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Zhou C, Bo W, El-Kassaby YA, Li W. Transcriptome profiles reveal response mechanisms and key role of PsNAC1 in Pinus sylvestris var. mongolica to drought stress. BMC PLANT BIOLOGY 2024; 24:343. [PMID: 38671396 PMCID: PMC11046967 DOI: 10.1186/s12870-024-05051-2] [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: 08/15/2023] [Accepted: 04/19/2024] [Indexed: 04/28/2024]
Abstract
BACKGROUND Drought stress severely impedes plant growth, and only a limited number of species exhibit long-term resistance to such conditions. Pinus sylvestris var. mongolica, a dominant tree species in arid and semi-arid regions of China, exhibits strong drought resistance and plays a crucial role in the local ecosystem. However, the molecular mechanisms underlying this resistance remain poorly understood. RESULTS Here, we conducted transcriptome sequence and physiological indicators analysis of needle samples during drought treatment and rehydration stages. De-novo assembly yielded approximately 114,152 unigenes with an N50 length of 1,363 bp. We identified 6,506 differentially expressed genes (DEGs), with the majority being concentrated in the heavy drought stage (4,529 DEGs). Functional annotation revealed enrichment of drought-related GO terms such as response to water (GO:0009415: enriched 108 genes) and response to water deprivation (GO:0009414: enriched 106 genes), as well as KEGG categories including MAPK signaling pathway (K04733: enriched 35 genes) and monoterpenoid biosynthesis (K21374: enriched 27 genes). Multiple transcription factor families and functional protein families were differentially expressed during drought treatment. Co-expression network analysis identified a potential drought regulatory network between cytochrome P450 genes (Unigene4122_c1_g1) and a core regulatory transcription factor Unigene9098_c3_g1 (PsNAC1) with highly significant expression differences. We validated PsNAC1 overexpression in Arabidopsis and demonstrated enhanced drought resistance. CONCLUSIONS These findings provide insight into the molecular basis of drought resistance in P. sylvestris var. mongolica and lay the foundation for further exploration of its regulatory network.
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Affiliation(s)
- Chengcheng Zhou
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Wenhao Bo
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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Niu X, Lai Z, Wang L, Ma R, Ren Y, Wang X, Cheng C, Wang T, Chen F, Xu Y. Co-Expression of JcNAC1- and JcZFP8-Improved Agronomic Traits of Tobacco and Enhanced Drought Resistance through NbbHLH1 and NbbHLH2. PLANTS (BASEL, SWITZERLAND) 2023; 12:3029. [PMID: 37687275 PMCID: PMC10490288 DOI: 10.3390/plants12173029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023]
Abstract
Previous studies have identified numerous transcription factors involved in drought response, each of which play different roles in plants. The objective of the present study was to evaluate the effectiveness of two transcription factors on drought response in Jatropha curcas L., JcNAC1 and JcZFP8. The overexpression of these transcription factors in tobacco (Nicotiana benthamiana L.) improved drought resistance, but JcZFP8 delayed germination and JcNAC1 reduced biomass and yield. By constitutively co-expressing these two genes in tobacco, drought resistance was improved, and the negative effects of each of them were overcome. The transgenic plants with double-gene co-expression showed stronger drought tolerance with 1.76-fold greater accumulation of proline and lower H2O2 and malondialdehyde (MDA) content to 43 and 65% of wildtype (WT) levels, respectively. The expression levels of NbbHLH1 and NbbHLH2 genes upregulated linearly with the increased drought tolerance of double genes co-expression plants. In drought conditions, the leaf water contents of bhlh1, bhlh2, and bhlh1bhlh2 deletion mutants obtained by CRISPR-CAS9 knockout technique were maintained at 99%, 97%, and 97% of WT. The bhlh1bhlh2 was found with lower germination rate but with higher reactive oxygen levels (1.64-fold H2O2 and 1.41-fold MDA levels). Thus, the co-expression of two transcription factors with different functions overcame the adverse traits brought by a single gene and enhanced the shared drought-tolerant traits, which can provide guidance on theory and selection of gene combinations for the application of multi-gene co-expression in agriculture in the future.
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Affiliation(s)
- Xianfei Niu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Zhiping Lai
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Linghui Wang
- College of Life Science and Food Engineering, Yibin University, Yibin 644000, China
| | - Rui Ma
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yingying Ren
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xueying Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Cheng Cheng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Ting Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Fang Chen
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Ying Xu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
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Han F, Wang P, Chen X, Zhao H, Zhu Q, Song Y, Nie Y, Li Y, Guo M, Niu S. An ethylene-induced NAC transcription factor acts as a multiple abiotic stress responsor in conifer. HORTICULTURE RESEARCH 2023; 10:uhad130. [PMID: 37560016 PMCID: PMC10407601 DOI: 10.1093/hr/uhad130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 06/13/2023] [Indexed: 08/11/2023]
Abstract
The proper response to various abiotic stresses is essential for plants' survival to overcome their sessile nature, especially for perennial trees with very long-life cycles. However, in conifers, the molecular mechanisms that coordinate multiple abiotic stress responses remain elusive. Here, the transcriptome response to various abiotic stresses like salt, cold, drought, heat shock and osmotic were systematically detected in Pinus tabuliformis (P. tabuliformis) seedlings. We found that four transcription factors were commonly induced by all tested stress treatments, while PtNAC3 and PtZFP30 were highly up-regulated and co-expressed. Unexpectedly, the exogenous hormone treatment assays and the content of the endogenous hormone indicates that the upregulation of PtNAC3 and PtZFP30 are mediated by ethylene. Time-course assay showed that the treatment by ethylene immediate precursor, 1-aminocyclopropane-1-carboxylic acid (ACC), activated the expression of PtNAC3 and PtZFP30 within 8 hours. We further confirm that the PtNAC3 can directly bind to the PtZFP30 promoter region and form a cascade. Overexpression of PtNAC3 enhanced unified abiotic stress tolerance without growth penalty in transgenic Arabidopsis and promoted reproductive success under abiotic stress by shortening the lifespan, suggesting it has great potential as a biological tool applied to plant breeding for abiotic stress tolerance. This study provides novel insights into the hub nodes of the abiotic stresses response network as well as the environmental adaptation mechanism in conifers, and provides a potential biofortification tool to enhance plant unified abiotic stress tolerance.
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Affiliation(s)
- Fangxu Han
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Peiyi Wang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xi Chen
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Huanhuan Zhao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Qianya Zhu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yitong Song
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yumeng Nie
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yue Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Meina Guo
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Shihui Niu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
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Deng H, Li Q, Cao R, Ren Y, Wang G, Guo H, Bu S, Liu J, Ma P. Overexpression of SmMYC2 enhances salt resistance in Arabidopsis thaliana and Salvia miltiorrhiza hairy roots. JOURNAL OF PLANT PHYSIOLOGY 2023; 280:153862. [PMID: 36399834 DOI: 10.1016/j.jplph.2022.153862] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/26/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
Soil salinity significantly affects both Salvia miltiorrhiza growth and development as well as seed germination throughout field cultivation and production. The basic helix-loop-helix (bHLH) transcription factor (TF) MYC2 contributes significantly to plant stress resistance as a key regulator of the jasmonic acid signaling pathway. In transgenic S. miltiorrhiza hairy roots, SmMYC2 has been shown to promote the accumulation of tanshinone and salvianolic acid, but its role in S. miltiorrhiza of resistance to abiotic stress is unclear. Herein, we found methyl jasmonate (MeJA), NaCl, and PEG treatment all significantly increased SmMYC2 expression. In response to salt stress, SmMYC2 overexpression in yeast increased its rate of growth. Additionally, overexpression of SmMYC2 transgenic Arabidopsis thaliana and S. miltiorrhiza hairy root showed that it might improve salt resistance in transgenic plant. In particular, compared to WT, overexpression of SmMYC2 transgenic Arabidopsis had higher levels of three antioxidant enzymes (superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT)), proline (Pro) content, and ABA-dependent and ABA-independent genes expression. They also had lower levels of malondialdehyde (MDA) and reactive oxygen species (ROS) accumulation. What's more, overexpression of SmMYC2 increases the expression of flavonoid synthesis genes and the accumulation of related components in Arabidopsis. These findings imply that SmMYC2 functions as a positive regulator that regulates plant tolerance to salt through ABA-dependent and independent signaling pathways.
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Affiliation(s)
- Huaiyu Deng
- College of Chemistry and Pharmacy, Northwest A&F University, Yangling, China
| | - Qi Li
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Ruizhi Cao
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Yafei Ren
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Guanfeng Wang
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Hongbo Guo
- College of Chemistry and Pharmacy, Northwest A&F University, Yangling, China
| | - Shuhai Bu
- College of Life Sciences, Northwest A&F University, Yangling, China.
| | - Jingying Liu
- College of Life Sciences, Northwest A&F University, Yangling, China.
| | - Pengda Ma
- College of Life Sciences, Northwest A&F University, Yangling, China.
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MicroRNA-mediated post-transcriptional regulation of Pinus pinaster response and resistance to pinewood nematode. Sci Rep 2022; 12:5160. [PMID: 35338210 PMCID: PMC8956650 DOI: 10.1038/s41598-022-09163-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/15/2022] [Indexed: 11/16/2022] Open
Abstract
Pine wilt disease (PWD), caused by the parasitic nematode Bursaphelenchus xylophilus, or pinewood nematode (PWN), is a serious threat to pine forests in Europe. Pinus pinaster is highly susceptible to the disease and it is currently the most affected European pine species. In this work, we investigated the role of small RNAs (sRNAs) in regulating P. pinaster–PWN interaction in an early stage of infection. After performing an artificial PWN inoculation assay, we have identified 105 plant microRNAs (miRNAs) responsive to PWN. Based on their predicted targets, part of these miRNAs was associated with roles in jasmonate-response pathway, ROS detoxification, and terpenoid biosynthesis. Furthermore, by comparing resistant and susceptible plants, eight miRNAs with putative functions in plant defence and resistance to PWN have been identified. Finally, we explored the possibility of bidirectional trans-kingdom RNA silencing, identifying several P. pinaster genes putatively targeted by PWN miRNAs, which was supported by degradome analysis. Targets for P. pinaster miRNAs were also predicted in PWN, suggesting a role for trans-kingdom miRNA transfer and gene silencing both in PWN parasitism as in P. pinaster resistance to PWD. Our results provide new insights into previously unexplored roles of sRNA post-transcriptional regulation in P. pinaster response and resistance to PWN.
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Zhao X, Huang LJ, Sun XF, Zhao LL, Wang PC. Transcriptomic and Metabolomic Analyses Reveal Key Metabolites, Pathways and Candidate Genes in Sophora davidii (Franch.) Skeels Seedlings Under Drought Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:785702. [PMID: 35310664 PMCID: PMC8924449 DOI: 10.3389/fpls.2022.785702] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 02/07/2022] [Indexed: 05/26/2023]
Abstract
Soil aridification and desertification are particularly prominent in China's karst areas, severely limiting crop yields and vegetation restoration. Therefore, it is very important to identify naturally drought-tolerant plant species. Sophora davidii (Franch.) Skeels is resistant to drought and soil infertility, is deeply rooted and is an excellent plant material for soil and water conservation. We studied the transcriptomic and metabolomic changes in S. davidii in response to drought stress (CK, control; LD, mild drought stress; MD, moderate drought stress; and SD, severe drought stress). Sophora davidii grew normally under LD and MD stress but was inhibited under SD stress; the malondialdehyde (MDA), hydrogen peroxide (H2O2), soluble sugar, proline, chlorophyll a, chlorophyll b and carotenoid contents and ascorbate peroxidase (APX) activity significantly increased, while the superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) activities and soluble protein content significantly decreased. In the LD/CK, MD/CK and SD/CK comparison groups, there were 318, 734 and 1779 DEGs, respectively, and 100, 168 and 281 differentially accumulated metabolites, respectively. Combined analysis of the transcriptomic and metabolomic data revealed the metabolic regulation of S. davidii in response to drought stress. First, key candidate genes such as PRR7, PRR5, GI, ELF3, PsbQ, PsaK, INV, AMY, E2.4.1.13, E3.2.1.2, NCED, PP2C, PYL, ABF, WRKY33, P5CS, PRODH, AOC3, HPD, GPX, GST, CAT and SOD1 may govern the drought resistance of S. davidii. Second, three metabolites (oxidised glutathione, abscisic acid and phenylalanine) were found to be related to drought tolerance. Third, several key candidate genes and metabolites involved in 10 metabolic pathways were identified, indicating that these metabolic pathways play an important role in the response to drought in S. davidii and possibly other plant species.
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Affiliation(s)
- Xin Zhao
- College of Animal Science, Guizhou University, Guiyang, China
| | - Li-Juan Huang
- College of Animal Science, Guizhou University, Guiyang, China
| | - Xiao-Fu Sun
- College of Animal Science, Guizhou University, Guiyang, China
| | - Li-Li Zhao
- College of Animal Science, Guizhou University, Guiyang, China
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7
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Bijali J, Halder T, Acharya K. Elucidation of the biochemical and molecular basis of the differential disease expression in two cultivars of chili ( Capsicum annuum) in response to Colletotrichum capsici infection. ACTA PHYSIOLOGIAE PLANTARUM 2021; 43:155. [PMID: 34776557 PMCID: PMC8578917 DOI: 10.1007/s11738-021-03334-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/22/2021] [Accepted: 11/02/2021] [Indexed: 06/13/2023]
Abstract
Chili plants are affected by the hemibiotrophic ascomycota fungus Colletotrichum capsici causing Anthracnose. Infection results in yield and marketability loss due to a decrease in the quality of fruits. The study of morphological symptom development in two cultivars, Bullet, and Beldanga, showed very different disease expression pattern. To understand the reasons behind such differential response, we investigated, in a time-dependent manner, biochemical activities of important defense enzymes, PR proteins, like peroxidase, polyphenol-oxidase, phenylalanine ammonia lyase, β-glucanase, chitinase, catalase, as well as phenols, flavonoids, chlorophyll and the key signaling molecule nitric oxide in their leaves. We further performed real-time nitric oxide (NO) detection studies. The results showed striking differences in the activity profile of these defense molecules through the course of the study. We monitored the gene expression levels of 12 important defense-related genes under in vivo condition. The transcription levels were mostly increased in the tolerant cultivar till 7 days post-infection (DPI), while downregulation of some of the genes were observed in the susceptible one. These data indicated that disease manifestation is a simulated response of these defense molecules which can nullify the effect of the pathogen and its products, when resistance occurs. Alternatively, the pathogen suppresses the host defense when the disease develops. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11738-021-03334-x.
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Affiliation(s)
- Jayeeta Bijali
- Molecular and Applied Mycology and Plant Pathology Laboratory Centre of Advanced Study, Department of Botany, University of Calcutta, Kolkata, West Bengal 700019 India
| | - Tanmoy Halder
- Plant Functional Genomics Lab, Department of Botany, Centre of Advanced Study, University of Calcutta, Kolkata, West Bengal 700019 India
| | - Krishnendu Acharya
- Molecular and Applied Mycology and Plant Pathology Laboratory Centre of Advanced Study, Department of Botany, University of Calcutta, Kolkata, West Bengal 700019 India
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Kim MH, Tran TNA, Cho JS, Park EJ, Lee H, Kim DG, Hwang S, Ko JH. Wood transcriptome analysis of Pinus densiflora identifies genes critical for secondary cell wall formation and NAC transcription factors involved in tracheid formation. TREE PHYSIOLOGY 2021; 41:1289-1305. [PMID: 33440425 DOI: 10.1093/treephys/tpab001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/04/2021] [Indexed: 05/27/2023]
Abstract
Although conifers have significant ecological and economic value, information on transcriptional regulation of wood formation in conifers is still limited. Here, to gain insight into secondary cell wall (SCW) biosynthesis and tracheid formation in conifers, we performed wood tissue-specific transcriptome analyses of Pinus densiflora (Korean red pine) using RNA sequencing. In addition, to obtain full-length transcriptome information, PacBio single molecule real-time iso-sequencing was carried out using RNAs from 28 tissues of P. densiflora. Subsequent comparative tissue-specific transcriptome analysis successfully pinpointed critical genes encoding key proteins involved in biosynthesis of the major secondary wall components (cellulose, galactoglucomannan, xylan and lignin). Furthermore, we predicted a total of 62 NAC (NAM, ATAF1/2 and CUC2) family transcription factor members and identified seven PdeNAC genes preferentially expressed in developing xylem tissues in P. densiflora. Protoplast-based transcriptional activation analysis found that four PdeNAC genes, homologous to VND, NST and SND/ANAC075, upregulated GUS activity driven by an SCW-specific cellulose synthase promoter. Consistently, transient overexpression of the four PdeNACs induced xylem vessel cell-like SCW deposition in both tobacco (Nicotiana benthamiana) and Arabidopsis leaves. Taken together, our data provide a foundation for further research to unravel transcriptional regulation of wood formation in conifers, especially SCW formation and tracheid differentiation.
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Affiliation(s)
- Min-Ha Kim
- Department of Plant & Environmental New Resources, Kyung Hee University, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
| | - Thi Ngoc Anh Tran
- Department of Plant & Environmental New Resources, Kyung Hee University, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
| | - Jin-Seong Cho
- Department of Plant & Environmental New Resources, Kyung Hee University, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
| | - Eung-Jun Park
- Division of Forest Biotechnology, National Institute of Forest Science, 39 Onjeong-ro, Suwon 16631, Republic of Korea
| | - Hyoshin Lee
- Division of Forest Biotechnology, National Institute of Forest Science, 39 Onjeong-ro, Suwon 16631, Republic of Korea
| | - Dong-Gwan Kim
- Department of Bioindustry and Bioresource Engineering, Department of Molecular Biology and Plant Engineering Research Institute, Sejong University, 209 Neungdong-ro, Seoul 05006, Republic of Korea
| | - Seongbin Hwang
- Department of Bioindustry and Bioresource Engineering, Department of Molecular Biology and Plant Engineering Research Institute, Sejong University, 209 Neungdong-ro, Seoul 05006, Republic of Korea
| | - Jae-Heung Ko
- Department of Plant & Environmental New Resources, Kyung Hee University, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
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Modesto I, Sterck L, Arbona V, Gómez-Cadenas A, Carrasquinho I, Van de Peer Y, Miguel CM. Insights Into the Mechanisms Implicated in Pinus pinaster Resistance to Pinewood Nematode. FRONTIERS IN PLANT SCIENCE 2021; 12:690857. [PMID: 34178007 PMCID: PMC8222992 DOI: 10.3389/fpls.2021.690857] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 05/17/2021] [Indexed: 05/27/2023]
Abstract
Pine wilt disease (PWD), caused by the plant-parasitic nematode Bursaphelenchus xylophilus, has become a severe environmental problem in the Iberian Peninsula with devastating effects in Pinus pinaster forests. Despite the high levels of this species' susceptibility, previous studies reported heritable resistance in P. pinaster trees. Understanding the basis of this resistance can be of extreme relevance for future programs aiming at reducing the disease impact on P. pinaster forests. In this study, we highlighted the mechanisms possibly involved in P. pinaster resistance to PWD, by comparing the transcriptional changes between resistant and susceptible plants after infection. Our analysis revealed a higher number of differentially expressed genes (DEGs) in resistant plants (1,916) when compared with susceptible plants (1,226). Resistance to PWN is mediated by the induction of the jasmonic acid (JA) defense pathway, secondary metabolism pathways, lignin synthesis, oxidative stress response genes, and resistance genes. Quantification of the acetyl bromide-soluble lignin confirmed a significant increase of cell wall lignification of stem tissues around the inoculation zone in resistant plants. In addition to less lignified cell walls, susceptibility to the pine wood nematode seems associated with the activation of the salicylic acid (SA) defense pathway at 72 hpi, as revealed by the higher SA levels in the tissues of susceptible plants. Cell wall reinforcement and hormone signaling mechanisms seem therefore essential for a resistance response.
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Affiliation(s)
- Inês Modesto
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia e Tecnologia Experimental, Oeiras, Portugal
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Lieven Sterck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Vicent Arbona
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castelló de la Plana, Spain
| | - Aurelio Gómez-Cadenas
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castelló de la Plana, Spain
| | - Isabel Carrasquinho
- Instituto Nacional Investigaciao Agraria e Veterinaria, Oeiras, Portugal
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Célia M. Miguel
- Instituto de Biologia e Tecnologia Experimental, Oeiras, Portugal
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
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10
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Munir N, Yukun C, Xiaohui C, Nawaz MA, Iftikhar J, Rizwan HM, Xu S, Yuling L, Xuhan X, Zhongxiong L. Genome-wide identification and comprehensive analyses of NAC transcription factor gene family and expression patterns during somatic embryogenesis in Dimocarpus longan Lour. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 157:169-184. [PMID: 33120109 DOI: 10.1016/j.plaphy.2020.10.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 10/06/2020] [Indexed: 05/23/2023]
Abstract
The NAM, ATAF1/2, and CUC2 form a huge plant-specific gene family of NAC TFs that are involved in the growth, development, and regulation of biotic and abiotic stress responses. Although the draft genome of longan (Dimocarpus longan Lour.) has been published, however the comprehensive data regarding the functions, evolution, and expression patterns of the NAC family are still unavailable. In this study, a comprehensive analysis of the NAC transcription factor family in longan was performed, and a total of 114 NAC genes were found. We investigated the NAC gene family exploring the phylogeny, domain conservation, intron/exon, motifs, cis-regulatory elements, protein-protein interaction, and expression profiles of RNA-seq samples in different tissues and early somatic embryogenesis of longan. Phylogenetic analysis showed that the genes with similar gene structure and motif distribution were clustered in the same group. Cis-element identification indicates the possible role of NAC genes in biological and physiological processes. Protein-protein interaction identified the DlNACs homologous with Arabidopsis proteins. We further investigated the expression pattern of DlNAC genes in different tissues (pulp, stem, large fruit, young fruit, and flower) during somatic embryogenesis at embryogenic callus (EC), incomplete compact pro-embryogenic cultures (ICpEC), and globular embryos (GE) stages. The qRT-PCR results showed that the DlNAC genes were expressed higher at EC and GE stage compared with ICpEC stage. In conclusion, our results provide insight into the evolution, diversity, and characterization of NAC genes in the longan and provide a base for understanding their biological roles and molecular mechanisms in plants.
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Affiliation(s)
- Nigarish Munir
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chen Yukun
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chen Xiaohui
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Muhammad Azher Nawaz
- Department of Horticulture, College of Agriculture, University of Sargodha, Sargodha, 40100, Pakistan
| | - Junaid Iftikhar
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hafiz Muhammad Rizwan
- Institute of Subtropical Fruit, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shen Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lin Yuling
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xu Xuhan
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Institute de la Recherché Interdisciplinary de Toulouse, IRIT-ARI, 31300, Toulouse, France.
| | - Lai Zhongxiong
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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11
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Yuan C, Li C, Lu X, Zhao X, Yan C, Wang J, Sun Q, Shan S. Comprehensive genomic characterization of NAC transcription factor family and their response to salt and drought stress in peanut. BMC PLANT BIOLOGY 2020; 20:454. [PMID: 33008287 PMCID: PMC7532626 DOI: 10.1186/s12870-020-02678-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 09/24/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Peanut is one of the most important oil crop species worldwide. NAC transcription factor (TF) genes play important roles in the salt and drought stress responses of plants by activating or repressing target gene expression. However, little is known about NAC genes in peanut. RESULTS We performed a genome-wide characterization of NAC genes from the diploid wild peanut species Arachis duranensis and Arachis ipaensis, which included analyses of chromosomal locations, gene structures, conserved motifs, expression patterns, and cis-acting elements within their promoter regions. In total, 81 and 79 NAC genes were identified from A. duranensis and A. ipaensis genomes. Phylogenetic analysis of peanut NACs along with their Arabidopsis and rice counterparts categorized these proteins into 18 distinct subgroups. Fifty-one orthologous gene pairs were identified, and 46 orthologues were found to be highly syntenic on the chromosomes of both A. duranensis and A. ipaensis. Comparative RNA sequencing (RNA-seq)-based analysis revealed that the expression of 43 NAC genes was up- or downregulated under salt stress and under drought stress. Among these genes, the expression of 17 genes in cultivated peanut (Arachis hypogaea) was up- or downregulated under both stresses. Moreover, quantitative reverse transcription PCR (RT-qPCR)-based analysis revealed that the expression of most of the randomly selected NAC genes tended to be consistent with the comparative RNA-seq results. CONCLUSION Our results facilitated the functional characterization of peanut NAC genes, and the genes involved in salt and drought stress responses identified in this study could be potential genes for peanut improvement.
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Affiliation(s)
- Cuiling Yuan
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Chunjuan Li
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Xiaodong Lu
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Xiaobo Zhao
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Caixia Yan
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Juan Wang
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Quanxi Sun
- Shandong Peanut Research Institute, Qingdao, 266100, China.
| | - Shihua Shan
- Shandong Peanut Research Institute, Qingdao, 266100, China.
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12
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Duan AQ, Tao JP, Jia LL, Tan GF, Liu JX, Li T, Chen LZ, Su XJ, Feng K, Xu ZS, Xiong AS. AgNAC1, a celery transcription factor, related to regulation on lignin biosynthesis and salt tolerance. Genomics 2020; 112:5254-5264. [PMID: 32976976 DOI: 10.1016/j.ygeno.2020.09.049] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/01/2020] [Accepted: 09/22/2020] [Indexed: 12/16/2022]
Abstract
The NAC transcription factor participates in various biotic and abiotic stress responses and plays a critical role in plant development. Lignin is a water-insoluble dietary fiber, but it is second only to cellulose in abundance. Celery is the main source of dietary fiber, but its quality and production are limited by various abiotic stresses. Here, AgNAC1 containing the NAM domain was identified from celery. AgNAC1 was found to be a nuclear protein. Transgenic Arabidopsis thaliana plants hosting AgNAC1 have longer root lengths and stomatal axis lengths than the wide type (WT). The evidence from lignin determination and expression levels of lignin-related genes indicated that AgNAC1 plays a vital role in lignin biosynthesis. Furthermore, the results of the physiological characterization and the drought and salt treatments indicate that AgNAC1-overexpressing plants are significantly resistive to salt stress. Under drought and salt treatments, the AgNAC1 transgenic Arabidopsis thaliana plants presented increased superoxide dismutase (SOD) and peroxidase (POD) activities and decreased malondialdehyde (MDA) content and size of stomatal apertures relatively to the WT plants. The AgNAC1 served as a positive regulator in inducing the expression of stress-responsive genes. Overall, the overexpressing AgNAC1 enhanced the plants' resistance to salt stress and played a regulatory role in lignin accumulation.
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Affiliation(s)
- Ao-Qi Duan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jian-Ping Tao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Li-Li Jia
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Guo-Fei Tan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang 55006, China
| | - Jie-Xia Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Tong Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Long-Zheng Chen
- Institute of Vegetable Crops, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing 210095, China
| | - Xiao-Jun Su
- Institute of Vegetable Crops, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing 210095, China
| | - Kai Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhi-Sheng Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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13
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Large-Scale Cloning and Comparative Analysis of TaNAC Genes in Response to Stripe Rust and Powdery Mildew in Wheat ( Triticum aestivum L.). Genes (Basel) 2020; 11:genes11091073. [PMID: 32932603 PMCID: PMC7564338 DOI: 10.3390/genes11091073] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/09/2020] [Accepted: 09/10/2020] [Indexed: 12/11/2022] Open
Abstract
The NAM, ATAF1/2, and CUC2 (NAC) transcription factors (TFs) constitute the largest plant-specific TF superfamily, and play important roles in various physiological processes, including stress responses. Stripe rust and powdery mildew are the most damaging of the fungal diseases that afflict wheat (Triticum aestivum L.). However, studies on Triticum aestivum NAC (TaNAC)s’ role in resistance to the two diseases are still limited, especially in an overall comparative analysis of TaNACs responding or not to fungal stress. In the present study, 186 TaNAC transcripts were obtained from the resistant hexaploid wheat line N9134 under fungal stress, and 180 new transcripts were submitted to GenBank. Statistical results show that 35.1% (54/154) of TaNAC genes responded to stripe rust and powdery mildew in the seedling stage. “Abnormal” coding transcripts of differentially expressed (DE)-TaNAC genes in wheat responding to fungal stress were found in a significantly higher proportion (24/117 vs. 8/69, p = 0.0098) than in non-DE-NACs. This hinted that the alternative splicing of TaNAC genes was active in transcriptional or post-transcriptional regulation during plant-pathogen interactions. Full-length NAC proteins were classified into nine groups via phylogenetic analysis. Multiple-sequence alignment revealed diversity in the C-terminal structural organization, but the differentially expressed gene (DEG)-encoding proteins enriched in Subgroups VI and VII were conserved, with WV[L/V]CR amino acid residues in Motif 7 following the NAM domain. Our data that showed TaNAC TFs responded to fungal disease, which was affected by expression levels and by the regulation of multifarious transcript variants. These data for TaNAC responses to stripe rust and/or powdery mildew and their numerous structural variants provide a good resource for NAC function–mechanism analysis in the context of biotic-stress tolerance in wheat.
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14
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Hernandez Y, Goswami K, Sanan‐Mishra N. Stress induced dynamic adjustment of conserved miR164:NAC module. PLANT-ENVIRONMENT INTERACTIONS (HOBOKEN, N.J.) 2020; 1:134-151. [PMID: 37283725 PMCID: PMC10168063 DOI: 10.1002/pei3.10027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 07/02/2020] [Accepted: 07/14/2020] [Indexed: 06/08/2023]
Abstract
Aims including the rationale Salinity and drought are the two major stresses limiting the productivity of economically important crops such as Glycine max (soybean). The incidence of these stresses during the pod development stages affects the quality and quantity of seeds, which compromise the yield of soybean. The miR164:NAC module has been shown to play a critical role in regulating the response to salt and drought stress in several plant species. However, biological role of miR164:NAC module in salt stress in soybean is not fully understood. Methods In this study, we identified 215 salt responsive miRNAs, using miScript miRNA array with a sensitive and a tolerant soybean genotype, William82 and INCASoy36, respectively. The targets of these salt regulated miRNAs were searched in the degradome datasets. Key results It was found that four salt stress deregulated miRNAs targeted the NAC transcription factor and among these miR164k and miR408d showed antagonistic expression in the two soybean genotypes. The expression of miR164k was higher in salt tolerant INCASoy36 as compared to salt sensitive William82, under unstressed conditions. However under salt stress, miR164k was downregulated in INCASoy36 (-2.65 fold), whereas it was upregulated in William82 (4.68 fold). A transient co-expression assay validated that gma-miR164k directs the cleavage of GmNAC1 transcript. Bioinformatics analysis revealed that the regulation of NAC transcription factor family by members of miR164 family is conserved across many species. The dynamic expression profiles of miR164 and NAC-TFs were captured in different tissues of rice, tobacco, and two soybean genotypes under drought and salt stress conditions. Main conclusion Collectively, our results suggest that genetically determined dynamic modulation of the conserved miR164:NAC-TF module may play an important role in determining the adaptive response of plants to stress.
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Affiliation(s)
- Yuniet Hernandez
- Plant RNAi Biology GroupInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia
| | - Kavita Goswami
- Plant RNAi Biology GroupInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia
| | - Neeti Sanan‐Mishra
- Plant RNAi Biology GroupInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia
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15
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Guo Y, Zhang H, Yuan Y, Cui X, Zhang L. Identification and characterization of NAC genes in response to abiotic stress conditions in Picea wilsonii using transcriptome sequencing. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1718550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Yuxiao Guo
- Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, The College of Forestry, Beijing Forestry University, Beijing, PR China
| | - Hehua Zhang
- Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, The College of Forestry, Beijing Forestry University, Beijing, PR China
| | - Yihang Yuan
- Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, The College of Forestry, Beijing Forestry University, Beijing, PR China
| | - Xiaoyue Cui
- Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, The College of Forestry, Beijing Forestry University, Beijing, PR China
| | - Lingyun Zhang
- Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, The College of Forestry, Beijing Forestry University, Beijing, PR China
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16
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Robledo‐Arnuncio JJ, Unger GM. Measuring viability selection from prospective cohort mortality studies: A case study in maritime pine. Evol Appl 2019; 12:863-877. [PMID: 31080501 PMCID: PMC6503825 DOI: 10.1111/eva.12729] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 10/05/2018] [Accepted: 10/15/2018] [Indexed: 11/27/2022] Open
Abstract
By changing the genetic background available for selection at subsequent life stages, stage-specific selection can define adaptive potential across the life cycle. We propose and evaluate here a neutrality test and a Bayesian method to infer stage-specific viability selection coefficients using sequential random genotypic samples drawn from a longitudinal cohort mortality study, within a generation. The approach is suitable for investigating selective mortality in large natural or experimental cohorts of any organism in which individual tagging and tracking are unfeasible. Numerical simulation results indicate that the method can discriminate loci under strong viability selection, and provided samples are large, yield accurate estimates of the corresponding selection coefficients. Genotypic frequency changes are largely driven by sampling noise under weak selection, however, compromising inference in that case. We apply the proposed methods to analyze viability selection operating at early recruitment stages in a natural maritime pine (Pinus pinaster Ait.) population. We measured temporal genotypic frequency changes at 384 candidate-gene SNP loci among seedlings sampled from the time of emergence in autumn until the summer of the following year, a period with high elimination rates. We detected five loci undergoing allele frequency changes larger than expected from stochastic mortality and sampling, with putative functions that could influence survival at early seedling stages. Our results illustrate how new statistical and sampling schemes can be used to conduct genomic scans of contemporary selection on specific life stages.
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Affiliation(s)
| | - Gregor M. Unger
- Department of Forest Ecology & GeneticsINIA‐CIFORMadridSpain
- Escuela Internacional de DoctoradoUniversidad Rey Juan CarlosMóstolesSpain
- Present address:
Department of Forest GeneticsFederal Research and Training Centre for ForestsNatural Hazards and LandscapeViennaAustria
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17
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Chakraborty R, Roy S. Evaluation of the diversity and phylogenetic implications of NAC transcription factor members of four reference species from the different embryophytic plant groups. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:347-359. [PMID: 30956419 PMCID: PMC6419696 DOI: 10.1007/s12298-018-0581-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 06/17/2018] [Accepted: 07/17/2018] [Indexed: 05/14/2023]
Abstract
NAC transcription factors (TFs) are one of the largest and important TF family that are involved in the regulation of plant growth and development. They are characterized by a highly conserved N-terminal domain and a variable C-terminal domain. In the present study, the amino acid sequences of NAC TFs from four embryophytic plant species viz. Arabidopsis thaliana (Angiosperm), Picea abies (Gymnosperm), Selaginella moellendorffii (Pteridophyte) and Physcomitrella patens (Bryophyte) as reference of the different plant groups were collected from the Plant Transcription Factor Database (PTFD) and the phylogenetic relationships were evaluated. The phylogenetic tree revealed that the majority of the NAC members were interspersed in the major subgroups that indicated the expansion of the NAC members predates the speciation events. Thirty one (31), five (05), one (1) and ten (10) paralog pairs were determined respectively for Arabidopsis, Picea, Selaginella and Physcomitrella. The structure-function relationship of paralog pairs were inferred from the phylogenetic tree of combined set of paralogous gene pairs by studying the prevalence of flanking regions and motif analysis of the NAC proteins. The motif analysis revealed the presence of an N-terminal conserved domain, a characteristic of the majority of NAC family proteins. Conserved motifs in the C-terminal region were absent in the majority of the protein sequences except few members in Arabidopsis and Physcomitrella. Also the time of gene duplication of the paralog pairs were calculated that revealed the duplication events occurred between 4.48 and 45.94 MYA Arabidopsis, 167.57-532.86 MYA in Picea, and 29.12-53.53 MYA in Physcomitrella.
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Affiliation(s)
- Rakhi Chakraborty
- Department of Botany, A.P.C. Roy Govt. College, Matigara, Siliguri, WB 734010 India
| | - Swarnendu Roy
- Molecular and Analytical Biochemistry Laboratory, Department of Botany, University of Gour Banga, Mokdumpur, Malda, WB 732103 India
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18
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Gautier F, Label P, Eliášová K, Leplé JC, Motyka V, Boizot N, Vondráková Z, Malbeck J, Trávníčková A, Le Metté C, Lesage-Descauses MC, Lomenech AM, Trontin JF, Costa G, Lelu-Walter MA, Teyssier C. Cytological, Biochemical and Molecular Events of the Embryogenic State in Douglas-fir ( Pseudotsuga menziesii [Mirb.]). FRONTIERS IN PLANT SCIENCE 2019; 10:118. [PMID: 30873184 PMCID: PMC6403139 DOI: 10.3389/fpls.2019.00118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/23/2019] [Indexed: 05/08/2023]
Abstract
Somatic embryogenesis techniques have been developed for most coniferous species, but only using very juvenile material. To extend the techniques' scope, better integrated understanding of the key biological, physiological and molecular characteristics of embryogenic state is required. Therefore, embryonal masses (EMs) and non-embryogenic calli (NECs) have been compared during proliferation at multiple levels. EMs and NECs originating from a single somatic embryo (isogenic lines) of each of three unrelated genotypes were used in the analyses, which included comparison of the lines' anatomy by transmission light microscopy, transcriptomes by RNAseq Illumina sequencing, proteomes by free-gel analysis, contents of endogenous phytohormones (indole-3-acetic acid, cytokinins and ABA) by LC-MS analysis, and soluble sugar contents by HPLC. EMs were characterized by upregulation (relative to levels in NECs) of transcripts, proteins, transcription factors and active cytokinins associated with cell differentiation accompanied by histological, carbohydrate content and genetic markers of cell division. In contrast, NECs were characterized by upregulation (relative to levels in EMs) of transcripts, proteins and products associated with responses to stimuli (ABA, degradation forms of cytokinins, phenols), oxidative stress (reactive oxygen species) and carbohydrate storage (starch). Sub-Network Enrichment Analyses that highlighted functions and interactions of transcripts and proteins that significantly differed between EMs and NECs corroborated these findings. The study shows the utility of a novel approach involving integrated multi-scale transcriptomic, proteomic, biochemical, histological and anatomical analyses to obtain insights into molecular events associated with embryogenesis and more specifically to the embryogenic state of cell in Douglas-fir.
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Affiliation(s)
- Florian Gautier
- BioForA, INRA, ONF, Orléans, France
- PEIRENE, Sylva LIM, Université de Limoges, Limoges, France
| | | | - Kateřina Eliášová
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | | | - Václav Motyka
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | | | - Zuzana Vondráková
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Jiří Malbeck
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Alena Trávníčková
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | | | | | - Anne-Marie Lomenech
- Centre de Génomique Fonctionnelle, Plateforme Protéome, University of Bordeaux, Bordeaux, France
| | | | - Guy Costa
- PEIRENE, Sylva LIM, Université de Limoges, Limoges, France
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Toffolatti SL, De Lorenzis G, Costa A, Maddalena G, Passera A, Bonza MC, Pindo M, Stefani E, Cestaro A, Casati P, Failla O, Bianco PA, Maghradze D, Quaglino F. Unique resistance traits against downy mildew from the center of origin of grapevine (Vitis vinifera). Sci Rep 2018; 8:12523. [PMID: 30131589 PMCID: PMC6104083 DOI: 10.1038/s41598-018-30413-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/30/2018] [Indexed: 11/17/2022] Open
Abstract
The Eurasian grapevine (Vitis vinifera), an Old World species now cultivated worldwide for high-quality wine production, is extremely susceptible to the agent of downy mildew, Plasmopara viticola. The cultivation of resistant V. vinifera varieties would be a sustainable way to reduce the damage caused by the pathogen and the impact of disease management, which involves the economic, health and environmental costs of frequent fungicide application. We report the finding of unique downy mildew resistance traits in a winemaking cultivar from the domestication center of V. vinifera, and characterize the expression of a range of genes associated with the resistance mechanism. Based on comparative experimental inoculations, confocal microscopy and transcriptomics analyses, our study shows that V. vinifera cv. Mgaloblishvili, native to Georgia (South Caucasus), exhibits unique resistance traits against P. viticola. Its defense response, leading to a limitation of P. viticola growth and sporulation, is determined by the overexpression of genes related to pathogen recognition, the ethylene signaling pathway, synthesis of antimicrobial compounds and enzymes, and the development of structural barriers. The unique resistant traits found in Mgaloblishvili highlight the presence of a rare defense system in V. vinifera against P. viticola which promises fresh opportunities for grapevine genetic improvement.
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Affiliation(s)
- Silvia Laura Toffolatti
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio e Agroenergia (DiSAA), via Celoria 2, 20133, Milano, Italy.
| | - Gabriella De Lorenzis
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio e Agroenergia (DiSAA), via Celoria 2, 20133, Milano, Italy.
| | - Alex Costa
- Università degli Studi di Milano, Dipartimento di Bioscienze (DBS), via Celoria 26, 20133, Milano, Italy
| | - Giuliana Maddalena
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio e Agroenergia (DiSAA), via Celoria 2, 20133, Milano, Italy
| | - Alessandro Passera
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio e Agroenergia (DiSAA), via Celoria 2, 20133, Milano, Italy
| | - Maria Cristina Bonza
- Università degli Studi di Milano, Dipartimento di Bioscienze (DBS), via Celoria 26, 20133, Milano, Italy
| | - Massimo Pindo
- Fondazione E. Mach, Centro Ricerca e Innovazione, Via E. Mach 1, 38010, San Michele all'Adige, (TN), Italy
| | - Erika Stefani
- Fondazione E. Mach, Centro Ricerca e Innovazione, Via E. Mach 1, 38010, San Michele all'Adige, (TN), Italy
| | - Alessandro Cestaro
- Fondazione E. Mach, Centro Ricerca e Innovazione, Via E. Mach 1, 38010, San Michele all'Adige, (TN), Italy
| | - Paola Casati
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio e Agroenergia (DiSAA), via Celoria 2, 20133, Milano, Italy
| | - Osvaldo Failla
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio e Agroenergia (DiSAA), via Celoria 2, 20133, Milano, Italy
| | - Piero Attilio Bianco
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio e Agroenergia (DiSAA), via Celoria 2, 20133, Milano, Italy
| | - David Maghradze
- Scientific - Research Center of Agriculture, Marshal Gelovani Avenue 6, 0159, Tbilisi, Georgia
- Faculty of Agricultural Sciences and Biosystems Engineering, Georgian Technical University, David Guramishvili Avenue 17, 0175, Tbilisi, Georgia
| | - Fabio Quaglino
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio e Agroenergia (DiSAA), via Celoria 2, 20133, Milano, Italy
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20
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Pascual MB, Llebrés M, Craven‐Bartle B, Cañas RA, Cánovas FM, Ávila C. PpNAC1, a main regulator of phenylalanine biosynthesis and utilization in maritime pine. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1094-1104. [PMID: 29055073 PMCID: PMC5902770 DOI: 10.1111/pbi.12854] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 09/13/2017] [Accepted: 10/16/2017] [Indexed: 05/14/2023]
Abstract
The transcriptional regulation of phenylalanine metabolism is particularly important in conifers, long-lived species that use large amounts of carbon in wood. Here, we show that the Pinus pinaster transcription factor, PpNAC1, is a main regulator of phenylalanine biosynthesis and utilization. A phylogenetic analysis classified PpNAC1 in the NST proteins group and was selected for functional characterization. PpNAC1 is predominantly expressed in the secondary xylem and compression wood of adult trees. Silencing of PpNAC1 in P. pinaster results in the alteration of stem vascular radial patterning and the down-regulation of several genes associated with cell wall biogenesis and secondary metabolism. Furthermore, transactivation and EMSA analyses showed that PpNAC1 is able to activate its own expression and PpMyb4 promoter, while PpMyb4 is able to activate PpMyb8, a transcriptional regulator of phenylalanine and lignin biosynthesis in maritime pine. Together, these results suggest that PpNAC1 is a functional ortholog of the ArabidopsisSND1 and NST1 genes and support the idea that key regulators governing secondary cell wall formation could be conserved between gymnosperms and angiosperms. Understanding the molecular switches controlling wood formation is of paramount importance for fundamental tree biology and paves the way for applications in conifer biotechnology.
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Affiliation(s)
- María Belén Pascual
- Departamento de Biología Molecular y BioquímicaFacultad de CienciasUniversidad de MálagaCampus Universitario de TeatinosMálagaSpain
| | - María‐Teresa Llebrés
- Departamento de Biología Molecular y BioquímicaFacultad de CienciasUniversidad de MálagaCampus Universitario de TeatinosMálagaSpain
| | - Blanca Craven‐Bartle
- Departamento de Biología Molecular y BioquímicaFacultad de CienciasUniversidad de MálagaCampus Universitario de TeatinosMálagaSpain
| | - Rafael A. Cañas
- Departamento de Biología Molecular y BioquímicaFacultad de CienciasUniversidad de MálagaCampus Universitario de TeatinosMálagaSpain
| | - Francisco M. Cánovas
- Departamento de Biología Molecular y BioquímicaFacultad de CienciasUniversidad de MálagaCampus Universitario de TeatinosMálagaSpain
| | - Concepción Ávila
- Departamento de Biología Molecular y BioquímicaFacultad de CienciasUniversidad de MálagaCampus Universitario de TeatinosMálagaSpain
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miRNA mediated regulation of NAC transcription factors in plant development and environment stress response. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.plgene.2017.05.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Berens ML, Berry HM, Mine A, Argueso CT, Tsuda K. Evolution of Hormone Signaling Networks in Plant Defense. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:401-425. [PMID: 28645231 DOI: 10.1146/annurev-phyto-080516-035544] [Citation(s) in RCA: 277] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Studies with model plants such as Arabidopsis thaliana have revealed that phytohormones are central regulators of plant defense. The intricate network of phytohormone signaling pathways enables plants to activate appropriate and effective defense responses against pathogens as well as to balance defense and growth. The timing of the evolution of most phytohormone signaling pathways seems to coincide with the colonization of land, a likely requirement for plant adaptations to the more variable terrestrial environments, which included the presence of pathogens. In this review, we explore the evolution of defense hormone signaling networks by combining the model plant-based knowledge about molecular components mediating phytohormone signaling and cross talk with available genome information of other plant species. We highlight conserved hubs in hormone cross talk and discuss evolutionary advantages of defense hormone cross talk. Finally, we examine possibilities of engineering hormone cross talk for improvement of plant fitness and crop production.
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Affiliation(s)
- Matthias L Berens
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
| | - Hannah M Berry
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523
| | - Akira Mine
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
| | - Cristiana T Argueso
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523
| | - Kenichi Tsuda
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
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23
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Santa Brigida AB, Rojas CA, Grativol C, de Armas EM, Entenza JOP, Thiebaut F, Lima MDF, Farrinelli L, Hemerly AS, Lifschitz S, Ferreira PCG. Sugarcane transcriptome analysis in response to infection caused by Acidovorax avenae subsp. avenae. PLoS One 2016; 11:e0166473. [PMID: 27936012 PMCID: PMC5147822 DOI: 10.1371/journal.pone.0166473] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 10/28/2016] [Indexed: 12/22/2022] Open
Abstract
Sugarcane is an important tropical crop mainly cultivated to produce ethanol and sugar. Crop productivity is negatively affected by Acidovorax avenae subsp avenae (Aaa), which causes the red stripe disease. Little is known about the molecular mechanisms triggered in response to the infection. We have investigated the molecular mechanism activated in sugarcane using a RNA-seq approach. We have produced a de novo transcriptome assembly (TR7) from sugarcane RNA-seq libraries submitted to drought and infection with Aaa. Together, these libraries present 247 million of raw reads and resulted in 168,767 reference transcripts. Mapping in TR7 of reads obtained from infected libraries, revealed 798 differentially expressed transcripts, of which 723 were annotated, corresponding to 467 genes. GO and KEGG enrichment analysis showed that several metabolic pathways, such as code for proteins response to stress, metabolism of carbohydrates, processes of transcription and translation of proteins, amino acid metabolism and biosynthesis of secondary metabolites were significantly regulated in sugarcane. Differential analysis revealed that genes in the biosynthetic pathways of ET and JA PRRs, oxidative burst genes, NBS-LRR genes, cell wall fortification genes, SAR induced genes and pathogenesis-related genes (PR) were upregulated. In addition, 20 genes were validated by RT-qPCR. Together, these data contribute to a better understanding of the molecular mechanisms triggered by the Aaa in sugarcane and opens the opportunity for the development of molecular markers associated with disease tolerance in breeding programs.
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Affiliation(s)
- Ailton B. Santa Brigida
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brasil
| | - Cristian A. Rojas
- Instituto Latino-Americano de Ciências da Vida e da Natureza, Universidade Federal da Integração Latino-Americana, Foz do Iguaçu, Paraná, Brasil
| | - Clícia Grativol
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, Brasil
| | - Elvismary M. de Armas
- Departamento de Informática, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brasil
| | - Júlio O. P. Entenza
- Departamento de Informática, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brasil
| | - Flávia Thiebaut
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brasil
| | - Marcelo de F. Lima
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, Brasil
| | | | - Adriana S. Hemerly
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brasil
| | - Sérgio Lifschitz
- Departamento de Informática, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brasil
| | - Paulo C. G. Ferreira
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brasil
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Merino I, Abrahamsson M, Sterck L, Craven-Bartle B, Canovas F, von Arnold S. Transcript profiling for early stages during embryo development in Scots pine. BMC PLANT BIOLOGY 2016; 16:255. [PMID: 27863470 PMCID: PMC5116219 DOI: 10.1186/s12870-016-0939-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/28/2016] [Indexed: 05/22/2023]
Abstract
BACKGROUND Characterization of the expression and function of genes regulating embryo development in conifers is interesting from an evolutionary point of view. However, our knowledge about the regulation of embryo development in conifers is limited. During early embryo development in Pinus species the proembyo goes through a cleavage process, named cleavage polyembryony, giving rise to four embryos. One of these embryos develops to a dominant embryo, which will develop further into a mature, cotyledonary embryo, while the other embryos, the subordinate embryos, are degraded. The main goal of this study has been to identify processes that might be important for regulating the cleavage process and for the development of a dominant embryo. RESULTS RNA samples from embryos and megagametophytes at four early developmental stages during seed development in Pinus sylvestris were subjected to high-throughput sequencing. A total of 6.6 million raw reads was generated, resulting in 121,938 transcripts, out of which 36.106 contained ORFs. 18,638 transcripts were differentially expressed (DETs) in embryos and megagametophytes. GO enrichment analysis of transcripts up-regulated in embryos showed enrichment for different cellular processes, while those up-regulated in megagametophytes were enriched for accumulation of storage material and responses to stress. The highest number of DETs was detected during the initiation of the cleavage process. Transcripts related to embryogenic competence, cell wall modifications, cell division pattern, axis specification and response to hormones and stress were highly abundant and differentially expressed during early embryo development. The abundance of representative DETs was confirmed by qRT-PCR analyses. CONCLUSION Based on the processes identified in the GO enrichment analyses and the expression of the selected transcripts we suggest that (i) processes related to embryogenic competence and cell wall loosening are involved in activating the cleavage process; (ii) apical-basal polarization is strictly regulated in dominant embryos but not in the subordinate embryos; (iii) the transition from the morphogenic phase to the maturation phase is not completed in subordinate embryos. This is the first genome-wide transcript expression profiling of the earliest stages during embryo development in a Pinus species. Our results can serve as a framework for future studies to reveal the functions of identified genes.
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Affiliation(s)
- Irene Merino
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7080, 750 07 Uppsala, Sweden
| | - Malin Abrahamsson
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7080, 750 07 Uppsala, Sweden
| | - Lieven Sterck
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, B-9000 Belgium
| | - Blanca Craven-Bartle
- Department of Molecular Biology and Biochemistry, School of Sciences, Campus de Teatinos, Universidad de Malaga, 29071 Malaga, Spain
| | - Francisco Canovas
- Department of Molecular Biology and Biochemistry, School of Sciences, Campus de Teatinos, Universidad de Malaga, 29071 Malaga, Spain
| | - Sara von Arnold
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7080, 750 07 Uppsala, Sweden
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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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Pascual MB, El-Azaz J, de la Torre FN, Cañas RA, Avila C, Cánovas FM. Biosynthesis and Metabolic Fate of Phenylalanine in Conifers. FRONTIERS IN PLANT SCIENCE 2016; 7:1030. [PMID: 27468292 PMCID: PMC4942462 DOI: 10.3389/fpls.2016.01030] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/30/2016] [Indexed: 05/18/2023]
Abstract
The amino acid phenylalanine (Phe) is a critical metabolic node that plays an essential role in the interconnection between primary and secondary metabolism in plants. Phe is used as a protein building block but it is also as a precursor for numerous plant compounds that are crucial for plant reproduction, growth, development, and defense against different types of stresses. The metabolism of Phe plays a central role in the channeling of carbon from photosynthesis to the biosynthesis of phenylpropanoids. The study of this metabolic pathway is particularly relevant in trees, which divert large amounts of carbon into the biosynthesis of Phe-derived compounds, particularly lignin, an important constituent of wood. The trunks of trees are metabolic sinks that consume a considerable percentage of carbon and energy from photosynthesis, and carbon is finally immobilized in wood. This paper reviews recent advances in the biosynthesis and metabolic utilization of Phe in conifer trees. Two alternative routes have been identified: the ancient phenylpyruvate pathway that is present in microorganisms, and the arogenate pathway that possibly evolved later during plant evolution. Additionally, an efficient nitrogen recycling mechanism is required to maintain sustained growth during xylem formation. The relevance of phenylalanine metabolic pathways in wood formation, the biotic interactions, and ultraviolet protection is discussed. The genetic manipulation and transcriptional regulation of the pathways are also outlined.
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Affiliation(s)
| | | | | | | | | | - Francisco M. Cánovas
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de MálagaMálaga, Spain
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Shiriga K, Sharma R, Kumar K, Yadav SK, Hossain F, Thirunavukkarasu N. Genome-wide identification and expression pattern of drought-responsive members of the NAC family in maize. Meta Gene 2014; 2:407-417. [PMID: 25606426 DOI: 10.1007/s00344-019-09984-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 04/09/2014] [Accepted: 05/03/2014] [Indexed: 05/28/2023] Open
Abstract
NAC proteins are plant-specific transcription factors (TFs). Although they play a pivotal role in regulating distinct biological processes, TFs in maize are yet to be investigated comprehensively. Within the maize genome, we identified 152 putative NAC domain-encoding genes (ZmNACs), including eight membrane-bound members, by systematic sequence analysis and physically mapped them onto ten chromosomes of maize. In silico analysis of the ZmNACs and comparison with similar genes in other plants such as Arabidopsis, rice, and soybean, revealed a similar NAC sequence architecture. Phylogenetically, the ZmNACs were arranged into six distinct subgroups (I-VI) possessing conserved motifs. Phylogenetic analysis using stress-related NAC TFs from Arabidopsis, rice, and soybean as seeding sequences identified 24 of the 152 ZmNACs (all from Group II) as putative stress-responsive genes, including one dehydration-responsive ZmSNAC1 gene reported earlier. One drought-tolerant genotype (HKI577) and one susceptible genotype (PC13T-3) were used for studying the expression pattern of the NAC genes during drought stress. qRT-PCR based expression profiles of 11 genes predicted to be related to stress confirmed strong differential gene expression during drought stress. Phylogenetic analyses revealed that ZmNAC18, ZmNAC51, ZmNAC145, and ZmNAC72, which were up-regulated in the tolerant genotype and down-regulated in the susceptible genotype, belonged to the same group to which also belong other drought-responsive genes, namely SNAC1, OsNAC6, ANAC019, and ANAC055, which act as a transcriptional activator and are strongly induced under stress from various abiotic sources. Differentially expressed ZmNAC genes, alone or in combination with each other or with other type(s) of TFs, may control the general cellular machinery and regulate stress-responsive downstream genes. Alternatively, they may serve as a platform to regulate a broad set of genes, which are subsequently fine-tuned by specific regulators. This genome-wide identification and expression profiling opens new avenues for systematic functional analysis of new members of the NAC gene family, which may be exploited in developing lines that are better adapted to drought.
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Affiliation(s)
- Kaliyugam Shiriga
- Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India ; School of Life Sciences, Singhania University, Rajasthan 333515, India
| | - Rinku Sharma
- Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Krishan Kumar
- School of Life Sciences, Singhania University, Rajasthan 333515, India
| | - Shiv Kumar Yadav
- Division of Seed Science and Technology, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Firoz Hossain
- Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India
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