling of the halophyte Suaeda maritima, which is an emerging plant model for research on salt tolerance. Illumina sequencing revealed 72,588 clustered transcripts, including 27,434 that were annotated using BLASTX. Salt application resulted in the 2-fold or greater upregulation of 647 genes and downregulation of 735 genes. Of these, 391 proteins were homologous to proteins in the COGs (cluster of orthologous groups) database, and the majorities were grouped into the poorly characterized category. Approximately 50% of the genes assigned to MapMan pathways showed homology to S. maritima. The majority of such genes represented transcription factors. Several genes also contributed to cell wall and carbohydrate metabolism, ion relation, redox responses and G protein, phosphoinositide and hormone signaling. Real-time PCR was used to validate the results of the deep sequencing for the most of the genes. This study demonstrates the expression of protein kinase C, the target of diacylglycerol in phosphoinositide signaling, for the first time in plants. This study further reveals that the biochemical and molecular responses occurring at several levels are associated with salt tolerance in S. maritima. At the structural level, adaptations to high salinity levels include the remodeling of cell walls and the modification of membrane lipids. At the cellular level, the accumulation of glycinebetaine and the sequestration and exclusion of Na+ appear to be important. Moreover, this study also shows that the processes related to salt tolerance might be highly complex, as reflected by the salt-induced enhancement of transcription factor expression, including hormone-responsive factors, and that this process might be initially triggered by G protein and phosphoinositide signaling.
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Affiliation(s)
- Sachin Ashruba Gharat
- Environmental Biotechnology Laboratory, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
| | - Shaifaly Parmar
- Environmental Biotechnology Laboratory, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
| | - Subodh Tambat
- Bionivid Technology Private Limited, 3rd Floor, 4C-209, 4th Cross, Near New Horizon College, Kasturi Nagar, Bangalore, 560043, Karnataka, India
| | - Madavan Vasudevan
- Bionivid Technology Private Limited, 3rd Floor, 4C-209, 4th Cross, Near New Horizon College, Kasturi Nagar, Bangalore, 560043, Karnataka, India
| | - Birendra Prasad Shaw
- Environmental Biotechnology Laboratory, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
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The De Novo Transcriptome and Its Functional Annotation in the Seed Beetle Callosobruchus maculatus. PLoS One 2016; 11:e0158565. [PMID: 27442123 PMCID: PMC4956038 DOI: 10.1371/journal.pone.0158565] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 06/19/2016] [Indexed: 12/25/2022] Open
Abstract
Despite their unparalleled biodiversity, the genomic resources available for beetles (Coleoptera) remain relatively scarce. We present an integrative and high quality annotated transcriptome of the beetle Callosobruchus maculatus, an important and cosmopolitan agricultural pest as well as an emerging model species in ecology and evolutionary biology. Using Illumina sequencing technology, we sequenced 492 million read pairs generated from 51 samples of different developmental stages (larvae, pupae and adults) of C. maculatus. Reads were de novo assembled using the Trinity software, into a single combined assembly as well as into three separate assemblies based on data from the different developmental stages. The combined assembly generated 218,192 transcripts and 145,883 putative genes. Putative genes were annotated with the Blast2GO software and the Trinotate pipeline. In total, 33,216 putative genes were successfully annotated using Blastx against the Nr (non-redundant) database and 13,382 were assigned to 34,100 Gene Ontology (GO) terms. We classified 5,475 putative genes into Clusters of Orthologous Groups (COG) and 116 metabolic pathways maps were predicted based on the annotation. Our analyses suggested that the transcriptional specificity increases with ontogeny. For example, out of 33,216 annotated putative genes, 51 were only expressed in larvae, 63 only in pupae and 171 only in adults. Our study illustrates the importance of including samples from several developmental stages when the aim is to provide an integrative and high quality annotated transcriptome. Our results will represent an invaluable resource for those working with the ecology, evolution and pest control of C. maculatus, as well for comparative studies of the transcriptomics and genomics of beetles more generally.
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Xu C, Tang X, Shao H, Wang H. Salinity Tolerance Mechanism of Economic Halophytes From Physiological to Molecular Hierarchy for Improving Food Quality. Curr Genomics 2016; 17:207-14. [PMID: 27252587 PMCID: PMC4869007 DOI: 10.2174/1389202917666160202215548] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 05/15/2015] [Accepted: 06/09/2015] [Indexed: 12/26/2022] Open
Abstract
Soil salinity is becoming the key constraints factor to agricultural production. Therefore, the plant especially the crops possessing capacities of salt tolerance will be of great economic significance. The adaptation or tolerance of plant to salinity stress involves a series of physiological, metabolic and molecular mechanisms. Halophytes are the kind of organisms which acquire special salt tolerance mechanisms to respond to the salt tress and ensure normal growth and development under saline conditions in their lengthy evolutionary adaptation, so understanding how halophytes respond to salinity stress will provide us with methods and tactics to foster and develop salt resistant varieties of crops. The strategies in physiological and molecular level adopted by halophytes are various including the changes in photosynthetic and transpiration rate, the sequestration of Na+ to extracellular or vacuole, the regulation of stomata aperture and stomatal density, the accumulation and synthesis of the phytohormones as well as the relevant gene expression underlying these physiological traits, such as the stress signal transduction, the regulation of the transcription factors, the activation and expression of the transporter genes, the activation or inhibition of the synthetases and so on. This review focuses on the research advances of the regulating mechanisms in halophytes from physiological to molecular, which render the halophytes tolerance and adaption to salinity stress.
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Affiliation(s)
- Chongzhi Xu
- College of Plant Science, Tarim University, Alar843300,Xinjiang, China
| | - Xiaoli Tang
- Key Laboratory of Coastal Biology & Bioresources Utilization, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Yantai 264003, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongbo Shao
- Key Laboratory of Coastal Biology & Bioresources Utilization, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Yantai 264003, China
- Institute of Agro-biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Hongyan Wang
- Key Laboratory of Coastal Biology & Bioresources Utilization, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Yantai 264003, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Yantai Academy of China Agriculture University, Yantai 264670, China
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Jin H, Dong D, Yang Q, Zhu D. Salt-Responsive Transcriptome Profiling of Suaeda glauca via RNA Sequencing. PLoS One 2016; 11:e0150504. [PMID: 26930632 PMCID: PMC4773115 DOI: 10.1371/journal.pone.0150504] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 02/15/2016] [Indexed: 12/04/2022] Open
Abstract
Background Suaeda glauca, a succulent halophyte of the Chenopodiaceae family, is widely distributed in coastal areas of China. Suaeda glauca is highly resistant to salt and alkali stresses. In the present study, the salt-responsive transcriptome of Suaeda glauca was analyzed to identify genes involved in salt tolerance and study halophilic mechanisms in this halophyte. Results Illumina HiSeq 2500 was used to sequence cDNA libraries from salt-treated and control samples with three replicates each treatment. De novo assembly of the six transcriptomes identified 75,445 unigenes. A total of 23,901 (31.68%) unigenes were annotated. Compared with transcriptomes from the three salt-treated and three salt-free samples, 231 differentially expressed genes (DEGs) were detected (including 130 up-regulated genes and 101 down-regulated genes), and 195 unigenes were functionally annotated. Based on the Gene Ontology (GO), Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) classifications of the DEGs, more attention should be paid to transcripts associated with signal transduction, transporters, the cell wall and growth, defense metabolism and transcription factors involved in salt tolerance. Conclusions This report provides a genome-wide transcriptional analysis of a halophyte, Suaeda glauca, under salt stress. Further studies of the genetic basis of salt tolerance in halophytes are warranted.
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Affiliation(s)
- Hangxia Jin
- Zhejiang Academy of Agricultural Science, Institute of Crops and Nuclear Technology Utilization, Hangzhou Zhejiang 310021, People’s Republic of China
| | - Dekun Dong
- Zhejiang Academy of Agricultural Science, Institute of Crops and Nuclear Technology Utilization, Hangzhou Zhejiang 310021, People’s Republic of China
| | - Qinghua Yang
- Zhejiang Academy of Agricultural Science, Institute of Crops and Nuclear Technology Utilization, Hangzhou Zhejiang 310021, People’s Republic of China
| | - Danhua Zhu
- Zhejiang Academy of Agricultural Science, Institute of Crops and Nuclear Technology Utilization, Hangzhou Zhejiang 310021, People’s Republic of China
- * E-mail:
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Sun X, Xu L, Wang Y, Luo X, Zhu X, Kinuthia KB, Nie S, Feng H, Li C, Liu L. Transcriptome-based gene expression profiling identifies differentially expressed genes critical for salt stress response in radish (Raphanus sativus L.). PLANT CELL REPORTS 2016; 35:329-46. [PMID: 26518430 DOI: 10.1007/s00299-015-1887-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Revised: 10/02/2015] [Accepted: 10/15/2015] [Indexed: 05/20/2023]
Abstract
Transcriptome-based gene expression analysis identifies many critical salt-responsive genes in radish and facilitates further dissecting the molecular mechanism underlying salt stress response. Salt stress severely impacts plant growth and development. Radish, a moderately salt-sensitive vegetable crop, has been studied for decades towards the physiological and biochemical performances under salt stress. However, no systematic study on isolation and identification of genes involved in salt stress response has been performed in radish, and the molecular mechanism governing this process is still indistinct. Here, the RNA-Seq technique was applied to analyze the transcriptomic changes on radish roots treated with salt (200 mM NaCl) for 48 h in comparison with those cultured in normal condition. Totally 8709 differentially expressed genes (DEGs) including 3931 up- and 4778 down-regulated genes were identified. Functional annotation analysis indicated that many genes could be involved in several aspects of salt stress response including stress sensing and signal transduction, osmoregulation, ion homeostasis and ROS scavenging. The association analysis of salt-responsive genes and miRNAs exhibited that 36 miRNA-mRNA pairs had negative correlationship in expression trends. Reverse-transcription quantitative PCR (RT-qPCR) analysis revealed that the expression profiles of DEGs were in line with results from the RNA-Seq analysis. Furthermore, the putative model of DEGs and miRNA-mediated gene regulation was proposed to elucidate how radish sensed and responded to salt stress. This study represents the first comprehensive transcriptome-based gene expression profiling under salt stress in radish. The outcomes of this study could facilitate further dissecting the molecular mechanism underlying salt stress response and provide a valuable platform for further genetic improvement of salt tolerance in radish breeding programs.
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Affiliation(s)
- Xiaochuan Sun
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014, People's Republic of China
| | - Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014, People's Republic of China
| | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014, People's Republic of China
| | - Xiaobo Luo
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Xianwen Zhu
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Karanja Benard Kinuthia
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Shanshan Nie
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014, People's Republic of China
| | - Haiyang Feng
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Chao Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014, People's Republic of China.
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Gharat SA, Shaw BP. Novel and conserved miRNAs in the halophyte Suaeda maritima identified by deep sequencing and computational predictions using the ESTs of two mangrove plants. BMC PLANT BIOLOGY 2015; 15:301. [PMID: 26714456 PMCID: PMC4696257 DOI: 10.1186/s12870-015-0682-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 12/13/2015] [Indexed: 05/23/2023]
Abstract
BACKGROUND Although miRNAs are reportedly involved in the salt stress tolerance of plants, miRNA profiling in plants has largely remained restricted to glycophytes, including certain crop species that do not exhibit any tolerance to salinity. Hence, this manuscript describes the results from the miRNA profiling of the halophyte Suaeda maritima, which is used worldwide to study salt tolerance in plants. RESULTS A total of 134 conserved miRNAs were identified from unique sRNA reads, with 126 identified using miRBase 21.0 and an additional eight identified using the Plant Non-coding RNA Database. The presence of the precursors of seven conserved miRNAs was validated in S. maritima. In addition, 13 novel miRNAs were predicted using the ESTs of two mangrove plants, Rhizophora mangle and Heritiera littoralis, and the precursors of seven miRNAs were found in S. maritima. Most of the miRNAs considered for characterization were responsive to NaCl application, indicating their importance in the regulation of metabolic activities in plants exposed to salinity. An expression study of the novel miRNAs in plants of diverse ecological and taxonomic groups revealed that two of the miRNAs, sma-miR6 and sma-miR7, were also expressed in Oryza sativa, whereas another two, sma-miR2 and sma-miR5, were only expressed in plants growing under the influence of seawater, similar to S. maritima. CONCLUSION The distribution of conserved miRNAs among only 25 families indicated the possibility of identifying a greater number of miRNAs with increase in knowledge of the genomes of more halophytes. The expression of two novel miRNAs, sma-miR2 and sma-miR5, only in plants growing under the influence of seawater suggested their metabolic regulatory roles specific to saline environments, and such behavior might be mediated by alterations in the expression of certain genes, modifications of proteins leading to changes in their activity and production of secondary metabolites as revealed by the miRNA target predictions. Moreover, the auxin responsive factor targeted by sma-miR7 could also be involved in salt tolerance because the target is conserved between species. This study also indicated that the transcriptome of one species can be successfully used to computationally predict the miRNAs in other species, especially those that have similar metabolism, even if they are taxonomically separated.
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Affiliation(s)
- Sachin Ashruba Gharat
- Environmental Biotechnology Laboratory, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India.
| | - Birendra Prasad Shaw
- Environmental Biotechnology Laboratory, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India.
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De novo transcriptome sequencing of Acer palmatum and comprehensive analysis of differentially expressed genes under salt stress in two contrasting genotypes. Mol Genet Genomics 2015; 291:575-86. [PMID: 26475609 DOI: 10.1007/s00438-015-1127-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 09/30/2015] [Indexed: 01/15/2023]
Abstract
Maple (Acer palmatum) is an important species for landscape planting worldwide. Salt stress affects the normal growth of the Maple leaf directly, leading to loss of esthetic value. However, the limited availability of Maple genomic information has hindered research on the mechanisms underlying this tolerance. In this study, we performed comprehensive analyses of the salt tolerance in two genotypes of Maple using RNA-seq. Approximately 146.4 million paired-end reads, representing 181,769 unigenes, were obtained. The N50 length of the unigenes was 738 bp, and their total length over 102.66 Mb. 14,090 simple sequence repeats and over 500,000 single nucleotide polymorphisms were identified, which represent useful resources for marker development. Importantly, 181,769 genes were detected in at least one library, and 303 differentially expressed genes (DEGs) were identified between salt-sensitive and salt-tolerant genotypes. Among these DEGs, 125 were upregulated and 178 were downregulated genes. Two MYB-related proteins and one LEA protein were detected among the first 10 most downregulated genes. Moreover, a methyltransferase-related gene was detected among the first 10 most upregulated genes. The three most significantly enriched pathways were plant hormone signal transduction, arginine and proline metabolism, and photosynthesis. The transcriptome analysis provided a rich genetic resource for gene discovery related to salt tolerance in Maple, and in closely related species. The data will serve as an important public information platform to further our understanding of the molecular mechanisms involved in salt tolerance in Maple.
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Uncovering the differential molecular basis of adaptive diversity in three Echinochloa leaf transcriptomes. PLoS One 2015; 10:e0134419. [PMID: 26266806 PMCID: PMC4534374 DOI: 10.1371/journal.pone.0134419] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 07/08/2015] [Indexed: 12/04/2022] Open
Abstract
Echinochloa is a major weed that grows almost everywhere in farmed land. This high prevalence results from its high adaptability to various water conditions, including upland and paddy fields, and its ability to grow in a wide range of climates, ranging from tropical to temperate regions. Three Echinochloa crus-galli accessions (EC-SNU1, EC-SNU2, and EC-SNU3) collected in Korea have shown diversity in their responses to flooding, with EC-SNU1 exhibiting the greatest growth among three accessions. In the search for molecular components underlying adaptive diversity among the three Echinochloa crus-galli accessions, we performed de novo assembly of leaf transcriptomes and investigated the pattern of differentially expressed genes (DEGs). Although the overall composition of the three leaf transcriptomes was well-conserved, the gene expression patterns of particular gene ontology (GO) categories were notably different among the three accessions. Under non-submergence growing conditions, five protein categories (serine/threonine kinase, leucine-rich repeat kinase, signaling-related, glycoprotein, and glycosidase) were significantly (FDR, q < 0.05) enriched in up-regulated DEGs from EC-SNU1. These up-regulated DEGs include major components of signal transduction pathways, such as receptor-like kinase (RLK) and calcium-dependent protein kinase (CDPK) genes, as well as previously known abiotic stress-responsive genes. Our results therefore suggest that diversified gene expression regulation of upstream signaling components conferred the molecular basis of adaptive diversity in Echinochloa crus-galli.
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