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Tabatabaeipour SN, Shiran B, Ravash R, Niazi A, Ebrahimie E. Comprehensive transcriptomic meta-analysis unveils new responsive genes to methyl jasmonate and ethylene in Catharanthusroseus. Heliyon 2024; 10:e27132. [PMID: 38449649 PMCID: PMC10915408 DOI: 10.1016/j.heliyon.2024.e27132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 02/23/2024] [Indexed: 03/08/2024] Open
Abstract
In Catharanthus roseus, vital plant hormones, namely methyl jasmonate (MeJA) and ethylene, serve as abiotic triggers, playing a crucial role in stimulating the production of specific secondary compounds with anticancer properties. Understanding how plants react to various stresses, stimuli, and the pathways involved in biosynthesis holds significant promise. The application of stressors like ethylene and MeJA induces the plant's defense mechanisms, leading to increased secondary metabolite production. To delve into the essential transcriptomic processes linked to hormonal responses, this study employed an integrated approach combining RNA-Seq data meta-analysis and system biology methodologies. Furthermore, the validity of the meta-analysis findings was confirmed using RT-qPCR. Within the meta-analysis, 903 genes exhibited differential expression (DEGs) when comparing normal conditions to those of the treatment. Subsequent analysis, encompassing gene ontology, KEGG, TF, and motifs, revealed that these DEGs were actively engaged in multiple biological processes, particularly in responding to various stresses and stimuli. Additionally, these genes were notably enriched in diverse biosynthetic pathways, including those related to TIAs, housing valuable medicinal compounds found in this plant. Furthermore, by conducting co-expression network analysis, we identified hub genes within modules associated with stress response and the production of TIAs. Most genes linked to the biosynthesis pathway of TIAs clustered within three specific modules. Noteworthy hub genes, including Helicase ATP-binding domain, hbdA, and ALP1 genes within the blue, turquoise, and green module networks, are presumed to play a role in the TIAs pathway. These identified candidate genes hold potential for forthcoming genetic and metabolic engineering initiatives aimed at augmenting the production of secondary metabolites and medicinal compounds within C. roseus.
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Affiliation(s)
- Seyede Nasim Tabatabaeipour
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran
| | - Behrouz Shiran
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran
- Institute of Biotechnology, Shahrekord University, P.O. Box 115, Shahrekord, Iran
| | - Rudabeh Ravash
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran
| | - Ali Niazi
- Department of Biotechnology, Faculty of Agriculture, Shiraz University, Shiraz, Iran
| | - Esmaeil Ebrahimie
- Department of Biotechnology, Faculty of Agriculture, Shiraz University, Shiraz, Iran
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, SA 5371, Australia
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Karami S, Shiran B, Ravash R, Fallahi H. A comprehensive analysis of transcriptomic data for comparison of plants with different photosynthetic pathways in response to drought stress. PLoS One 2023; 18:e0287761. [PMID: 37368898 DOI: 10.1371/journal.pone.0287761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 06/11/2023] [Indexed: 06/29/2023] Open
Abstract
The main factor leading to a decrease in crop productivity is abiotic stresses, particularly drought. Plants with C4 and CAM photosynthesis are better adapted to drought-prone areas than C3 plants. Therefore, it is beneficial to compare the stress response of plants with different photosynthetic pathways. Since most crops are C3 and C4 plants, this study focused on conducting an RNA-seq meta-analysis to investigate and compare how C3 and C4 plants respond to drought stress at the gene expression level in their leaves. Additionally, the accuracy of the meta-analysis results was confirmed with RT-qPCR. Based on the functional enrichment and network analysis, hub genes related to ribosomal proteins and photosynthesis were found to play a potential role in stress response. Moreover, our findings suggest that the low abundant amino acid degradation pathway, possibly through providing ATP source for the TCA cycle, in both groups of plants and the activation of the OPPP pathway in C4 plants, through providing the electron source required by this plant, can help to improve drought stress tolerance.
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Affiliation(s)
- Shima Karami
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran
| | - Behrouz Shiran
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran
- Institute of Biotechnology, Shahrekord University, Shahrekord, Iran
| | - Rudabeh Ravash
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran
| | - Hossein Fallahi
- Department of Biology, Faculty of Sciences, Razi University, Kermanshah, Iran
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Shojaee S, Ravash R, Shiran B, Ebrahimie E. Meta-analysis highlights the key drought responsive genes in genes: PEPC and TaSAG7 are hubs response networks. J Genet Eng Biotechnol 2022; 20:127. [PMID: 36053361 PMCID: PMC9468207 DOI: 10.1186/s43141-022-00395-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 06/14/2022] [Indexed: 11/29/2022]
Abstract
Background Wheat is the most important cereal. One of the environmental stresses is drought that harm the production of many cereals and every year due to low rainfall and frequent droughts, the need to produce plants resistant to this stress is felt. Therefore, identification and evaluation of the genes involved in the production of this resistance in plants are of great importance. By identifying these genes and changing their expression, it is possible to produce resistant plants that can tolerate dehydration and drought, with at least a qualitative and quantitative reduction in yield. Results Based on the meta-analysis results obtained in this study, in resistant cultivars ~ 4% (2394/61290) of the probe IDs decreased and ~ 4.5% (2670/61290) increased expression, furthermore in susceptible cultivars ~ 7% (4183/61290) of probe IDs decreased and ~ 6% (3591/61290) increased expression (P value ≤ 0.05). List of up- and downregulated genes was revealed, among the expressed genes of transcription factors Myb3, ethylene-responsive 5a, MIKC-type MADS-box WM24B, and salinity inducible ERF4 in resistant cultivars and transcription factors WRKY15, MADS-box TaAGL8, WRKY39, and Myb in susceptible cultivars, they showed a significant increase in expression, these transcription factors are of great importance in drought stress. Among them, ethylene responsive 5a in resistant cultivars by 3 times and Myb in susceptible cultivars by 2.6 times have shown the highest expression change. Using Cytoscape Hub software, the Phosphoenolpyruvate carboxylase (PEPC) and lyase isocitrate (TaSAG7) genes, which have significantly different expressions in resistant and susceptible wheat cultivars. PEPC and TaSAG7 genes were upregulated in resistant wheat cultivars as well as down regulated in susceptible cultivars. Also, the qPCR results of selected genes were consistent with the outcomes of the meta-analysis. Conclusions All microarray data were collected from the NCBI Gene Expression Omnibus site. Libraries with drought-tolerant and susceptible cultivars for wheat were considered under the stress and control conditions from whole leaf tissue. By meta-analysis combined the purposeful results of multiple experiments, and found list of genes expressed in reverse between the two cultivars. These genes can distinguish between different susceptible and resistant wheat cultivars. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-022-00395-4.
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Affiliation(s)
- Sahar Shojaee
- Department of Plant Breeding and Biotechnology, Shahrekord University, Shahr-e Kord, Iran
| | - Rudabeh Ravash
- Department of Plant Breeding and Biotechnology Faculty of Agriculture, Shahrekord University, Shahr-e Kord, Iran.
| | - Behrouz Shiran
- Department of Plant Breeding and Biotechnology Faculty of Agriculture, Shahrekord University, Shahr-e Kord, Iran
| | - Esmaeil Ebrahimie
- Genomics Research Platform, School of Agriculture, Biomedicine and Environment, Melbourne, La Trobe University, Victoria, 3086, Australia.,Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, South Australia, 5371, Australia
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Rajpal VR, Sharma S, Kumar A, Chand S, Joshi L, Chandra A, Babbar S, Goel S, Raina SN, Shiran B. "Is Omicron mild"? Testing this narrative with the mutational landscape of its three lineages and response to existing vaccines and therapeutic antibodies. J Med Virol 2022; 94:3521-3539. [PMID: 35355267 PMCID: PMC9088584 DOI: 10.1002/jmv.27749] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/10/2022] [Accepted: 03/28/2022] [Indexed: 11/12/2022]
Abstract
SARS-CoV-2 Omicron with its lineages BA.1, BA.2, and BA.3 has triggered a fresh wave of Covid-19 infections. Though, Omicron has, so far, produced mild symptoms, its genome contains 60 mutations including 37 in the spike protein and 15 in the receptor-binding domain. Thirteen sites conserved in previous SARS-CoV-2 variants carry mutations in Omicron. Many mutations have shown evolution under positive selection. Omicron's giant mutational leap has raised concerns as there are signs of higher virus infectivity rate, pathogenesis, reinfection, and immune evasion. Preliminary studies have reported waning of immunity after two-dose primary vaccine regime, need for the boosters, folds reduction in vaccine effectiveness and neutralizing antibodies even after boosting and significant neutralization resistance with the therapeutic monoclonal, polyclonal, and convalescent antibodies against Omicron. The narrative that "Omicron is mild," therefore, needs time to be tested with a deeper, scientific dwelling into the facts.
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Affiliation(s)
| | - Shashi Sharma
- Division of VirologyDefence Research and Development EstablishmentGwaliorMadhya PradeshIndia
| | - Avinash Kumar
- Department of BotanyVinoba Bhave UniversityHazaribagJharkhandIndia
| | - Shweta Chand
- Department of BotanyHansraj College, University of DelhiDelhiIndia
| | - Lata Joshi
- Department of BotanyHansraj College, University of DelhiDelhiIndia
| | - Atika Chandra
- Department of BotanyMaitreyi College, University of DelhiDelhiIndia
| | - Sadhna Babbar
- Department of BotanySwami Shraddhanand College, University of DelhiDelhiIndia
| | | | - Soom Nath Raina
- Department of BiotechnologyAmity Institute of Biotechnology, Amity University Uttar PradeshNoidaUttar PradeshIndia
| | - Behrouz Shiran
- Department of Plant Breeding and BiotechnologyShahrekord UniversityShahrekordIran
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Jafari M, Shiran B, Rabiei G, Ravash R, Sayed Tabatabaei BE, Martínez-Gómez P. Identification and verification of seed development related miRNAs in kernel almond by small RNA sequencing and qPCR. PLoS One 2021; 16:e0260492. [PMID: 34851991 PMCID: PMC8635354 DOI: 10.1371/journal.pone.0260492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 11/10/2021] [Indexed: 12/02/2022] Open
Abstract
Many studies have investigated the role of miRNAs on the yield of various plants, but so far, no report is available on the identification and role of miRNAs in fruit and seed development of almonds. In this study, preliminary analysis by high-throughput sequencing of short RNAs of kernels from the crosses between almond cultivars 'Sefid' × 'Mamaee' (with small and large kernels, respectively) and 'Sefid' × 'P. orientalis' (with small kernels) showed that the expressions of several miRNAs such as Pdu-miR395a-3p, Pdu-miR8123-5p, Pdu-miR482f, Pdu-miR6285, and Pdu-miR396a were significantly different. These miRNAs targeted genes encoding different proteins such as NYFB-3, SPX1, PGSIP3 (GUX2), GH3.9, and BEN1. The result of RT-qPCR revealed that the expression of these genes showed significant differences between the crosses and developmental stages of the seeds, suggesting that these genes might be involved in controlling kernel size because the presence of these miRNAs had a negative effect on their target genes. Pollen source can influence kernel size by affecting hormonal signaling and metabolic pathways through related miRNAs, a phenomenon known as xenia.
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Affiliation(s)
- Marjan Jafari
- Department of Horticulture, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran
| | - Behrouz Shiran
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran
- Institute of Biotechnology, Shahrekord University, Shahrekord, Iran
| | - Gholamreza Rabiei
- Department of Horticulture, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran
| | - Roudabeh Ravash
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran
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Eshaghi M, Shiran B, Fallahi H, Ravash R, Đeri BB. Identification of genes involved in steroid alkaloid biosynthesis in Fritillaria imperialis via de novo transcriptomics. Genomics 2019; 111:1360-1372. [DOI: 10.1016/j.ygeno.2018.09.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 08/15/2018] [Accepted: 09/14/2018] [Indexed: 01/22/2023]
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Aroee F, Azizi H, Shiran B, Pirali Kheirabadi K. Molecular identification of Nosema species in provinces of Fars, Chaharmahal and Bakhtiari and Isfahan (Southwestern Iran). Asian Pac J Trop Biomed 2017. [DOI: 10.1016/j.apjtb.2016.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Karimi M, Ghazanfari F, Fadaei A, Ahmadi L, Shiran B, Rabei M, Fallahi H. The Small-RNA Profiles of Almond (Prunus dulcis Mill.) Reproductive Tissues in Response to Cold Stress. PLoS One 2016; 11:e0156519. [PMID: 27253370 PMCID: PMC4890778 DOI: 10.1371/journal.pone.0156519] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 05/16/2016] [Indexed: 11/20/2022] Open
Abstract
Spring frost is an important environmental stress that threatens the production of Prunus trees. However, little information is available regarding molecular response of these plants to the frost stress. Using high throughput sequencing, this study was conducted to identify differentially expressed miRNAs, both the conserved and the non-conserved ones, in the reproductive tissues of almond tolerant H genotype under cold stress. Analysis of 50 to 58 million raw reads led to identification of 174 unique conserved and 59 novel microRNAs (miRNAs). Differential expression pattern analysis showed that 50 miRNA families were expressed differentially in one or both of almond reproductive tissues (anther and ovary). Out of these 50 miRNA families, 12 and 15 displayed up-regulation and down-regulation, respectively. The distribution of conserved miRNA families indicated that miR482f harbor the highest number of members. Confirmation of miRNAs expression patterns by quantitative real- time PCR (qPCR) was performed in cold tolerant (H genotype) alongside a sensitive variety (Sh12 genotype). Our analysis revealed differential expression for 9 miRNAs in anther and 3 miRNAs in ovary between these two varieties. Target prediction of miRNAs followed by differential expression analysis resulted in identification of 83 target genes, mostly transcription factors. This study comprehensively catalogued expressed miRNAs under different temperatures in two reproductive tissues (anther and ovary). Results of current study and the previous RNA-seq study, which was conducted in the same tissues by our group, provide a unique opportunity to understand the molecular basis of responses of almond to cold stress. The results can also enhance the possibility for gene manipulation to develop cold tolerant plants.
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Affiliation(s)
- Marzieh Karimi
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, P.O.Box 115, Iran
| | - Farahnaz Ghazanfari
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, P.O.Box 115, Iran
| | - Adeleh Fadaei
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, P.O.Box 115, Iran
| | - Laleh Ahmadi
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, P.O.Box 115, Iran
| | - Behrouz Shiran
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, P.O.Box 115, Iran
- Institute of Biotechnology, Shahrekord University, Shahrekord, P.O.Box 115, Iran
| | - Mohammad Rabei
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, P.O.Box 115, Iran
| | - Hossein Fallahi
- Department of Biology, School of Sciences, Razi University, Bagh-e-Abrisham Kermanshah, Iran
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
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Kharazian N, Rahimi S, Shiran B. Genetic diversity and morphological variability of fifteen Stachys (Lamiaceae) species from Iran using morphological and ISSR molecular markers. Biologia (Bratisl) 2015. [DOI: 10.1515/biolog-2015-0051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Alisoltani A, Fallahi H, Shiran B, Alisoltani A, Ebrahimie E. RNA-Seq SSRs and small RNA-Seq SSRs: New approaches in cancer biomarker discovery. Gene 2015; 560:34-43. [DOI: 10.1016/j.gene.2015.01.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 12/02/2014] [Accepted: 01/13/2015] [Indexed: 11/24/2022]
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Ebrahimi Khaksefidi R, Mirlohi S, Khalaji F, Fakhari Z, Shiran B, Fallahi H, Rafiei F, Budak H, Ebrahimie E. Differential expression of seven conserved microRNAs in response to abiotic stress and their regulatory network in Helianthus annuus. Front Plant Sci 2015; 6:741. [PMID: 26442054 PMCID: PMC4585256 DOI: 10.3389/fpls.2015.00741] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 08/31/2015] [Indexed: 05/03/2023]
Abstract
Biotic and abiotic stresses affect plant development and production through alternation of the gene expression pattern. Gene expression itself is under the control of different regulators such as miRNAs and transcription factors (TFs). MiRNAs are known to play important roles in regulation of stress responses via interacting with their target mRNAs. Here, for the first time, seven conserved miRNAs, associated with drought, heat, salt and cadmium stresses were characterized in sunflower. The expression profiles of miRNAs and their targets were comparatively analyzed between leaves and roots of plants grown under the mentioned stress conditions. Gene ontology analysis of target genes revealed that they are involved in several important pathways such as auxin and ethylene signaling, RNA mediated silencing and DNA methylation processes. Gene regulatory network highlighted the existence of cross-talks between these stress-responsive miRNAs and the other stress responsive genes in sunflower. Based on network analysis, we suggest that some of these miRNAs in sunflower such as miR172 and miR403 may play critical roles in epigenetic responses to stress. It seems that depending on the stress type, theses miRNAs target several pathways and cellular processes to help sunflower to cope with drought, heat, salt and cadmium stress conditions in a tissue-associated manner.
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Affiliation(s)
| | - Shirin Mirlohi
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord UniversityShahrekord, Iran
| | - Fahimeh Khalaji
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord UniversityShahrekord, Iran
| | - Zahra Fakhari
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord UniversityShahrekord, Iran
| | - Behrouz Shiran
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord UniversityShahrekord, Iran
- Department of Agricultural Biotechnology, Institute of Biotechnology, Shahrekord UniversityShahrekord, Iran
- *Correspondence: Behrouz Shiran, Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, PO Box 115, Shahrekord 8818634141, Iran ;
| | - Hossein Fallahi
- Department of Biology, School of Sciences, Razi UniversityKermanshah, Iran
| | - Fariba Rafiei
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord UniversityShahrekord, Iran
| | - Hikmet Budak
- Biological Sciences and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci UniversityIstanbul, Turkey
| | - Esmaeil Ebrahimie
- Faculty of Agriculture, Institute of Biotechnology, Shiraz UniversityShiraz, Iran
- Department of Genetics and Evolution, School of Biological Sciences, University of AdelaideAdelaide, SA, Australia
- School of Biological Sciences, Faculty of Science and Engineering, Flinders UniversityAdelaide, Australia
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12
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Mousavi S, Alisoltani A, Shiran B, Fallahi H, Ebrahimie E, Imani A, Houshmand S. De novo transcriptome assembly and comparative analysis of differentially expressed genes in Prunus dulcis Mill. in response to freezing stress. PLoS One 2014; 9:e104541. [PMID: 25122458 PMCID: PMC4133227 DOI: 10.1371/journal.pone.0104541] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 07/13/2014] [Indexed: 11/18/2022] Open
Abstract
Almond (Prunus dulcis Mill.), one of the most important nut crops, requires chilling during winter to develop fruiting buds. However, early spring chilling and late spring frost may damage the reproductive tissues leading to reduction in the rate of productivity. Despite the importance of transcriptional changes and regulation, little is known about the almond’s transcriptome under the cold stress conditions. In the current reserch, we used RNA-seq technique to study the response of the reporuductive tissues of almond (anther and ovary) to frost stress. RNA sequencing resulted in more than 20 million reads from anther and ovary tissues of almond, individually. About 40,000 contigs were assembled and annotated denovo in each tissue. Profile of gene expression in ovary showed significant alterations in 5,112 genes, whereas in anther 6,926 genes were affected by freezing stress. Around two thousands of these genes were common altered genes in both ovary and anther libraries. Gene ontology indicated the involvement of differentially expressed (DE) genes, responding to freezing stress, in metabolic and cellular processes. qRT-PCR analysis verified the expression pattern of eight genes randomley selected from the DE genes. In conclusion, the almond gene index assembled in this study and the reported DE genes can provide great insights on responses of almond and other Prunus species to abiotic stresses. The obtained results from current research would add to the limited available information on almond and Rosaceae. Besides, the findings would be very useful for comparative studies as the number of DE genes reported here is much higher than that of any previous reports in this plant.
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Affiliation(s)
- Sadegh Mousavi
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran
| | - Arghavan Alisoltani
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran
| | - Behrouz Shiran
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran
- Institute of Biotechnology, Shahrekord University, Shahrekord, Iran
- * E-mail:
| | - Hossein Fallahi
- Department of Biology, School of Sciences, Razi University, Bagh-e-Abrisham Kermanshah, Iran
| | - Esameil Ebrahimie
- Department of Crop Production and Plant Breeding, Faculty of Agriculture, Shiraz University, Shiraz, Iran
- School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, Australia
| | - Ali Imani
- Department of Horticulture, Seed and Plant Improvement Institute (SPII), Karaj, Iran
| | - Saadollah Houshmand
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran
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Badfar-Chaleshtori S, Shiran B, Kohgard M, Mommeni H, Hafizi A, Khodambashi M, Mirakhorli N, Sorkheh K. Assessment of genetic diversity and structure of Imperial Crown (Fritillaria imperialis L.) populations in the Zagros region of Iran using AFLP, ISSR and RAPD markers and implications for its conservation. BIOCHEM SYST ECOL 2012. [DOI: 10.1016/j.bse.2011.12.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Ji X, Dong B, Shiran B, Talbot MJ, Edlington JE, Hughes T, White RG, Gubler F, Dolferus R. Control of abscisic acid catabolism and abscisic acid homeostasis is important for reproductive stage stress tolerance in cereals. Plant Physiol 2011; 156:647-62. [PMID: 21502188 PMCID: PMC3177265 DOI: 10.1104/pp.111.176164] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Accepted: 04/17/2011] [Indexed: 05/18/2023]
Abstract
Drought stress at the reproductive stage causes pollen sterility and grain loss in wheat (Triticum aestivum). Drought stress induces abscisic acid (ABA) biosynthesis genes in anthers and ABA accumulation in spikes of drought-sensitive wheat varieties. In contrast, drought-tolerant wheat accumulates lower ABA levels, which correlates with lower ABA biosynthesis and higher ABA catabolic gene expression (ABA 8'-hydroxylase). Wheat TaABA8'OH1 deletion lines accumulate higher spike ABA levels and are more drought sensitive. ABA treatment of the spike mimics the effect of drought, causing high levels of sterility. ABA treatment represses the anther cell wall invertase gene TaIVR1, and drought-tolerant lines appeared to be more sensitive to the effect of ABA. Drought-induced sterility shows similarity to cold-induced sterility in rice (Oryza sativa). In cold-stressed rice, the rate of ABA accumulation was similar in cold-sensitive and cold-tolerant lines during the first 8 h of cold treatment, but in the tolerant line, ABA catabolism reduced ABA levels between 8 and 16 h of cold treatment. The ABA biosynthesis gene encoding 9-cis-epoxycarotenoid dioxygenase in anthers is mainly expressed in parenchyma cells surrounding the vascular bundle of the anther. Transgenic rice lines expressing the wheat TaABA8'OH1 gene under the control of the OsG6B tapetum-specific promoter resulted in reduced anther ABA levels under cold conditions. The transgenic lines showed that anther sink strength (OsINV4) was maintained under cold conditions and that this correlated with improved cold stress tolerance. Our data indicate that ABA and ABA 8'-hydroxylase play an important role in controlling anther ABA homeostasis and reproductive stage abiotic stress tolerance in cereals.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Rudy Dolferus
- Commonwealth Scientific and Industrial Research Organization Plant Industry, Canberra, Australian Capital Territory 2601, Australia
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Ji X, Shiran B, Wan J, Lewis DC, Jenkins CLD, Condon AG, Richards RA, Dolferus R. Importance of pre-anthesis anther sink strength for maintenance of grain number during reproductive stage water stress in wheat. Plant Cell Environ 2010; 33:926-42. [PMID: 20199626 DOI: 10.1111/j.1365-3040.2010.02130.x] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Reproductive stage water stress leads to spikelet sterility in wheat. Whereas drought stress at anthesis affects mainly grain size, stress at the young microspore stage of pollen development is characterized by abortion of pollen development and reduction in grain number. We identified genetic variability for drought tolerance at the reproductive stage. Drought-tolerant wheat germplasm is able to maintain carbohydrate accumulation in the reproductive organs throughout the stress treatment. Starch depletion in the ovary of drought-sensitive wheat is reversible upon re-watering and cross-pollination experiments indicate that the ovary is more resilient than the anther. The effect on anthers and pollen fertility is irreversible, suggesting that pollen sterility is the main cause of grain loss during drought conditions in wheat. The difference in storage carbohydrate accumulation in drought-sensitive and drought-tolerant wheat is correlated with differences in sugar profiles, cell wall invertase gene expression and expression of fructan biosynthesis genes in anther and ovary (sucrose : sucrose 1-fructosyl-transferase, 1-SST; sucrose : fructan 6-fructosyl-transferase, 6-SFT). Our results indicate that the ability to control and maintain sink strength and carbohydrate supply to anthers may be the key to maintaining pollen fertility and grain number in wheat and this mechanism may also provide protection against other abiotic stresses.
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Affiliation(s)
- Xuemei Ji
- CSIRO Plant Industry, Canberra, Australian Capital Territory 2601, Australia
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Ravash R, Shiran B, Alavi AA, Bayat F, Rajaee S, Zervakis GI. Genetic variability and molecular phylogeny of Pleurotus eryngii species-complex isolates from Iran, and notes on the systematics of Asiatic populations. Mycol Prog 2009. [DOI: 10.1007/s11557-009-0624-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Rani V, Singh KP, Shiran B, Nandy S, Goel S, Devarumath RM, Sreenath HL, Raina SN. Evidence for new nuclear and mitochondrial genome organizations among high-frequency somatic embryogenesis-derived plants of allotetraploid Coffea arabica L. (Rubiaceae). Plant Cell Rep 2000; 19:1013-1020. [PMID: 30754832 DOI: 10.1007/s002990000228] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The most important commercial species of coffee, Coffea arabica, which produces 73% of the world's coffee crop and almost all of the coffee in Latin America, is the only tetraploid (allotetraploid, 2n=4x=44) species known in the genus. High-frequency somatic embryogenesis, plant regeneration and plant recovery were achieved from leaf explants of a mature, elite plant of C. arabica cv. Cauvery (S-4347) using a two-step culture method. To assess the genetic integrity of the nuclear, mitochondrial and chloroplast genomes among the hardened regenerants, we employed multiple DNA markers (RFLP, RAPD, ISSR) for sampling various regions of the genome. Although the nuclear and mitochondrial genomes of the mother plant and five ramets derived from the mother ortet were similar in organization, this was not so in the somatic embryo-derived plants where both nuclear and mitochondrial genomes changed in different, characteristic ways and produced novel genome organizations. A total of 480 genetic loci, based on the data obtained from a total of 16 nuclear, mitochondrial and chloroplast gene probes, in combination with nine restriction enzyme digests, 38 RAPD and 17 SSR primers, were scored in 27 somatic embryo-derived plants and the single control. Among these, 44 loci were observed to be polymorphic. A relatively low level of polymorphism (4.36%) was found in the nuclear genome, while polymorphism in the mitochondrial genome (41%) was much higher. No polymorphism was detected in the chloroplast genome. The polymorphism in the mitochondrial genome was found in only 4 plants. Such selective polymorphism was not true for the nuclear genome. Thus, this in-depth and comprehensive study demonstrates, for the first time, the presence of subtle genetic variability and novel genome organizations in the commercially well-established somatic embryogenesis-derived plants of this important coffee species.
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Affiliation(s)
- V Rani
- Laboratory of Cellular and Molecular Cytogenetics, Department of Botany, University of Delhi, Delhi 110 007, India e-mail: Fax: +91-11-7256541, , , , , , IN
| | - K P Singh
- Laboratory of Cellular and Molecular Cytogenetics, Department of Botany, University of Delhi, Delhi 110 007, India e-mail: Fax: +91-11-7256541, , , , , , IN
| | - B Shiran
- Laboratory of Cellular and Molecular Cytogenetics, Department of Botany, University of Delhi, Delhi 110 007, India e-mail: Fax: +91-11-7256541, , , , , , IN
| | - S Nandy
- Laboratory of Cellular and Molecular Cytogenetics, Department of Botany, University of Delhi, Delhi 110 007, India e-mail: Fax: +91-11-7256541, , , , , , IN
| | - S Goel
- Laboratory of Cellular and Molecular Cytogenetics, Department of Botany, University of Delhi, Delhi 110 007, India e-mail: Fax: +91-11-7256541, , , , , , IN
| | - R M Devarumath
- Laboratory of Cellular and Molecular Cytogenetics, Department of Botany, University of Delhi, Delhi 110 007, India e-mail: Fax: +91-11-7256541, , , , , , IN
| | - H L Sreenath
- Laboratory of Cellular and Molecular Cytogenetics, Department of Botany, University of Delhi, Delhi 110 007, India e-mail: Fax: +91-11-7256541, , , , , , IN
| | - S N Raina
- Laboratory of Cellular and Molecular Cytogenetics, Department of Botany, University of Delhi, Delhi 110 007, India e-mail: Fax: +91-11-7256541, , , , , , IN
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