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Payne D, Li Y, Govindan G, Kumar A, Thomas J, Addo-Quaye CA, Pereira A, Sunkar R. High Daytime Temperature Responsive MicroRNA Profiles in Developing Grains of Rice Varieties with Contrasting Chalkiness. Int J Mol Sci 2023; 24:11631. [PMID: 37511395 PMCID: PMC10380806 DOI: 10.3390/ijms241411631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
High temperature impairs starch biosynthesis in developing rice grains and thereby increases chalkiness, affecting the grain quality. Genome encoded microRNAs (miRNAs) fine-tune target transcript abundances in a spatio-temporal specific manner, and this mode of gene regulation is critical for a myriad of developmental processes as well as stress responses. However, the role of miRNAs in maintaining rice grain quality/chalkiness during high daytime temperature (HDT) stress is relatively unknown. To uncover the role of miRNAs in this process, we used five contrasting rice genotypes (low chalky lines Cyp, Ben, and KB and high chalky lines LaGrue and NB) and compared the miRNA profiles in the R6 stage caryopsis samples from plants subjected to prolonged HDT (from the onset of fertilization through R6 stage of caryopsis development). Our small RNA analysis has identified approximately 744 miRNAs that can be grouped into 291 families. Of these, 186 miRNAs belonging to 103 families are differentially regulated under HDT. Only two miRNAs, Osa-miR444f and Osa-miR1866-5p, were upregulated in all genotypes, implying that the regulations greatly varied between the genotypes. Furthermore, not even a single miRNA was commonly up/down regulated specifically in the three tolerant genotypes. However, three miRNAs (Osa-miR1866-3p, Osa-miR5150-3p and canH-miR9774a,b-3p) were commonly upregulated and onemiRNA (Osa-miR393b-5p) was commonly downregulated specifically in the sensitive genotypes (LaGrue and NB). These observations suggest that few similarities exist within the low chalky or high chalky genotypes, possibly due to high genetic variation. Among the five genotypes used, Cypress and LaGrue are genetically closely related, but exhibit contrasting chalkiness under HDT, and thus, a comparison between them is most relevant. This comparison revealed a general tendency for Cypress to display miRNA regulations that could decrease chalkiness under HDT compared with LaGrue. This study suggests that miRNAs could play an important role in maintaining grain quality in HDT-stressed rice.
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Affiliation(s)
- David Payne
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Yongfang Li
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Ganesan Govindan
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Anuj Kumar
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Julie Thomas
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Charles A Addo-Quaye
- Department of Computer Science and Cybersecurity, Metropolitan State University, Saint Paul, MN 55106, USA
| | - Andy Pereira
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
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2
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Wang M, Yang C, Wei K, Zhao M, Shen L, Ji J, Wang L, Zhang D, Guo J, Zheng Y, Yu J, Zhu M, Liu H, Li YF. Temporal expression study of miRNAs in the crown tissues of winter wheat grown under natural growth conditions. BMC Genomics 2021; 22:793. [PMID: 34736408 PMCID: PMC8567549 DOI: 10.1186/s12864-021-08048-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 09/30/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Winter wheat requires prolonged exposure to low temperature to initiate flowering (vernalization). Shoot apical meristem of the crown is the site of cold perception, which produces leaf primordia during vegetative growth before developing into floral primordia at the initiation of the reproductive phase. Although many essential genes for winter wheat cold acclimation and floral initiation have been revealed, the importance of microRNA (miRNA) meditated post-transcriptional regulation in crowns is not well understood. To understand the potential roles of miRNAs in crown tissues, we performed a temporal expression study of miRNAs in crown tissues at the three-leaf stage, winter dormancy stage, spring green-up stage, and jointing stage of winter wheat grown under natural growth conditions. RESULTS In total, 348 miRNAs belonging to 298 miRNA families, were identified in wheat crown tissues. Among them, 92 differentially expressed miRNAs (DEMs) were found to be significantly regulated from the three-leaf stage to the jointing stage. Most of these DEMs were highly expressed at the three-leaf stage and winter dormancy stage, and then declined in later stages. Six DEMs, including miR156a-5p were markedly induced during the winter dormancy stage. Eleven DEMs, including miR159a.1, miR390a-5p, miR393-5p, miR160a-5p, and miR1436, were highly expressed at the green-up stage. Twelve DEMs, such as miR172a-5p, miR394a, miR319b-3p, and miR9676-5p were highly induced at the jointing stage. Moreover, 14 novel target genes of nine wheat or Pooideae-specific miRNAs were verified using RLM-5' RACE assay. Notably, six mTERFs and two Rf1 genes, which are associated with mitochondrial gene expression, were confirmed as targets of three wheat-specific miRNAs. CONCLUSIONS The present study not only confirmed the known miRNAs associated with phase transition and floral development, but also identified a number of wheat or Pooideae-specific miRNAs critical for winter wheat cold acclimation and floral development. Most importantly, this study provided experimental evidence that miRNA could regulate mitochondrial gene expression by targeting mTERF and Rf1 genes. Our study provides valuable information for further exploration of the mechanism of miRNA mediated post-transcriptional regulation during winter wheat vernalization and inflorescent initiation.
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Affiliation(s)
- Menglei Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China.,Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang, 453007, China.,Present address: National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Chenhui Yang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Kangning Wei
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Miao Zhao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Liqiang Shen
- Jindal School of Management, University of Texas at Dallas, 800 W Campbell RD, Richardson, TX, 75080, USA
| | - Jie Ji
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Li Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China.,Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang, 453007, China
| | - Daijing Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Junqiang Guo
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Yun Zheng
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Juanjuan Yu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China.,Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang, 453007, China
| | - Mo Zhu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China.,Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang, 453007, China
| | - Haiying Liu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Yong-Fang Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China. .,Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang, 453007, China.
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3
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Distinct Evolutionary Profiles and Functions of microRNA156 and microRNA529 in Land Plants. Int J Mol Sci 2021; 22:ijms222011100. [PMID: 34681763 PMCID: PMC8541648 DOI: 10.3390/ijms222011100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/23/2021] [Accepted: 10/11/2021] [Indexed: 01/14/2023] Open
Abstract
MicroRNA156 (miR156) and miR529 have high sequence similarity and recognize overlapping sites in the same target genes, SQUAMOSA promoter binding protein-like (SPL or SBP box) genes, making it difficult to accurately distinguish their roles in regulatory networks that affect numerous biological functions. Here, we collected data about miR156 and miR529 family members from representative land plants and performed sequence comparisons, phylogenetic analysis, small RNA sequencing, and parallel analysis of RNA ends (PARE) analysis to dissect their evolutionary and functional differences. Although miR156 and miR529 are highly similar, there are differences in their mismatch-sensitive regions, which are essential for target recognition. In land plants, miR156 precursors are conserved mainly within the hairpin region, whereas miR529 precursors are conserved outside the hairpin region, including both the 5’ and 3’ arms. Phylogenetic analysis showed that MIR156 and MIR529 evolved independently, through divergent evolutionary patterns. The two genes also exhibit different expression patterns, with MIR529 preferentially expressed in reproductive tissues and MIR156 in other tissues. PARE analysis revealed that miR156 and miR529 possess specific targets in addition to common targets in maize, pointing to functional differences between them. Based on our findings, we developed a method for the rapid identification of miR529 and miR156 family members and uncovered the evolutionary divergence of these families, providing insights into their different regulatory roles in plant growth and development.
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4
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Natarajan P, Ahn E, Reddy UK, Perumal R, Prom LK, Magill C. RNA-Sequencing in Resistant (QL3) and Susceptible (Theis) Sorghum Cultivars Inoculated With Johnsongrass Isolates of Colletotrichum sublineola. Front Genet 2021; 12:722519. [PMID: 34456979 PMCID: PMC8385561 DOI: 10.3389/fgene.2021.722519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 07/22/2021] [Indexed: 12/02/2022] Open
Abstract
Gene expression was analyzed at 0- and 24-h post-inoculation of two inbred sorghum cultivars known to differ in response to inoculation with Colletotrichum sublineola, the fungal pathogen that causes anthracnose. QL3 is reported to have quantitative resistance, while Theis is susceptible to most pathotypes of the pathogen; RNASeq identified over 3,000 specific genes in both cultivars as showing significant changes in expression following inoculation; in all but one gene, the changes in QL3 and Thies were in the same direction. Many other genes showed significant changes in only one of the two cultivars. Overall, more genes were downregulated than upregulated. Differences in changes in expression levels of a few genes suggested potential roles for the difference in disease response between QL3 and Theis, but did not identify known resistance genes. Gene ontology (GO) and pathway enrichment analysis identified upregulation of 23 transcription factor encoding genes as well as genes involved in the production of secondary metabolites, which are part of a typical host defense reaction.
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Affiliation(s)
- Purushothaman Natarajan
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, West Virginia, WV, United States
| | - Ezekiel Ahn
- Department of Plant Pathology and Microbiology, Texas A & M University, College Station, TX, United States
| | - Umesh K Reddy
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, West Virginia, WV, United States
| | - Ramasamy Perumal
- Agricultural Research Center, Kansas State University, Hays, KS, United States
| | - Louis K Prom
- Crop Germplasm Research Unit, USDA-ARS Southern Plains Agricultural Research Center, College Station, TX, United States
| | - Clint Magill
- Department of Plant Pathology and Microbiology, Texas A & M University, College Station, TX, United States
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5
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Endophytic Microbiome Responses to Sulfur Availability in Beta vulgaris (L.). Int J Mol Sci 2021; 22:ijms22137184. [PMID: 34281236 PMCID: PMC8269133 DOI: 10.3390/ijms22137184] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/20/2021] [Accepted: 06/22/2021] [Indexed: 11/17/2022] Open
Abstract
Sulfur is an essential plant macronutrient, and its adequate supply allows an efficient root storage and sugar extractability in sugar beets (Beta vulgaris L.). In this study, we investigated the effect of changes in sulfur availability on the endophytic community structure of sugar beets. Plants were hydroponically grown in a complete nutrient solution (S-supplied), a nutrient solution without MgSO4 (S-deprived), and a nutrient solution without MgSO4 for six days and resupplied with 100 μM MgSO4 for 48 h (S-resupplied). The sulfur status was monitored by inductively coupled plasma ICP–OES, and combustion analysis together with the evaluation of microRNA395 as a biomarker for sulfate status. Metabarcoding of the bacterial 16S rRNA gene was carried out in order to determine leaf endophytic community structure. The Shannon diversity index significantly differed (p < 0.05) between sulfate-supplied and sulfate-deprived seedlings. Validation by Real-Time PCR showed a significant increase (p < 0.05) of Burkholderia spp. in sulfate-deprived plants as compared to sulfate-supplied ones. The study sheds new light on the effects of nutrient deficiency on the microbiome of sugar beet plants.
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6
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Jia W, Lin K, Lou T, Feng J, Lv S, Jiang P, Yi Z, Zhang X, Wang D, Guo Z, Tang Y, Qiu R, Li Y. Comparative analysis of sRNAs, degradome and transcriptomics in sweet sorghum reveals the regulatory roles of miRNAs in Cd accumulation and tolerance. PLANTA 2021; 254:16. [PMID: 34185181 DOI: 10.1007/s00425-021-03669-2] [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: 12/03/2020] [Accepted: 06/20/2021] [Indexed: 06/13/2023]
Abstract
Key miRNAs including sbi-miR169p/q, sbi-miR171g/j, sbi-miR172a/c/d, sbi-miR172e, sbi-miR319a/b, sbi-miR396a/b, miR408, sbi-miR5384, sbi-miR5565e and nov_23 were identified to function in the regulation of Cd accumulation and tolerance. As an energy plant, sweet sorghum shows great potential in the phytoremediation of Cd-contaminated soils. However, few studies have focused on the regulatory roles of miRNAs and their targets under Cd stress. In this study, comparative analysis of sRNAs, degradome and transcriptomics was conducted in high-Cd accumulation (H18) and low-Cd accumulation (L69) genotypes of sweet sorghum. A total of 38 conserved and 23 novel miRNAs with differential expressions were identified under Cd stress or between H18 and L69, and 114 target genes of 41 miRNAs were validated. Furthermore, 25 miRNA-mRNA pairs exhibited negatively correlated expression profiles and sbi-miR172e together with its target might participate in the distinct Cd tolerance between H18 and L69 as well as sbi-miR172a/c/d. Additionally, two groups of them: miR169p/q-nov_23 and miR408 were focused through the co-expression analysis, which might be involved in Cd uptake and tolerance by regulating their targets associated with transmembrane transportation, cytoskeleton activity, cell wall construction and ROS (reactive oxygen species) homeostasis. Further experiments exhibited that cell wall components of H18 and L69 were different when exposed to cadmium, which might be regulated by miR169p/q, miR171g/j, miR319a/b, miR396a/b, miR5384 and miR5565e through their targets. Through this study, we aim to reveal the potential miRNAs involved in sweet sorghum in response to Cd stress and provide references for developing high-Cd accumulation or high Cd-resistant germplasm of sweet sorghum that can be used in phytoremediation.
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Affiliation(s)
- Weitao Jia
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, People's Republic of China
| | - Kangqi Lin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Tengxue Lou
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Juanjuan Feng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
| | - Sulian Lv
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
| | - Ping Jiang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
| | - Ze Yi
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xuan Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Duoliya Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Zijing Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yetao Tang
- Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, People's Republic of China
| | - Rongliang Qiu
- Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, People's Republic of China
| | - Yinxin Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China.
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7
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Muslu T, Biyiklioglu-Kaya S, Akpinar BA, Yuce M, Budak H. Pan-Genome miRNomics in Brachypodium. PLANTS 2021; 10:plants10050991. [PMID: 34065739 PMCID: PMC8156279 DOI: 10.3390/plants10050991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/17/2021] [Accepted: 05/12/2021] [Indexed: 01/14/2023]
Abstract
Pan-genomes are efficient tools for the identification of conserved and varying genomic sequences within lineages of a species. Investigating genetic variations might lead to the discovery of genes present in a subset of lineages, which might contribute into beneficial agronomic traits such as stress resistance or yield. The content of varying genomic regions in the pan-genome could include protein-coding genes as well as microRNA(miRNAs), small non-coding RNAs playing key roles in the regulation of gene expression. In this study, we performed in silico miRNA identification from the genomic sequences of 54 lineages of Brachypodium distachyon, aiming to explore varying miRNA contents and their functional interactions. A total of 115 miRNA families were identified in 54 lineages, 56 of which were found to be present in all lineages. The miRNA families were classified based on their conservation among lineages and potential mRNA targets were identified. Obtaining information about regulatory mechanisms stemming from these miRNAs offers strong potential to provide a better insight into the complex traits that were potentially present in some lineages. Future work could lead us to introduce these traits to different lineages or other economically important plant species in order to promote their survival in different environmental conditions.
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Affiliation(s)
- Tugdem Muslu
- Faculty of Engineering and Natural Sciences, Molecular Biology, Genetics and Bioengineering Program, Sabanci University, Istanbul 34956, Turkey; (T.M.); (S.B.-K.)
| | - Sezgi Biyiklioglu-Kaya
- Faculty of Engineering and Natural Sciences, Molecular Biology, Genetics and Bioengineering Program, Sabanci University, Istanbul 34956, Turkey; (T.M.); (S.B.-K.)
| | | | - Meral Yuce
- Sabanci University SUNUM Nanotechnology Research and Application Centre, Sabanci University, Istanbul 34956, Turkey;
| | - Hikmet Budak
- Montana BioAgriculture, Inc., Missoula, MT 59802, USA;
- Correspondence:
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8
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Sun X, Zheng H, Li J, Liu L, Zhang X, Sui N. Comparative Transcriptome Analysis Reveals New lncRNAs Responding to Salt Stress in Sweet Sorghum. Front Bioeng Biotechnol 2020; 8:331. [PMID: 32351954 PMCID: PMC7174691 DOI: 10.3389/fbioe.2020.00331] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 03/25/2020] [Indexed: 12/18/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) can enhance plant stress resistance by regulating the expression of functional genes. Sweet sorghum is a salt-tolerant energy crop. However, little is known about how lncRNAs in sweet sorghum respond to salt stress. In this study, we identified 126 and 133 differentially expressed lncRNAs in the salt-tolerant M-81E and the salt-sensitive Roma strains, respectively. Salt stress induced three new lncRNAs in M-81E and inhibited two new lncRNAs in Roma. These lncRNAs included lncRNA13472, lncRNA11310, lncRNA2846, lncRNA26929, and lncRNA14798, which potentially function as competitive endogenous RNAs (ceRNAs) that influence plant responses to salt stress by regulating the expression of target genes related to ion transport, protein modification, transcriptional regulation, and material synthesis and transport. Additionally, M-81E had a more complex ceRNA network than Roma. This study provides new information regarding lncRNAs and the complex regulatory network underlying salt-stress responses in sweet sorghum.
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Affiliation(s)
- Xi Sun
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Hongxiang Zheng
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Jinlu Li
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Luning Liu
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.,College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiansheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Na Sui
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
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9
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Nagaraju M, Reddy PS, Kumar SA, Kumar A, Rajasheker G, Rao DM, Kavi Kishor PB. Genome-wide identification and transcriptional profiling of small heat shock protein gene family under diverse abiotic stress conditions in Sorghum bicolor (L.). Int J Biol Macromol 2019; 142:822-834. [PMID: 31622710 DOI: 10.1016/j.ijbiomac.2019.10.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/16/2019] [Accepted: 10/02/2019] [Indexed: 11/24/2022]
Abstract
The small heat shock proteins (sHsps/Hsp20s) are the molecular chaperones that maintain proper folding, trafficking and disaggregation of proteins under diverse abiotic stress conditions. In the present investigation, a genome-wide scan revealed the presence of a total of 47 sHsps in Sorghum bicolor (SbsHsps), distributed across 10 subfamilies, the major subfamily being P (plastid) group with 17 genes. Chromosomes 1 and 3 appear as the hot spot regions for SbsHsps, and majority of them were found acidic, hydrophilic, unstable and intron less. Interestingly, promoter analysis indicated that they are associated with both biotic and abiotic stresses, as well as plant development. Sorghum sHsps exhibited 15 paralogous and 20 orthologous duplications. Expression analysis of 15 genes selected from different subfamilies showed high transcript levels in roots and leaves implying that they are likely to participate in the developmental processes. SbsHsp genes were highly induced by diverse abiotic stresses inferring their critical role in mediating the environmental stress responses. Gene expression data revealed that SbsHsp-02 is a candidate gene expressed in all the tissues under varied stress conditions tested. Our results contribute to the understanding of the complexity of SbsHsp genes and help to analyse them further for functional validation.
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Affiliation(s)
- M Nagaraju
- Department of Genetics, Osmania University, Hyderabad 500 007, India; Biochemistry Division, ICMR-National Institute of Nutrition, Hyderabad 500 007, India
| | - Palakolanu Sudhakar Reddy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, India
| | - S Anil Kumar
- Department of Biotechnology, Vignan's Foundation for Science, Technology and Research, Vadlamudi, Guntur, Andhra Pradesh 522 213, India
| | - Anuj Kumar
- Advance Center for Computational & Applied Biotechnology, Uttarakhand Council for Biotechnology (UCB), Dehradun 248 007, India
| | - G Rajasheker
- Department of Genetics, Osmania University, Hyderabad 500 007, India
| | - D Manohar Rao
- Department of Genetics, Osmania University, Hyderabad 500 007, India.
| | - P B Kavi Kishor
- Department of Genetics, Osmania University, Hyderabad 500 007, India.
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10
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Dhaka N, Sharma S, Vashisht I, Kandpal M, Sharma MK, Sharma R. Small RNA profiling from meiotic and post-meiotic anthers reveals prospective miRNA-target modules for engineering male fertility in sorghum. Genomics 2019; 112:1598-1610. [PMID: 31521711 DOI: 10.1016/j.ygeno.2019.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 08/30/2019] [Accepted: 09/11/2019] [Indexed: 02/06/2023]
Abstract
Understanding male gametophyte development is essential to augment hybrid production in sorghum. Although small RNAs are known to critically influence anther/pollen development, their roles in sorghum reproduction have not been deciphered yet. Here, we report small RNA profiling and high-confidence annotation of microRNAs (miRNAs) from meiotic and post-meiotic anthers in sorghum. We identified 262 miRNAs (82 known and 180 novel), out of which 58 (35 known and 23 novel) exhibited differential expression between two stages. Out of 35 differentially expressed known miRNAs, 13 are known to regulate anther/pollen development in other plant species. We also demonstrated conserved spatiotemporal patterns of 21- and 24-nt phasiRNAs and their respective triggers, miR2118 and miR2275, in sorghum anthers as evidenced in other monocots. miRNA target identification yielded 5622 modules, of which 46 modules comprising 16 known and 8 novel miRNA families with 38 target genes are prospective candidates for engineering male fertility in grasses.
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Affiliation(s)
- Namrata Dhaka
- Crop Genetics & Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067, India
| | - Shalini Sharma
- Crop Genetics & Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067, India
| | - Ira Vashisht
- Crop Genetics & Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067, India
| | - Manu Kandpal
- Crop Genetics & Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067, India
| | - Manoj Kumar Sharma
- Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067, India
| | - Rita Sharma
- Crop Genetics & Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067, India.
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Li YF, Wei K, Wang M, Wang L, Cui J, Zhang D, Guo J, Zhao M, Zheng Y. Identification and Temporal Expression Analysis of Conserved and Novel MicroRNAs in the Leaves of Winter Wheat Grown in the Field. Front Genet 2019; 10:779. [PMID: 31552091 PMCID: PMC6737308 DOI: 10.3389/fgene.2019.00779] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 07/23/2019] [Indexed: 11/28/2022] Open
Abstract
Cold acclimation and vegetative/reproductive transition are two important evolutionary adaptive mechanisms for winter wheat surviving the freezing temperature in winter and successful seeds setting in the next year. MicroRNA (miRNA) is a class of regulatory small RNAs (sRNAs), which plays critical roles in the growth and development of plants. However, the regulation mechanism of miRNAs during cold acclimation and vegetative/reproductive transition of winter wheat is not much understood. In this study, four sRNA libraries from leaves of winter wheat grown in the field at the three-leaf stage, winter dormancy stage, spring green-up stage, and jointing stage were analyzed to identify known and novel miRNAs and to understand their potential roles in the growth and development of winter wheat. We examined miRNA expression using a high-throughput sequencing technique. A total of 373 known, 55 novel, and 27 putative novel miRNAs were identified. Ninety-one miRNAs were found to be differentially expressed at the four stages. Among them, the expression of six known and eight novel miRNAs was significantly suppressed at the winter dormancy stage, whereas the expression levels of seven known and eight novel miRNAs were induced at this stage; three known miRNAs and three novel miRNAs were significantly induced at the spring green-up stage; six known miRNAs were induced at the spring green-up stage and reached the highest expression level at the jointing stage; and 20 known miRNAs and 10 novel miRNAs were significantly induced at the jointing stage. Expression of a number of representative differentially expressed miRNAs was verified using quantitative real-time polymerase chain reaction (qRT-PCR). Potential target genes for known and novel miRNAs were predicted. Moreover, six novel target genes for four Pooideae species-specific miRNAs and two novel miRNAs were verified using the RNA ligase-mediated 5'-rapid amplification of cDNA ends (RLM-5'RACE) technique. These results indicate that miRNAs are key non-coding regulatory factors modulating the growth and development of wheat. Our study provides valuable information for in-depth understanding of the regulatory mechanism of miRNAs in cold acclimation and vegetative/reproductive transition of winter wheat grown in the field.
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Affiliation(s)
- Yong-Fang Li
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Kangning Wei
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Menglei Wang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Li Wang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Junxia Cui
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Daijing Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Junqiang Guo
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, China
| | - Miao Zhao
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Yun Zheng
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
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Galdino JH, Eguiluz M, Guzman F, Margis R. Novel and Conserved miRNAs Among Brazilian Pine and Other Gymnosperms. Front Genet 2019; 10:222. [PMID: 30984236 PMCID: PMC6448024 DOI: 10.3389/fgene.2019.00222] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 02/28/2019] [Indexed: 01/01/2023] Open
Abstract
The knowledge about plant miRNAs has increased exponentially, with thousands of miRNAs been reported in different plant taxa using high throughput sequencing technologies and bioinformatic tools. Nevertheless, several groups of plants remain unexplored, and the gap of knowledge about conifer miRNAs is considerable. There is no sequence or functional information available on miRNAs in Araucariaceae. This group is represented in Brazil by only one species, Araucaria angustifolia, an endangered species known as Brazilian pine. In the present study, Brazilian pine has its transcriptome explored with respect to small RNAs, representing the first description in a member of the Araucariaceae family. The screening for conserved miRNAs in Brazilian pine revealed 115 sequences of 30 miRNA families. A total of 106 precursors sequences were predicted. Forty one comprised conserved miRNAs from 16 families, whereas 65 were annotated as novel miRNAs. The comparison of Brazilian pine precursors with sRNA libraries of other five conifer species indicates that 9 out 65 novel miRNAs are conserved among gymnosperms, while 56 seems to be specific for Brazilian pine or restricted to Araucariaceae family. Analysis comparing novel Brazilian pine miRNAs precursors and Araucaria cunninghamii RNA-seq data identified seven orthologs between both species. Mature miRNA identified by bioinformatics predictions were validated using stem-loop RT-qPCR assays. The expression pattern of conserved and novel miRNAs was analyzed in five different tissues of 3-month-old Araucaria seedlings. The present study provides insights about the nature and composition of miRNAs in an Araucariaceae species, with valuable information on miRNAs diversity and conservation in this taxon.
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Affiliation(s)
- José Henrique Galdino
- Programa de Pós-graduação e Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - Maria Eguiluz
- Programa de Pós-graduação e Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - Frank Guzman
- Programa de Pós-graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - Rogerio Margis
- Programa de Pós-graduação e Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
- Programa de Pós-graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
- Departamento de Biofísica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
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Sanjari S, Shirzadian-Khorramabad R, Shobbar ZS, Shahbazi M. Systematic analysis of NAC transcription factors' gene family and identification of post-flowering drought stress responsive members in sorghum. PLANT CELL REPORTS 2019; 38:361-376. [PMID: 30627770 DOI: 10.1007/s00299-019-02371-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/02/2019] [Indexed: 05/25/2023]
Abstract
SbNAC genes (131) encoding 183 proteins were identified from the sorghum genome and characterized. The expression patterns of SbSNACs were evaluated at three sampling time points under post-flowering drought stress. NAC proteins are specific transcription factors in plants, playing vital roles in development and response to various environmental stresses. Despite the fact that Sorghum bicolor is well-known for its drought-tolerance, it suffers from grain yield loss due to pre and post-flowering drought stress. In the present study, 131 SbNAC genes encoding 183 proteins were identified from the sorghum genome. The phylogenetic trees were constructed based on the NAC domains of sorghum, and also based on sorghum with Arabidopsis and 8 known NAC domains of other plants, which classified the family into 15 and 19 subfamilies, respectively. Based on the obtained results, 13 SbNAC proteins joined the SNAC subfamily, and these proteins are expected to be involved in response to abiotic stresses. Promoter analysis revealed that all SbNAC genes comprise different stress-associated cis-elements in their promoters. UTRs analysis indicated that 101 SbNAC transcripts had upstream open reading frames, while 39 of the transcripts had internal ribosome entry sites in their 5'UTR. Moreover, 298 miRNA target sites were predicted to exist in the UTRs of SbNAC transcripts. The expression patterns of SbSNACs were evaluated in three genotypes at three sampling time points under post-flowering drought stress. Based on the results, it could be suggested that some gene members are involved in response to drought stress at the post-flowering stage since they act as positive or negative transcriptional regulators. Following further functional analyses, some of these genes might be perceived to be promising candidates for breeding programs to enhance drought tolerance in crops.
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Affiliation(s)
- Sepideh Sanjari
- Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | - Reza Shirzadian-Khorramabad
- Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | - Zahra-Sadat Shobbar
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Education and Extension Organization (AREEO), Karaj, Iran.
| | - Maryam Shahbazi
- Department of Molecular Physiology, Agricultural Biotechnology Research Institute of Iran, Education and Extension Organization (AREEO), Karaj, Iran
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Akbudak MA, Filiz E, Kontbay K. DREB2 (dehydration-responsive element-binding protein 2) type transcription factor in sorghum ( Sorghum bicolor): genome-wide identification, characterization and expression profiles under cadmium and salt stresses. 3 Biotech 2018; 8:426. [PMID: 30305995 DOI: 10.1007/s13205-018-1454-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/24/2018] [Indexed: 10/28/2022] Open
Abstract
Biotic and abiotic stresses negatively affect fitness, biomass production, and crop yield in plants. The dehydration-responsive element-binding proteins (DREB) are important transcription factors (TFs), and are induced by abiotic and biotic stresses. In this study, genome-wide identification, in silico sequence, and phylogenetic analyses and expression analyses of DREB2 genes under cadmium (Cd) and salt (NaCl) stresses in sorghum (Sorghum bicolor, Sb) were performed. Six putative SbDREB2 genes were identified in sorghum genome and all contained AP2 domain (PF00847). Nucleotide diversities in SbDREB2 genes were calculated as π: 0.53 and θ: 0.39, respectively. While exon numbers of them were either one or two, length of SbDREB2 proteins ranged from 238 to 388 amino acid residues. Fifty-six cis-acting regulatory elements, which are tissue specific, light, hormone, and stress responsive, were identified in the promotor regions of SbDREB2 genes. Analyses on digital expression data indicated that SbDREB2A and SbDREB2B are more expressed genes than other SbDREB genes in sorghum. Under Cd and NaCl stresses, expressions of SbDREB2 genes were induced at different levels. All SbDREB2 genes in root were up-regulated under salt stress. In case of Cd stress, SbDREB2D gene was particularly up-regulated in leaves and roots. Co-expression analyses revealed four of TFs in co-expression network, indicating that they have roles in transcriptional cascade. Furthermore, five miRNA target regions were identified for four SbDREB2 genes, indicating their roles in post-transcriptional regulation. The predicted 3D structure of SbDREB2 proteins showed some structural divergences and structure overlap between rice and sorghum varied at between 26.58 and 50%. Finally, obtained data could be used in breeding of stress-tolerant plants, particularly genetically engineered DREB2 expressing plants. Findings in this study would also contribute to the understanding of DREB2 genes in plants, especially in sorghum.
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Moradi K, Khalili F. Assessment of pattern expression of miR172 and miR169 in response to drought stress in Echinacea purpurea L. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2018. [DOI: 10.1016/j.bcab.2018.08.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Njaci I, Williams B, Castillo-González C, Dickman MB, Zhang X, Mundree S. Genome-Wide Investigation of the Role of MicroRNAs in Desiccation Tolerance in the Resurrection Grass Tripogon loliiformis. PLANTS (BASEL, SWITZERLAND) 2018; 7:E68. [PMID: 30200279 PMCID: PMC6161015 DOI: 10.3390/plants7030068] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/24/2018] [Accepted: 08/29/2018] [Indexed: 12/15/2022]
Abstract
Drought causes approximately two-thirds of crop and yield loss worldwide. To sustain future generations, there is a need to develop robust crops with enhanced water use efficiency. Resurrection plants are naturally resilient and tolerate up to 95% water loss with the ability to revive upon watering. Stress is genetically encoded and resilient species may garner tolerance by tightly regulating the expression of stress-related genes. MicroRNAs (miRNAs) post-transcriptionally regulate development and other stress response processes in eukaryotes. However, their role in resurrection plant desiccation tolerance is poorly understood. In this study, small RNA sequencing and miRNA expression profiling was conducted using Tripogon loliiformis plants subjected to extreme water deficit conditions. Differentially expressed miRNA profiles, target mRNAs, and their regulatory processes were elucidated. Gene ontology enrichment analysis revealed that development, stress response, and regulation of programmed cell death biological processes; Oxidoreductase and hydrolyase molecular activities; and SPL, MYB, and WRKY transcription factors were targeted by miRNAs during dehydration stress, indicating the indispensable regulatory role of miRNAs in desiccation tolerance. This study provides insights into the molecular mechanisms of desiccation tolerance in the resurrection plant T. loliiformis. This information will be useful in devising strategies for crop improvement on enhanced drought tolerance and water use efficiency.
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Affiliation(s)
- Isaac Njaci
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD 4000, Australia.
| | - Brett Williams
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD 4000, Australia.
| | - Claudia Castillo-González
- Department of Biochemistry and Biophysics, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA.
| | - Martin B Dickman
- Department of Plant Pathology and Microbiology, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA.
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA.
| | - Sagadevan Mundree
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD 4000, Australia.
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18
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Srivastava S, Sharma A. Study of microRNA mediated gene regulation in Striga hermonthica through in-silico approach. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.aggene.2017.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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19
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Li M, Liang Z, He S, Zeng Y, Jing Y, Fang W, Wu K, Wang G, Ning X, Wang L, Li S, Tan H, Tan F. Genome-wide identification of leaf abscission associated microRNAs in sugarcane (Saccharum officinarum L.). BMC Genomics 2017; 18:754. [PMID: 28946845 PMCID: PMC5613641 DOI: 10.1186/s12864-017-4053-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/11/2017] [Indexed: 11/16/2022] Open
Abstract
Background Sugarcane (Saccharum officinarum L.) is an economically important crop, mainly due to the production of sugar and biofuel (Azevedo RA, Carvalho RF, Cia MC, & Gratão PL, Trop Plant Biol 4:42-51, 2011). Grown mainly in tropical and subtropical countries, sugarcane is a highly polyploid plant with up to ten copies of each chromosome, which increases the difficulties of genome assembly and genetic, physiologic and biochemical analyses. The increasing demands of sugar and the increasing cost of sugarcane harvest require sugarcane varieties which can shed their leaves during the maturity time, so it is important to study the mechanism of leaf abscission in sugarcane. Results To improve the understanding of miRNA roles in sugarcane leaf abscission, we reported the genome-wide characterization of miRNAs and their putative targets in sugarcane using deep sequencing for six small RNA libraries. In total, 93 conserved miRNAs and 454 novel miRNAs were identified in sugarcane using previously reported transcriptome as reference. Among them, 25 up-regulated and 13 down-regulated miRNAs were identified in leaf abscission sugarcane plants (LASP) compared to leaf packaging sugarcane plants (LPSP). Target prediction revealed several miRNA-mRNA modules including miR156-SPL, miR319-TPR2, miR396-GRF and miR408-LAC3 might be involved in the sugarcane leaf abscission. KEGG pathway enrichment analysis showed differentially expressed miRNAs may regulate pathways like “plant hormone signal transduction” and “plant-pathogen interaction”, which is consistent with previous transcriptome study. In addition, we identified 96 variant miRNAs with 135 single nucleotide polymorphisms (SNPs). The expression of sugarcane miRNAs and variant miRNAs were confirmed by qRT-PCR. We identified a possible poaceae specific miRNA called miR5384 for the first time in sugarcane. Conclusions We not only reported miR5384, a possible poaceae specific miRNA, for the first time in sugarcane but also presented some miRNA-mRNA modules including miR156-SPL, miR319-TPR2, miR396-GRF and miR408-LAC in sugarcane. These modules might be involved in the regulation of sugarcane leaf abscission during the maturity time. All of these findings may lay ground work for future application of sugarcane breeding program and benefit research studies of sugarcane miRNAs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4053-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ming Li
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China.
| | - Zhaoxu Liang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Shanshan He
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Yuan Zeng
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Yan Jing
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Weikuan Fang
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Kaichao Wu
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Guanyu Wang
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Xia Ning
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Lunwang Wang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Song Li
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Hongwei Tan
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Fang Tan
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
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Bai B, Shi B, Hou N, Cao Y, Meng Y, Bian H, Zhu M, Han N. microRNAs participate in gene expression regulation and phytohormone cross-talk in barley embryo during seed development and germination. BMC PLANT BIOLOGY 2017; 17:150. [PMID: 28877679 PMCID: PMC5586051 DOI: 10.1186/s12870-017-1095-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 08/22/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND Small RNA and degradome sequencing have identified a large number of miRNA-target pairs in plant seeds. However, detailed spatial and temporal studies of miRNA-mediated regulation, which can reflect links between seed development and germination are still lacking. RESULTS In this study, we extended our investigation on miRNAs-involved gene regulation by a combined analysis of seed maturation and germination in barley. Through bioinformatics analysis of small RNA sequencing data, a total of 1324 known miRNA families and 448 novel miRNA candidates were identified. Of those, 16 known miRNAs with 40 target genes, and three novel miRNAs with four target genes were confirmed based on degradome sequencing data. Conserved miRNA families such as miR156, miR168, miR166, miR167, and miR894 were highly expressed in embryos of developing and germinating seeds. A barley-specific miRNA, miR5071, which was predicted to target an OsMLA10-like gene, accumulated at a high level, suggesting its involvement in defence response during these two developmental stages. Based on target prediction and Kyoto Encyclopedia of Genes and Genomes analysis of putative targets, nine highly expressed miRNAs were found to be related to phytohormone signalling and hormone cross-talk. Northern blot and qRT-PCR analysis showed that these miRNAs displayed differential expression patterns during seed development and germination, indicating their different roles in hormone signalling pathways. In addition, we showed that miR393 affected seed development through targeting two genes encoding the auxin receptors TIR1/AFBs in barley, as over-expression of miR393 led to an increased length-width ratio of seeds, whereas target mimic (MIM393)-mediated inhibition of its activity decreased the 1000-grain weight of seeds. Furthermore, the expression of auxin-responsive genes, abscisic acid- and gibberellic acid-related genes was altered in miR393 misexpression lines during germination and early seedling growth. CONCLUSIONS Our work indicates that miRNA-target pairs participate in gene expression regulation and hormone interaction in barley embryo and provides evidence that miR393-mediated auxin response regulation affects grain development and influences gibberellic acid and abscisic acid homeostasis during germination.
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Affiliation(s)
- Bin Bai
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou 310058 China
| | - Bo Shi
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou 310058 China
| | - Ning Hou
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou 310058 China
| | - Yanli Cao
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou 310058 China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, Hangzhou 310036 China
| | - Hongwu Bian
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou 310058 China
| | - Muyuan Zhu
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou 310058 China
| | - Ning Han
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou 310058 China
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Ghorecha V, Zheng Y, Liu L, Sunkar R, Krishnayya NSR. MicroRNA dynamics in a wild and cultivated species of Convolvulaceae exposed to drought stress. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:291-300. [PMID: 28461718 PMCID: PMC5391358 DOI: 10.1007/s12298-017-0426-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 02/14/2017] [Accepted: 03/03/2017] [Indexed: 05/14/2023]
Abstract
Agricultural productivity is severely hampered by drought in many parts of the globe. It is well-known that wild plant species can tolerate drought better when compared with their closely related cultivated plant species. Better drought adaptation of wild species over cultivated ones is accounted for their ability to differentially regulate gene expression. miRNAs, known to regulate gene expression at the post-transcriptional level, are admitted to play an important role in plant adaptation to stresses. This study aims at evaluating miRNA dynamics in a drought-tolerant wild Ipomoea campanulata L. and drought-sensitive cultivated Jacquemontia pentantha (Jacq.) of the family Convolvulaceae under ex situ drought. Sequencing profiles revealed that 34 conserved miRNA families were analogous between the two species. Drought altered expression levels of several of these miRNAs in both the species. Drought-tolerant I. campanulata showed upregulation of miR398, miR168, miR858, miR162 and miR408, while miR394 and miR171 were downregulated. Drought-sensitive J. pentantha showed upregulation of miR394, miR156, miR160, miR164, miR167, miR172, miR319, miR395, miR396, miR403 and downregulation of miR157. Basal miRNA levels and their drought mediated regulation were very different between the two species. Differential drought sensitivities of these two plant species can be attributed to these innate variations in miRNA levels and their expression.
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Affiliation(s)
- Vallabhi Ghorecha
- Ecology Laboratory, Botany Department, Faculty of Science, M.S. University of Baroda, Baroda, 390002 India
| | - Yun Zheng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727, South Jingming Road, Kunming, 650500 Yunnan China
| | - Li Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727, South Jingming Road, Kunming, 650500 Yunnan China
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74074 USA
| | - N. S. R. Krishnayya
- Ecology Laboratory, Botany Department, Faculty of Science, M.S. University of Baroda, Baroda, 390002 India
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Mangrauthia SK, Bhogireddy S, Agarwal S, Prasanth VV, Voleti SR, Neelamraju S, Subrahmanyam D. Genome-wide changes in microRNA expression during short and prolonged heat stress and recovery in contrasting rice cultivars. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2399-2412. [PMID: 28407080 PMCID: PMC5447883 DOI: 10.1093/jxb/erx111] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
MicroRNAs (miRNAs) are known to regulate expression of genes under stress. We report here the deep sequencing of small RNAs expressed during control, short and prolonged heat stress and recovery. Genome-wide identification of miRNAs in tolerant (Nagina 22) and susceptible (Vandana) rice cultivars was performed in 16 samples representing root and shoot of 13-day-old seedlings. The expression profile of miRNAs was analysed in 36 pairwise combinations to identify the genotype-, treatment- and tissue-dependent expression of miRNAs. Small-RNA sequencing of 16 libraries yielded ~271 million high-quality raw sequences; 162 miRNA families were identified. The highly expressed miRNAs in rice tissues were miR166, miR168, miR1425, miR529, mR162, miR1876, and miR1862. Expression of osa-miR1436, osa-miR5076, osa-miR5161, and osa-miR6253 was observed only in stressed tissue of both genotypes indicating their general role in heat stress response. Expression of osa-miR1439, osa-miR1848, osa-miR2096, osa-miR2106, osa-miR2875, osa-miR3981, osa-miR5079, osa-miR5151, osa-miR5484, osa-miR5792, and osa-miR5812 was observed only in Nagina 22 during high temperature, suggesting a specific role of these miRNAs in heat stress tolerance. This study provides details of the repertoire of miRNAs expressed in root and shoot of heat susceptible and tolerant rice genotypes under heat stress and recovery.
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Affiliation(s)
| | | | - Surekha Agarwal
- ICAR-Indian Institute of Rice Research, Hyderabad 500030,India
| | | | - S R Voleti
- ICAR-Indian Institute of Rice Research, Hyderabad 500030,India
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Djami-Tchatchou AT, Sanan-Mishra N, Ntushelo K, Dubery IA. Functional Roles of microRNAs in Agronomically Important Plants-Potential as Targets for Crop Improvement and Protection. FRONTIERS IN PLANT SCIENCE 2017; 8:378. [PMID: 28382044 PMCID: PMC5360763 DOI: 10.3389/fpls.2017.00378] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/06/2017] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs that have recently emerged as important regulators of gene expression, mainly through cleavage and/or translation inhibition of the target mRNAs during or after transcription. miRNAs play important roles by regulating a multitude of biological processes in plants which include maintenance of genome integrity, development, metabolism, and adaptive responses toward environmental stresses. The increasing population of the world and their food demands requires focused efforts for the improvement of crop plants to ensure sustainable food production. Manipulation of mRNA transcript abundance via miRNA control provides a unique strategy for modulating differential plant gene expression and miRNAs are thus emerging as the next generation targets for genetic engineering for improvement of the agronomic properties of crops. However, a deeper understanding of its potential and the mechanisms involved will facilitate the design of suitable strategies to obtain the desirable traits with minimum trade-offs in the modified crops. In this regard, this review highlights the diverse roles of conserved and newly identified miRNAs in various food and industrial crops and recent advances made in the uses of miRNAs to improve plants of agronomically importance so as to significantly enhance crop yields and increase tolerance to various environmental stress agents of biotic-or abiotic origin.
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Affiliation(s)
- Arnaud T. Djami-Tchatchou
- Department of Agriculture and Animal Health, University of South Africa (Florida Campus)Pretoria, South Africa
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and BiotechnologyNew Delhi, India
| | - Khayalethu Ntushelo
- Department of Agriculture and Animal Health, University of South Africa (Florida Campus)Pretoria, South Africa
| | - Ian A. Dubery
- Department of Biochemistry, University of Johannesburg (Auckland Park Kingsway Campus)Johannesburg, South Africa
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Abstract
Background Emerging evidence indicates that plant miRNAs can present within human circulating system through dietary intake and regulate human gene expression. Hence we deduced that comestible plants miRNAs can be identified in the public available small RNA sequencing data sets. Results In this study, we identified abundant plant miRNAs sequences from 410 human plasma small RNA sequencing data sets. One particular plant miRNA miR2910, conserved in fruits and vegetables, was found to present in high relative amount in the plasma samples. This miRNA, with same 6mer and 7mer-A1 target seed sequences as hsa-miR-4259 and hsa-miR-4715-5p, was predicted to target human JAK-STAT signaling pathway gene SPRY4 and transcription regulation genes. Conclusions Through analysis of public available plasma small RNA sequencing data, we found the supporting evidence for the plant miRNAs cross kingdom RNAi within human circulating system. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3502-3) contains supplementary material, which is available to authorized users.
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Zheng Y, Hivrale V, Zhang X, Valliyodan B, Lelandais-Brière C, Farmer AD, May GD, Crespi M, Nguyen HT, Sunkar R. Small RNA profiles in soybean primary root tips under water deficit. BMC SYSTEMS BIOLOGY 2016; 10:126. [PMID: 28105955 PMCID: PMC5249032 DOI: 10.1186/s12918-016-0374-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Soybean (Glycine max) production is significantly hampered by frequent droughts in many regions of the world including the United States. Identifying microRNA (miRNA)-controlled posttranscriptional gene regulation under drought will enhance our understanding of molecular basis of drought tolerance in this important cash crop. Indeed, miRNA profiles in soybean exposed to drought were studied but not from the primary root tips, which is not only a main zone of water uptake but also critical for water stress sensing and signaling. METHODS Here we report miRNA profiles specifically from well-watered and water-stressed primary root tips (0 to 8 mm from the root apex) of soybean. Small RNA sequencing confirmed the expression of vastly diverse miRNA (303 individual miRNAs) population, and, importantly several conserved miRNAs were abundantly expressed in primary root tips. RESULTS Notably, 12 highly conserved miRNA families were differentially regulated in response to water-deficit; six were upregulated while six others were downregulated at least by one fold (log2) change. Differentially regulated soybean miRNAs are targeting genes include auxin response factors, Cu/Zn Superoxide dismutases, laccases and plantacyanin and several others. CONCLUSIONS These results highlighted the importance of miRNAs in primary root tips both under control and water-deficit conditions; under control conditions, miRNAs could be important for cell division, cell elongation and maintenance of the root apical meristem activity including quiescent centre whereas under water stress differentially regulated miRNAs could decrease auxin signaling and oxidative stress as well as other metabolic processes that save energy and water.
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Affiliation(s)
- Yun Zheng
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Vandana Hivrale
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Xiaotuo Zhang
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Babu Valliyodan
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Christine Lelandais-Brière
- Institut of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University of "Paris-Sud", Batiment 630, 91405, Orsay, France
- Institut of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University of "Paris-Diderot", Sorbonne Paris-Cité, 91405 Orsay,, Paris, France
| | - Andrew D Farmer
- National Center for Genome Resources, Santa Fe, New Mexico, NM, 87505, USA
| | - Gregory D May
- National Center for Genome Resources, Santa Fe, New Mexico, NM, 87505, USA
- Present address: Pioneer Hi-Bred International, Inc, Johnston, IA, 50131, USA
| | - Martin Crespi
- Institut of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University of "Paris-Sud", Batiment 630, 91405, Orsay, France
- Institut of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University of "Paris-Diderot", Sorbonne Paris-Cité, 91405 Orsay,, Paris, France
| | - Henry T Nguyen
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA.
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Hamza NB, Sharma N, Tripathi A, Sanan-Mishra N. MicroRNA expression profiles in response to drought stress in Sorghum bicolor. Gene Expr Patterns 2016; 20:88-98. [PMID: 26772909 DOI: 10.1016/j.gep.2016.01.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 12/18/2015] [Accepted: 01/04/2016] [Indexed: 01/08/2023]
Abstract
The regulatory role of small non-coding RNAs that are 20-24 nucleotides in length has become the foremost area of research for biologists. A major class of small RNAs represented by the microRNAs (miRNAs), has been implicated in various aspects of plant development including leaf pattering, meristem function, root patterning etc. Recent findings support that miRNAs are regulated by drought and other abiotic stresses in various plant species. In this study, were report the expression profiling of 8 known abiotic stress deregulated miRNAs in 11 elite sorghum genotypes, under watered and drought conditions. Significant deregulation was observed with miR396, miR393, miR397-5p, miR166, miR167 and miR168. Among these, the expression levels of sbi-miR396 and sbi-miR398 were the highest in all the genotypes. The expression of sbi-miR396 was maximum in the grain sorghum HSD3226 under well-watered conditions and the profile shifted towards HSD3221 under drought stress. Forage accessions, N98 and Atlas, showed an opposite behavior in expression patterns of miR397-5p in drought physiologies. Such dynamic expression patterns could be indicative of prevailing drought tolerant mechanisms present in these sorghum accessions. This data provides insights into sorghum miRNAs which may have potential use in improving drought tolerance in sorghum and other cereal crops.
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Affiliation(s)
- Nada Babiker Hamza
- Department of Molecular Biology, Commission for Biotechnology and Genetic Engineering, National Center for Research, P.O. Box: 2404, Khartoum, Sudan.
| | - Neha Sharma
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, ArunaAsaf Ali Marg, New Delhi, 110067, India
| | - Anita Tripathi
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, ArunaAsaf Ali Marg, New Delhi, 110067, India
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, ArunaAsaf Ali Marg, New Delhi, 110067, India.
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Srivastava S, Zheng Y, Kudapa H, Jagadeeswaran G, Hivrale V, Varshney RK, Sunkar R. High throughput sequencing of small RNA component of leaves and inflorescence revealed conserved and novel miRNAs as well as phasiRNA loci in chickpea. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 235:46-57. [PMID: 25900565 DOI: 10.1016/j.plantsci.2015.03.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 02/27/2015] [Accepted: 03/03/2015] [Indexed: 05/04/2023]
Abstract
Among legumes, chickpea (Cicer arietinum L.) is the second most important crop after soybean. MicroRNAs (miRNAs) play important roles by regulating target gene expression important for plant development and tolerance to stress conditions. Additionally, recently discovered phased siRNAs (phasiRNAs), a new class of small RNAs, are abundantly produced in legumes. Nevertheless, little is known about these regulatory molecules in chickpea. The small RNA population was sequenced from leaves and flowers of chickpea to identify conserved and novel miRNAs as well as phasiRNAs/phasiRNA loci. Bioinformatics analysis revealed 157 miRNA loci for the 96 highly conserved and known miRNA homologs belonging to 38 miRNA families in chickpea. Furthermore, 20 novel miRNAs belonging to 17 miRNA families were identified. Sequence analysis revealed approximately 60 phasiRNA loci. Potential target genes likely to be regulated by these miRNAs were predicted and some were confirmed by modified 5' RACE assay. Predicted targets are mostly transcription factors that might be important for developmental processes, and others include superoxide dismutases, plantacyanin, laccases and F-box proteins that could participate in stress responses and protein degradation. Overall, this study provides an inventory of miRNA-target gene interactions for chickpea, useful for the comparative analysis of small RNAs among legumes.
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Affiliation(s)
- Sangeeta Srivastava
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078 USA
| | - Yun Zheng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727, South Jingming Road, Kunming, Yunnan 650500, China
| | - Himabindu Kudapa
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502324, India
| | - Guru Jagadeeswaran
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078 USA
| | - Vandana Hivrale
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078 USA
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502324, India; School of Plant Biology and Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078 USA.
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28
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Zheng LL, Qu LH. Application of microRNA gene resources in the improvement of agronomic traits in rice. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:329-36. [PMID: 25583449 DOI: 10.1111/pbi.12321] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/02/2014] [Accepted: 12/02/2014] [Indexed: 05/20/2023]
Abstract
microRNAs (miRNAs) are important nonprotein-coding genes that are involved in almost all biological processes, including cell differentiation and fate determination, developmental regulation, and immune responses. Investigations have shown that some miRNAs can highly affect plant agricultural traits, including virus resistance, nematode resistance, drought and salinity tolerance, heavy metal detoxification, biomass yield, grain yield, fruit development and flower development. Therefore, these miRNAs are considered a newly identified gene resource for the genetic improvement of crops. In this review, we will summarize the recent findings of the rice miRNA-directed regulatory network, which controls agronomic traits such as yield, quality and stress tolerance, and explore the outlook for the uses of these miRNA-associated traits in rice biotechnology.
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Affiliation(s)
- Ling-Ling Zheng
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, China
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29
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Trumbo JL, Zhang B, Stewart CN. Manipulating microRNAs for improved biomass and biofuels from plant feedstocks. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:337-54. [PMID: 25707745 DOI: 10.1111/pbi.12319] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 11/25/2014] [Accepted: 11/29/2014] [Indexed: 05/22/2023]
Abstract
Petroleum-based fuels are nonrenewable and unsustainable. Renewable sources of energy, such as lignocellulosic biofuels and plant metabolite-based drop-in fuels, can offset fossil fuel use and reverse environmental degradation through carbon sequestration. Despite these benefits, the lignocellulosic biofuels industry still faces many challenges, including the availability of economically viable crop plants. Cell wall recalcitrance is a major economic barrier for lignocellulosic biofuels production from biomass crops. Sustainability and biomass yield are two additional, yet interrelated, foci for biomass crop improvement. Many scientists are searching for solutions to these problems within biomass crop genomes. MicroRNAs (miRNAs) are involved in almost all biological and metabolic process in plants including plant development, cell wall biosynthesis and plant stress responses. Because of the broad functions of their targets (e.g. auxin response factors), the alteration of plant miRNA expression often results in pleiotropic effects. A specific miRNA usually regulates a biologically relevant bioenergy trait. For example, relatively low miR156 overexpression leads to a transgenic feedstock with enhanced biomass and decreased recalcitrance. miRNAs have been overexpressed in dedicated bioenergy feedstocks such as poplar and switchgrass yielding promising results for lignin reduction, increased plant biomass, the timing of flowering and response to harsh environments. In this review, we present the status of miRNA-related research in several major biofuel crops and relevant model plants. We critically assess published research and suggest next steps for miRNA manipulation in feedstocks for increased biomass and sustainability for biofuels and bioproducts.
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Affiliation(s)
- Jennifer Lynn Trumbo
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, USA; Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
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30
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Katiyar A, Smita S, Muthusamy SK, Chinnusamy V, Pandey DM, Bansal KC. Identification of novel drought-responsive microRNAs and trans-acting siRNAs from Sorghum bicolor (L.) Moench by high-throughput sequencing analysis. FRONTIERS IN PLANT SCIENCE 2015; 6:506. [PMID: 26236318 PMCID: PMC4504434 DOI: 10.3389/fpls.2015.00506] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 06/23/2015] [Indexed: 05/03/2023]
Abstract
Small non-coding RNAs (sRNAs) namely microRNAs (miRNAs) and trans-acting small interfering RNAs (tasi-RNAs) play a crucial role in post-transcriptional regulation of gene expression and thus the control plant development and stress responses. In order to identify drought-responsive miRNAs and tasi-RNAs in sorghum, we constructed small RNA libraries from a drought tolerant (M35-1) and susceptible (C43) sorghum genotypes grown under control and drought stress conditions, and sequenced by Illumina Genome Analyzer IIx. Ninety seven conserved and 526 novel miRNAs representing 472 unique miRNA families were identified from sorghum. Ninety-six unique miRNAs were found to be regulated by drought stress, of which 32 were up- and 49 were down-regulated (fold change ≥ 2 or ≤ -2) at least in one genotype, while the remaining 15 miRNAs showed contrasting drought-regulated expression pattern between genotypes. A maximum of 17 and 18 miRNAs was differentially regulated under drought stress condition in the sensitive and tolerant genotypes, respectively. These results suggest that genotype dependent stress responsive regulation of miRNAs may contribute, at least in part, to the differential drought tolerance of sorghum genotypes. We also identified two miR390-directed TAS3 gene homologs and the auxin response factors as tasi-RNA targets. We predicted more than 1300 unique target genes for the novel and conserved miRNAs. These target genes were predicted to be involved in different cellular, metabolic, response to stimulus, biological regulation, and developmental processes. Genome-wide identification of stress-responsive miRNAs, tasi-RNAs and their targets identified in this study will be useful in unraveling the molecular mechanisms underlying drought stress responses and genetic improvement of biomass production and stress tolerance in sorghum.
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Affiliation(s)
- Amit Katiyar
- Indian Council of Agricultural Research-National Bureau of Plant Genetic ResourcesNew Delhi, India
- Department of Biotechnology, Birla Institute of Technology, MesraRanchi, India
| | - Shuchi Smita
- Indian Council of Agricultural Research-National Bureau of Plant Genetic ResourcesNew Delhi, India
- Department of Biotechnology, Birla Institute of Technology, MesraRanchi, India
| | - Senthilkumar K. Muthusamy
- Indian Council of Agricultural Research-National Research Centre on Plant BiotechnologyNew Delhi, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, Indian Council of Agricultural Research-Indian Agricultural Research InstituteNew Delhi, India
| | - Dev M. Pandey
- Department of Biotechnology, Birla Institute of Technology, MesraRanchi, India
| | - Kailash C. Bansal
- Indian Council of Agricultural Research-National Bureau of Plant Genetic ResourcesNew Delhi, India
- *Correspondence: Kailash C. Bansal, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources (NBPGR), IARI Pusa Campus, New Delhi 110012, India
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31
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Feng H, Wang B, Zhang Q, Fu Y, Huang L, Wang X, Kang Z. Exploration of microRNAs and their targets engaging in the resistance interaction between wheat and stripe rust. FRONTIERS IN PLANT SCIENCE 2015; 6:469. [PMID: 26175740 PMCID: PMC4485317 DOI: 10.3389/fpls.2015.00469] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 06/12/2015] [Indexed: 05/02/2023]
Abstract
Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat worldwide. miRNAs are important regulators, they play very central roles in plant organ development, vegetable phase change and defense responses. In this study, two miRNA libraries from wheat cultivar Xingzi 9104 (XZ) challenged with the avirulent Pst race CYR32 and sterile water were constructed, respectively. A total of 596 miRNA candidates were obtained. 420 wheat-specific candidate miRNAs were screened in adult plants challenged with Pst using microarray-based analyses. We analyzed the abundance of candidate miRNAs, and the levels of a subset of candidate miRNAs were determined by quantitative real time PCR (qRT-PCR). The qRT-PCR results indicated that some miRNAs were involved in the incompatible interaction between wheat and Pst. In addition, we identified some miRNAs differentially expressed in different leaves. Additionally, the target genes of wheat miRNAs were confirmed by using degradome sequencing technology. Most of the annotated target genes are related to signal transduction, energy metabolism, and other functions. We selected some target genes for relative expression analysis using qRT-PCR, and found that RabGAP/TBC domain-containing protein, zinc finger protein and Cysteine-rich receptor-like protein kinase 41 may play important role in the incompatible interaction between XZ and CYR32. Intriguingly, miRNAs and target gene seem to form a complicated regulation network that regulates the wheat-Pst interaction. Our data provide the foundation for evaluating the important regulatory roles of miRNAs in the wheat-Pst interaction.
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Affiliation(s)
- Hao Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Bing Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Qiong Zhang
- College of Life Sciences, Northwest A&F UniversityYangling, China
| | - Yanping Fu
- College of Life Sciences, Northwest A&F UniversityYangling, China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Xiaojie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F UniversityYangling, China
- *Correspondence: Zhensheng Kang and Xiaojie Wang, State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3#, Yangling, Shaanxi 712100, China ;
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F UniversityYangling, China
- *Correspondence: Zhensheng Kang and Xiaojie Wang, State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3#, Yangling, Shaanxi 712100, China ;
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Jagadeeswaran G, Li YF, Sunkar R. Redox signaling mediates the expression of a sulfate-deprivation-inducible microRNA395 in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 77:85-96. [PMID: 24164591 DOI: 10.1111/tpj.12364] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 10/09/2013] [Accepted: 10/18/2013] [Indexed: 05/07/2023]
Abstract
MicroRNA395 (miR395) is a conserved miRNA that targets a low-affinity sulfate transporter (AST68) and three ATP sulfurylases (APS1, APS3 and APS4) in higher plants. In this study, At2g28780 was confirmed as another target of miR395 in Arabidopsis. Interestingly, several dicots contained genes homologous to At2g28780 and a cognate miR395 complementary site but possess a gradient of mismatches at the target site. It is well established that miR395 is induced during S deprivation in Arabidopsis; however, the signaling pathways that mediate this regulation are unknown. Several findings in the present study demonstrate that redox signaling plays an important role in induction of miR395 during S deprivation. These include the following results: (i) glutathione (GSH) supplementation suppressed miR395 induction in S-deprived plants (ii) miR395 is induced in Arabidopsis seedlings exposed to Arsenate or Cu(2+) , which induces oxidative stress (iii), S deprivation-induced oxidative stress, and (iv) compromised induction of miR395 during S deprivation in cad2 mutant (deficient in GSH biosynthesis) that is defective in glutaredoxin-dependent redox signaling and ntra/ntrb (defective in thioredoxin reductases a and b) double mutants that are defective in thioredoxin-dependent redox signaling. Collectively, these findings strongly support the involvement of redox signaling in inducing the expression of miR395 during S deprivation in Arabidopsis.
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Affiliation(s)
- Guru Jagadeeswaran
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 740748, USA
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Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon. Genome Biol 2013; 14:R145. [PMID: 24367943 PMCID: PMC4053937 DOI: 10.1186/gb-2013-14-12-r145] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 12/24/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The wild grass Brachypodium distachyon has emerged as a model system for temperate grasses and biofuel plants. However, the global analysis of miRNAs, molecules known to be key for eukaryotic gene regulation, has been limited in B. distachyon to studies examining a few samples or that rely on computational predictions. Similarly an in-depth global analysis of miRNA-mediated target cleavage using parallel analysis of RNA ends (PARE) data is lacking in B. distachyon. RESULTS B. distachyon small RNAs were cloned and deeply sequenced from 17 libraries that represent different tissues and stresses. Using a computational pipeline, we identified 116 miRNAs including not only conserved miRNAs that have not been reported in B. distachyon, but also non-conserved miRNAs that were not found in other plants. To investigate miRNA-mediated cleavage function, four PARE libraries were constructed from key tissues and sequenced to a total depth of approximately 70 million sequences. The roughly 5 million distinct genome-matched sequences that resulted represent an extensive dataset for analyzing small RNA-guided cleavage events. Analysis of the PARE and miRNA data provided experimental evidence for miRNA-mediated cleavage of 264 sites in predicted miRNA targets. In addition, PARE analysis revealed that differentially expressed miRNAs in the same family guide specific target RNA cleavage in a correspondingly tissue-preferential manner. CONCLUSIONS B. distachyon miRNAs and target RNAs were experimentally identified and analyzed. Knowledge gained from this study should provide insights into the roles of miRNAs and the regulation of their targets in B. distachyon and related plants.
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Yi F, Xie S, Liu Y, Qi X, Yu J. Genome-wide characterization of microRNA in foxtail millet (Setaria italica). BMC PLANT BIOLOGY 2013; 13:212. [PMID: 24330712 PMCID: PMC3878754 DOI: 10.1186/1471-2229-13-212] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 11/27/2013] [Indexed: 05/23/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are a class of short non-coding, endogenous RNAs that play key roles in many biological processes in both animals and plants. Although many miRNAs have been identified in a large number of organisms, the miRNAs in foxtail millet (Setaria italica) have, until now, been poorly understood. RESULTS In this study, two replicate small RNA libraries from foxtail millet shoots were sequenced, and 40 million reads representing over 10 million unique sequences were generated. We identified 43 known miRNAs, 172 novel miRNAs and 2 mirtron precursor candidates in foxtail millet. Some miRNA*s of the known and novel miRNAs were detected as well. Further, eight novel miRNAs were validated by stem-loop RT-PCR. Potential targets of the foxtail millet miRNAs were predicted based on our strict criteria. Of the predicted target genes, 79% (351) had functional annotations in InterPro and GO analyses, indicating the targets of the miRNAs were involved in a wide range of regulatory functions and some specific biological processes. A total of 69 pairs of syntenic miRNA precursors that were conserved between foxtail millet and sorghum were found. Additionally, stem-loop RT-PCR was conducted to confirm the tissue-specific expression of some miRNAs in the four tissues identified by deep-sequencing. CONCLUSIONS We predicted, for the first time, 215 miRNAs and 447 miRNA targets in foxtail millet at a genome-wide level. The precursors, expression levels, miRNA* sequences, target functions, conservation, and evolution of miRNAs we identified were investigated. Some of the novel foxtail millet miRNAs and miRNA targets were validated experimentally.
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Affiliation(s)
- Fei Yi
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shaojun Xie
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yuwei Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xin Qi
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jingjuan Yu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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Turner M, Adhikari S, Subramanian S. Optimizing stem-loop qPCR assays through multiplexed cDNA synthesis of U6 and miRNAs. PLANT SIGNALING & BEHAVIOR 2013; 8:24918. [PMID: 23673353 PMCID: PMC4010539 DOI: 10.4161/psb.24918] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 05/03/2013] [Indexed: 05/18/2023]
Abstract
We recently reported that hairpin (or stem-loop) priming is better-suited than polyA tailing to generate cDNA for plant microRNA qPCR. One major limitation of this method is the need to perform individual cDNA synthesis reactions for the reference gene and test miRNAs. Here, we report a novel fusion primer that allows multiplexed hairpin cDNA synthesis of the most-commonly used reference gene, nucleolar small RNA U6, together with test miRNAs. We also propose the use of miR1515 as a house keeping control for tropical legumes. We show that multiplexed cDNA synthesis does not result in loss of sensitivity and reduces the amount of RNA required for miRNA gene expression assays.
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Affiliation(s)
- Marie Turner
- Department of Plant Science; South Dakota State University; Brookings, SD USA
| | - Sajag Adhikari
- Department of Plant Science; South Dakota State University; Brookings, SD USA
| | - Senthil Subramanian
- Department of Plant Science; South Dakota State University; Brookings, SD USA
- Department of Biology & Microbiology; South Dakota State University; Brookings, SD USA
- Correspondence to: Senthil Subramanian,
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Li YF, Zheng Y, Jagadeeswaran G, Sunkar R. Characterization of small RNAs and their target genes in wheat seedlings using sequencing-based approaches. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 203-204:17-24. [PMID: 23415324 DOI: 10.1016/j.plantsci.2012.12.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 12/20/2012] [Accepted: 12/23/2012] [Indexed: 05/24/2023]
Abstract
Wheat is the most highly cultivated plant species for its grain production throughout the world. Because small RNA-dependent gene regulation is critical for successful completion of plant life cycle including its productivity, identification of not only miRNAs but also confirming their targets in wheat is important. To identify small RNAs including novel miRNAs as well as miRNA targets in wheat, we constructed small RNA and degradome libraries from wheat seedlings. Small RNA analysis resulted in identification of most conserved miRNAs including novel miRNAs that can be grouped into 32 miRNA families. The sequence analysis also led to the characterization of two abundantly expressed rRNA-derived small RNAs. To identify miRNA targets, degradome library was sequenced and the bioinformatic analysis confirmed 53 genes as targets for miRNAs and Tas3-siRNAs. Degradome analysis also confirmed a conserved fine-tuning mechanism of Tas3-siRNA abundance by siRNA-mediated silencing of TAS3 transcripts in diverse plant species. These findings added additional information to the small RNA knowledge-base in wheat.
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Affiliation(s)
- Yong-Fang Li
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
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Carnavale Bottino M, Rosario S, Grativol C, Thiebaut F, Rojas CA, Farrineli L, Hemerly AS, Ferreira PCG. High-throughput sequencing of small RNA transcriptome reveals salt stress regulated microRNAs in sugarcane. PLoS One 2013; 8:e59423. [PMID: 23544066 PMCID: PMC3609749 DOI: 10.1371/journal.pone.0059423] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 02/14/2013] [Indexed: 12/15/2022] Open
Abstract
Salt stress is a primary cause of crop losses worldwide, and it has been the subject of intense investigation to unravel the complex mechanisms responsible for salinity tolerance. MicroRNA is implicated in many developmental processes and in responses to various abiotic stresses, playing pivotal roles in plant adaptation. Deep sequencing technology was chosen to determine the small RNA transcriptome of Saccharum sp cultivars grown on saline conditions. We constructed four small RNAs libraries prepared from plants grown on hydroponic culture submitted to 170 mM NaCl and harvested after 1 h, 6 hs and 24 hs. Each library was sequenced individually and together generated more than 50 million short reads. Ninety-eight conserved miRNAs and 33 miRNAs* were identified by bioinformatics. Several of the microRNA showed considerable differences of expression in the four libraries. To confirm the results of the bioinformatics-based analysis, we studied the expression of the 10 most abundant miRNAs and 1 miRNA* in plants treated with 170 mM NaCl and in plants with a severe treatment of 340 mM NaCl. The results showed that 11 selected miRNAs had higher expression in samples treated with severe salt treatment compared to the mild one. We also investigated the regulation of the same miRNAs in shoots of four cultivars grown on soil treated with 170 mM NaCl. Cultivars could be grouped according to miRNAs expression in response to salt stress. Furthermore, the majority of the predicted target genes had an inverse regulation with their correspondent microRNAs. The targets encode a wide range of proteins, including transcription factors, metabolic enzymes and genes involved in hormone signaling, probably assisting the plants to develop tolerance to salinity. Our work provides insights into the regulatory functions of miRNAs, thereby expanding our knowledge on potential salt-stressed regulated genes.
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Affiliation(s)
- Mariana Carnavale Bottino
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Sabrina Rosario
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Clicia Grativol
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Flávia Thiebaut
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | | | | | - Adriana Silva Hemerly
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Paulo Cavalcanti Gomes Ferreira
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ, Brazil
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Identification and comparative profiling of microRNAs in wild-type Xanthoceras sorbifolia and its double flower mutant. Genes Genomics 2012. [DOI: 10.1007/s13258-012-0065-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Jagadeeswaran G, Nimmakayala P, Zheng Y, Gowdu K, Reddy UK, Sunkar R. Characterization of the small RNA component of leaves and fruits from four different cucurbit species. BMC Genomics 2012; 13:329. [PMID: 22823569 PMCID: PMC3431224 DOI: 10.1186/1471-2164-13-329] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 06/29/2012] [Indexed: 12/31/2022] Open
Abstract
Background MicroRNAs (miRNAs) are a class of non-coding small RNAs involved in post-transcriptional regulation of gene expression critical for plant growth and development, stress responses and other diverse biological processes in plants. The Cucurbitaceae or cucurbit family represents some of economically important species, particularly those with edible and medicinal fruits. Genomic tools for the molecular analysis of members of this family are just emerging. Partial draft genome sequence became available recently for cucumber and watermelon facilitating investigation of the small RNA component of the transcriptomes in cucurbits. Results We generated four small RNA libraries from bottle gourd (Lagenaria siceraria), Cucurbita moschata, Cucurbita pepo, and, watermelon (Citrullus lanatus var. lanatus) in order to identify conserved and novel lineage specific miRNAs in these cucurbits. Deep sequencing of small RNA libraries from these species resulted in 1,597,263, 532,948, 601,388, and 493,384 unique sRNA reads from bottle gourd, moschata, pepo and watermelon, respectively. Sequence analysis of these four libraries resulted in identification of 21 miRNA families that are highly conserved and 8 miRNA families that are moderately conserved in diverse dicots. We also identified 4 putative novel miRNAs in these plant species. Furthermore, the tasiRNAs were identified and their biogenesis was determined in these cucurbits. Small RNA blot analysis or q-PCR analyses of leaf and fruit tissues of these cucurbits showed differential expression of several conserved miRNAs. Interestingly, the abundance of several miRNAs in leaves and fruits of closely related C. moschata and C. pepo was also distinctly different. Target genes for the most conserved miRNAs are also predicted. Conclusion High-throughput sequencing of small RNA libraries from four cucurbit species has provided a glimpse of small RNA component in their transcriptomes. The analysis also showed considerable variation within four cucurbit species with regards to expression of individual miRNAs.
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Affiliation(s)
- Guru Jagadeeswaran
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
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Thiebaut F, Grativol C, Carnavale-Bottino M, Rojas CA, Tanurdzic M, Farinelli L, Martienssen RA, Hemerly AS, Ferreira PCG. Computational identification and analysis of novel sugarcane microRNAs. BMC Genomics 2012; 13:290. [PMID: 22747909 PMCID: PMC3464620 DOI: 10.1186/1471-2164-13-290] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Accepted: 05/02/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND MicroRNA-regulation of gene expression plays a key role in the development and response to biotic and abiotic stresses. Deep sequencing analyses accelerate the process of small RNA discovery in many plants and expand our understanding of miRNA-regulated processes. We therefore undertook small RNA sequencing of sugarcane miRNAs in order to understand their complexity and to explore their role in sugarcane biology. RESULTS A bioinformatics search was carried out to discover novel miRNAs that can be regulated in sugarcane plants submitted to drought and salt stresses, and under pathogen infection. By means of the presence of miRNA precursors in the related sorghum genome, we identified 623 candidates of new mature miRNAs in sugarcane. Of these, 44 were classified as high confidence miRNAs. The biological function of the new miRNAs candidates was assessed by analyzing their putative targets. The set of bona fide sugarcane miRNA includes those likely targeting serine/threonine kinases, Myb and zinc finger proteins. Additionally, a MADS-box transcription factor and an RPP2B protein, which act in development and disease resistant processes, could be regulated by cleavage (21-nt-species) and DNA methylation (24-nt-species), respectively. CONCLUSIONS A large scale investigation of sRNA in sugarcane using a computational approach has identified a substantial number of new miRNAs and provides detailed genotype-tissue-culture miRNA expression profiles. Comparative analysis between monocots was valuable to clarify aspects about conservation of miRNA and their targets in a plant whose genome has not yet been sequenced. Our findings contribute to knowledge of miRNA roles in regulatory pathways in the complex, polyploidy sugarcane genome.
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Affiliation(s)
- Flávia Thiebaut
- Laboratorio de Biologia Molecular de Plantas, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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