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Liu H, Yu M, Zhou S, Wang Y, Xia Z, Wang Z, Song B, An M, Wu Y. Unveiling novel anti-viral mechanisms of ε-poly-l-lysine on tobacco mosaic virus-infected Nicotiana tabacum through microRNA and transcriptome sequencing. Int J Biol Macromol 2024; 268:131628. [PMID: 38631577 DOI: 10.1016/j.ijbiomac.2024.131628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/30/2024] [Accepted: 04/13/2024] [Indexed: 04/19/2024]
Abstract
MicroRNAs (miRNAs) play important roles in plant defense against various pathogens. ε-poly-l-lysine (ε-PL), a natural anti-microbial peptide produced by microorganisms, effectively suppresses tobacco mosaic virus (TMV) infection. To investigate the anti-viral mechanism of ε-PL, the expression profiles of miRNAs in TMV-infected Nicotiana tabacum after ε-PL treatment were analyzed. The results showed that the expression levels of 328 miRNAs were significantly altered by ε-PL. Degradome sequencing was used to identify their target genes. Integrative analysis of miRNAs target genes and gene-enriched GO/KEGG pathways indicated that ε-PL regulates the expression of miRNAs involved in critical pathways of plant hormone signal transduction, host defense response, and plant pathogen interaction. Subsequently, virus induced gene silencing combined with the short tandem targets mimic technology was used to analyze the function of these miRNAs and their target genes. The results indicated that silencing miR319 and miR164 reduced TMV accumulation in N. benthamiana, indicating the essential roles of these miRNAs and their target genes during ε-PL-mediated anti-viral responses. Collectively, this study reveals that microbial source metabolites can inhibit plant viruses by regulating crucial host miRNAs and further elucidate anti-viral mechanisms of ε-PL.
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Affiliation(s)
- He Liu
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China; State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, Guizhou 550025, China
| | - Miao Yu
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Shidong Zhou
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Yan Wang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Zihao Xia
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Zhiping Wang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Baoan Song
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, Guizhou 550025, China
| | - Mengnan An
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China.
| | - Yuanhua Wu
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China.
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Malankar NN, Kondhare KR, Saha K, Mantri M, Banerjee AK. The phased short-interfering RNA siRD29(-) regulates GIBBERELLIN 3-OXIDASE 3 during stolon-to-tuber transitions in potato. PLANT PHYSIOLOGY 2023; 193:2555-2572. [PMID: 37691396 DOI: 10.1093/plphys/kiad493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 08/10/2023] [Accepted: 08/22/2023] [Indexed: 09/12/2023]
Abstract
Phased short-interfering RNAs (phasiRNAs) fine tune various stages of growth, development, and stress responses in plants. Potato (Solanum tuberosum) tuberization is a complex process, wherein a belowground modified stem (stolon) passes through developmental stages like swollen stolon and minituber before it matures to a potato. Previously, we identified several phasiRNA-producing loci (PHAS) from stolon-to-tuber transition stages. However, whether phasiRNAs mediate tuber development remains unknown. Here, we show that a gene encoding NB-ARC DOMAIN-CONTAINING DISEASE RESISTANCE PROTEIN (StRGA4; a PHAS locus) is targeted by Stu-microRNA482c to generate phasiRNAs. Interestingly, we observed that one of the phasiRNAs, referred as short-interfering RNA D29(-), i.e. siRD29(-), targets the gibberellin (GA) biosynthesis gene GIBBERELLIN 3-OXIDASE 3 (StGA3ox3). Since regulation of bioactive GA levels in stolons controls tuber development, we hypothesized that a gene regulatory module, Stu-miR482c-StRGA4-siRD29(-)-StGA3ox3, could govern tuber development. Through transient expression assays and small RNA sequencing, generation of siRD29(-) and its phase was confirmed in planta. Notably, the expression of StGA3ox3 was higher in swollen stolon compared to stolon, whereas siRD29(-) showed a negative association with StGA3ox3 expression. Antisense (AS) lines of StGA3ox3 produced more tubers compared to wild type. As expected, StRGA4 overexpression (OE) lines had high levels of siRD29(-) and mimicked the phenotypes of StGA3ox3-AS lines, indicating the functionality of this module in potato. In vitro tuberization assays (with or without a GA inhibitor) using StGA3ox3 antisense lines and overexpression lines of StGA3ox3 or StRGA4 revealed that StGA3ox3 controls the tuber stalk development. Taken together, our findings suggest that a phasiRNA, siRD29(-), mediates the regulation of StGA3ox3 during stolon-to-tuber transitions in potato.
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Affiliation(s)
- Nilam N Malankar
- Biology Division, Indian Institute of Science Education and Research (IISER Pune), Pune, 411008 Maharashtra, India
| | - Kirtikumar R Kondhare
- Biology Division, Indian Institute of Science Education and Research (IISER Pune), Pune, 411008 Maharashtra, India
- Biochemical Sciences Division, CSIR - National Chemical Laboratory (CSIR-NCL), Pune, 411008 Maharashtra, India
| | - Kishan Saha
- Biology Division, Indian Institute of Science Education and Research (IISER Pune), Pune, 411008 Maharashtra, India
| | - Mohit Mantri
- Biology Division, Indian Institute of Science Education and Research (IISER Pune), Pune, 411008 Maharashtra, India
| | - Anjan K Banerjee
- Biology Division, Indian Institute of Science Education and Research (IISER Pune), Pune, 411008 Maharashtra, India
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Liu X, Gao T, Liu C, Mao K, Gong X, Li C, Ma F. Fruit crops combating drought: Physiological responses and regulatory pathways. PLANT PHYSIOLOGY 2023; 192:1768-1784. [PMID: 37002821 PMCID: PMC10315311 DOI: 10.1093/plphys/kiad202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
Drought is a common stress in agricultural production. Thus, it is imperative to understand how fruit crops respond to drought and to develop drought-tolerant varieties. This paper provides an overview of the effects of drought on the vegetative and reproductive growth of fruits. We summarize the empirical studies that have assessed the physiological and molecular mechanisms of the drought response in fruit crops. This review focuses on the roles of calcium (Ca2+) signaling, abscisic acid (ABA), reactive oxygen species signaling, and protein phosphorylation underlying the early drought response in plants. We review the resulting downstream ABA-dependent and ABA-independent transcriptional regulation in fruit crops under drought stress. Moreover, we highlight the positive and negative regulatory mechanisms of microRNAs in the drought response of fruit crops. Lastly, strategies (including breeding and agricultural practices) to improve the drought resistance of fruit crops are outlined.
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Affiliation(s)
- Xiaomin Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Tengteng Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Changhai Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Ke Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xiaoqing Gong
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Chao Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
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Ahmad I, Soni SK, M M, Pandey D. In-silico mining and characterization of MYB family genes in wilt-resistant hybrid guava (Psidium guajava × Psidium molle). J Genet Eng Biotechnol 2023; 21:74. [PMID: 37389653 DOI: 10.1186/s43141-023-00528-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 06/20/2023] [Indexed: 07/01/2023]
Abstract
BACKGROUND The MYB family is one of the most significant groups of transcription factors in plants. However, several MYBs have been linked to secondary metabolism and are important for determining the color of fruit's peel and pulp. Despite being a substantial fruit crop in tropical and subtropical areas of the world, wilt-resistant hybrid guava (Psidium guajava × Psidium molle; PGPM) has not yet been the subject of a thorough examination. This study's goal was to assess the expression of MYB in guava fruit pulp, roots, and seeds to predict its function by in silico analysis of the guava root transcriptome data. RESULTS In the current study, we have mined the MYBs family of MYB genes from the transcriptome of the PGPM guava root. We have mined 15 distinct MYB transcription factor genes/transcripts viz MYB3, MYB4, MYB23, MYB86, MYB90, MYB308, MYB5, MYB82, MYB114, MYB6, MYB305, MYB44, MYB51, MYB46, and MYB330. From the analyses, it was found that R2-MYB and R3-MYB domains are conserved in all known guava MYB proteins. The expression of six different MYB TFs was examined using semi-quantitative RT-PCR in "Shweta" pulp (white colour pulp), "Lalit" pulp (red color pulp), "Lalit" root, and "Lalit" seed. CONCLUSION There were 15 MYB family members observed in guava. They were unequally distributed across the chromosomes, most likely as a result of gene duplication. Additionally, the expression patterns of the particular MYBs showed that MYB may be involved in the control of wilt, fruit ripening, seed development, and root development. Our results allow for a more thorough functional characterization of the guava MYB family genes and open the door to additional research into one essential MYB transcription factor family of genes and its involvement in the growth and ripening of guava fruit.
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Affiliation(s)
- Israr Ahmad
- Division of Crop Improvement and Biotechnology, ICAR-Central Institute for Subtropical Horticulture, Rehmankhera, P.O. Kakori, Lucknow, Uttar Pradesh, 226101, India.
| | - Sumit K Soni
- Division of Crop Improvement and Biotechnology, ICAR-Central Institute for Subtropical Horticulture, Rehmankhera, P.O. Kakori, Lucknow, Uttar Pradesh, 226101, India.
| | - Muthukumar M
- Division of Crop Improvement and Biotechnology, ICAR-Central Institute for Subtropical Horticulture, Rehmankhera, P.O. Kakori, Lucknow, Uttar Pradesh, 226101, India
| | - Devendra Pandey
- Division of Crop Improvement and Biotechnology, ICAR-Central Institute for Subtropical Horticulture, Rehmankhera, P.O. Kakori, Lucknow, Uttar Pradesh, 226101, India
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Wang WQ, Moss SMA, Zeng L, Espley RV, Wang T, Lin-Wang K, Fu BL, Schwinn KE, Allan AC, Yin XR. The red flesh of kiwifruit is differentially controlled by specific activation-repression systems. THE NEW PHYTOLOGIST 2022; 235:630-645. [PMID: 35348217 DOI: 10.1111/nph.18122] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
Abstract
Anthocyanins are visual cues for pollination and seed dispersal. Fruit containing anthocyanins also appeals to consumers due to its appearance and health benefits. In kiwifruit (Actinidia spp.) studies have identified at least two MYB activators of anthocyanin, but their functions in fruit and the mechanisms by which they act are not fully understood. Here, transcriptome and small RNA high-throughput sequencing were used to comprehensively identify contributors to anthocyanin accumulation in kiwifruit. Stable overexpression in vines showed that both 35S::MYB10 and MYB110 can upregulate anthocyanin biosynthesis in Actinidia chinensis fruit, and that MYB10 overexpression resulted in anthocyanin accumulation which was limited to the inner pericarp, suggesting that repressive mechanisms underlie anthocyanin biosynthesis in this species. Furthermore, motifs in the C-terminal region of MYB10/110 were shown to be responsible for the strength of activation of the anthocyanic response. Transient assays showed that both MYB10 and MYB110 were not directly cleaved by miRNAs, but that miR828 and its phased small RNA AcTAS4-D4(-) efficiently targeted MYB110. Other miRNAs were identified, which were differentially expressed between the inner and outer pericarp, and cleavage of SPL13, ARF16, SCL6 and F-box1, all of which are repressors of MYB10, was observed. We conclude that it is the differential expression and subsequent repression of MYB activators that is responsible for variation in anthocyanin accumulation in kiwifruit species.
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Affiliation(s)
- Wen-Qiu Wang
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Horticulture Department, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Sarah M A Moss
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Palmerston North, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Lihui Zeng
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Richard V Espley
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Tianchi Wang
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Kui Lin-Wang
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Bei-Ling Fu
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Horticulture Department, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Kathy E Schwinn
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Palmerston North, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Andrew C Allan
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Xue-Ren Yin
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Horticulture Department, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
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6
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Tirumalai V, Narjala A, Swetha C, Sundar GVH, Sujith TN, Shivaprasad PV. Cultivar-specific miRNA-mediated RNA silencing in grapes. PLANTA 2022; 256:17. [PMID: 35737180 DOI: 10.1007/s00425-022-03934-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/28/2022] [Indexed: 06/15/2023]
Abstract
In-depth comparative degradome analysis of two domesticated grape cultivars with diverse secondary metabolite accumulation reveals differential miRNA-mediated targeting. Small (s)RNAs such as micro(mi)RNAs and secondary small interfering (si) often work as negative switches of gene expression. In plants, it is well known that miRNAs target and cleave mRNAs that have high sequence complementarity. However, it is not known if there are variations in miRNA-mediated targeting between subspecies and cultivars that have been subjected to vast genetic modifications through breeding and other selections. Here, we have used PAREsnip2 tool for analysis of degradome datasets derived from two contrasting domesticated grape cultivars having varied fruit color, habit and leaf shape. We identified several interesting variations in sRNA targeting using degradome and 5'RACE analysis between two contrasting grape cultivars that was further correlated using RNA-seq analysis. Several of the differences we identified are associated with secondary metabolic pathways. We propose possible means by which sRNAs might contribute to diversity in secondary metabolites and other development pathways between two domesticated cultivars of grapes.
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Affiliation(s)
- Varsha Tirumalai
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
- SASTRA University, Thirumalaisamudram, Thanjavur, 613401, India
| | - Anushree Narjala
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
- SASTRA University, Thirumalaisamudram, Thanjavur, 613401, India
| | - Chenna Swetha
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
- SASTRA University, Thirumalaisamudram, Thanjavur, 613401, India
| | - G Vivek Hari Sundar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - T N Sujith
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - P V Shivaprasad
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India.
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Mora J, Pott DM, Osorio S, Vallarino JG. Regulation of Plant Tannin Synthesis in Crop Species. Front Genet 2022; 13:870976. [PMID: 35586570 PMCID: PMC9108539 DOI: 10.3389/fgene.2022.870976] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/28/2022] [Indexed: 11/26/2022] Open
Abstract
Plant tannins belong to the antioxidant compound family, which includes chemicals responsible for protecting biological structures from the harmful effects of oxidative stress. A wide range of plants and crops are rich in antioxidant compounds, offering resistance to biotic, mainly against pathogens and herbivores, and abiotic stresses, such as light and wound stresses. These compounds are also related to human health benefits, offering protective effects against cardiovascular and neurodegenerative diseases in addition to providing anti-tumor, anti-inflammatory, and anti-bacterial characteristics. Most of these compounds are structurally and biosynthetically related, being synthesized through the shikimate-phenylpropanoid pathways, offering several classes of plant antioxidants: flavonoids, anthocyanins, and tannins. Tannins are divided into two major classes: condensed tannins or proanthocyanidins and hydrolysable tannins. Hydrolysable tannin synthesis branches directly from the shikimate pathway, while condensed tannins are derived from the flavonoid pathway, one of the branches of the phenylpropanoid pathway. Both types of tannins have been proposed as important molecules for taste perception of many fruits and beverages, especially wine, besides their well-known roles in plant defense and human health. Regulation at the gene level, biosynthesis and degradation have been extensively studied in condensed tannins in crops like grapevine (Vitis vinifera), persimmon (Diospyros kaki) and several berry species due to their high tannin content and their importance in the food and beverage industry. On the other hand, much less information is available regarding hydrolysable tannins, although some key aspects of their biosynthesis and regulation have been recently discovered. Here, we review recent findings about tannin metabolism, information that could be of high importance for crop breeding programs to obtain varieties with enhanced nutritional characteristics.
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Affiliation(s)
| | | | | | - José G. Vallarino
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”—Consejo Superior de Investigaciones Científicas-Universidad de Málaga- (IHSM-CSIC-UMA), Málaga, Spain
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8
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Jyothsna S, Alagu M. Role of phasiRNAs in plant-pathogen interactions: molecular perspectives and bioinformatics tools. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:947-961. [PMID: 35722509 PMCID: PMC9203634 DOI: 10.1007/s12298-022-01189-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/01/2022] [Accepted: 05/18/2022] [Indexed: 05/03/2023]
Abstract
The genome of an organism is regulated in concert with the organized action of various genetic regulators at different hierarchical levels. Small non-coding RNAs are one of these regulators, among which microRNAs (miRNAs), a distinguished sRNA group with decisive functions in the development, growth and stress-responsive activities of both plants as well as animals, are keenly explored over a good number of years. Recent studies in plants revealed that apart from the silencing activity exhibited by miRNAs on their targets, miRNAs of specific size and structural features can direct the phasing pattern of their target loci to form phased secondary small interfering RNAs (phasiRNAs). These trigger-miRNAs were identified to target both coding and long non-coding RNAs that act as potent phasiRNA precursors or PHAS loci. The phasiRNAs produced thereby exhibit a role in enhancing further downstream regulation either on their own precursors or on those transcripts that are distinct from their genetic source of origin. Hence, these tiny regulators can stimulate an elaborative cascade of interacting RNA networks via cis and trans-regulatory mechanisms. Our review focuses on the comprehensive understanding of phasiRNAs and their trigger miRNAs, by giving much emphasis on their role in the regulation of plant defense responses, together with a summary of the computational tools available for the prediction of the same.
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Affiliation(s)
- S. Jyothsna
- Department of Genomic Science, Central University of Kerala, Periye, Kasaragod, Kerala 671316 India
| | - Manickavelu Alagu
- Department of Genomic Science, Central University of Kerala, Periye, Kasaragod, Kerala 671316 India
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9
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Ivanova Z, Minkov G, Gisel A, Yahubyan G, Minkov I, Toneva V, Baev V. The Multiverse of Plant Small RNAs: How Can We Explore It?
. Int J Mol Sci 2022; 23:ijms23073979. [PMID: 35409340 PMCID: PMC8999349 DOI: 10.3390/ijms23073979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/28/2022] [Accepted: 03/31/2022] [Indexed: 12/22/2022] Open
Abstract
Plant small RNAs (sRNAs) are a heterogeneous group of noncoding RNAs with a length of 20–24 nucleotides that are widely studied due to their importance as major regulators in various biological processes. sRNAs are divided into two main classes—microRNAs (miRNAs) and small interfering RNAs (siRNAs)—which differ in their biogenesis and functional pathways. Their identification and enrichment with new structural variants would not be possible without the use of various high-throughput sequencing (NGS) techniques, allowing for the detection of the total population of sRNAs in plants. Classifying sRNAs and predicting their functional role based on such high-performance datasets is a nontrivial bioinformatics task, as plants can generate millions of sRNAs from a variety of biosynthetic pathways. Over the years, many computing tools have been developed to meet this challenge. Here, we review more than 35 tools developed specifically for plant sRNAs over the past few years and explore some of their basic algorithms for performing tasks related to predicting, identifying, categorizing, and quantifying individual sRNAs in plant samples, as well as visualizing the results of these analyzes. We believe that this review will be practical for biologists who want to analyze their plant sRNA datasets but are overwhelmed by the number of tools available, thus answering the basic question of how to choose the right one for a particular study.
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Affiliation(s)
- Zdravka Ivanova
- Institute of Molecular Biology and Biotechnologies, 4108 Markovo, Bulgaria; (Z.I.); (G.M.); (I.M.); (V.T.)
| | - Georgi Minkov
- Institute of Molecular Biology and Biotechnologies, 4108 Markovo, Bulgaria; (Z.I.); (G.M.); (I.M.); (V.T.)
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 4000 Plovdiv, Bulgaria;
| | - Andreas Gisel
- Institute of Biomedical Technologies (ITB), CNR, 70126 Bari, Italy;
| | - Galina Yahubyan
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 4000 Plovdiv, Bulgaria;
| | - Ivan Minkov
- Institute of Molecular Biology and Biotechnologies, 4108 Markovo, Bulgaria; (Z.I.); (G.M.); (I.M.); (V.T.)
- Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Valentina Toneva
- Institute of Molecular Biology and Biotechnologies, 4108 Markovo, Bulgaria; (Z.I.); (G.M.); (I.M.); (V.T.)
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 4000 Plovdiv, Bulgaria;
| | - Vesselin Baev
- Institute of Molecular Biology and Biotechnologies, 4108 Markovo, Bulgaria; (Z.I.); (G.M.); (I.M.); (V.T.)
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 4000 Plovdiv, Bulgaria;
- Correspondence:
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10
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Ding T, Tomes S, Gleave AP, Zhang H, Dare AP, Plunkett B, Espley RV, Luo Z, Zhang R, Allan AC, Zhou Z, Wang H, Wu M, Dong H, Liu C, Liu J, Yan Z, Yao JL. microRNA172 targets APETALA2 to regulate flavonoid biosynthesis in apple (Malus domestica). HORTICULTURE RESEARCH 2022; 9:uhab007. [PMID: 35039839 PMCID: PMC8846330 DOI: 10.1093/hr/uhab007] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 01/18/2022] [Accepted: 10/02/2021] [Indexed: 05/24/2023]
Abstract
MicroRNA172 (miR172) plays a role in regulating a diverse range of plant developmental processes, including flowering, fruit development and nodulation. However, its role in regulating flavonoid biosynthesis is unclear. In this study, we show that transgenic apple plants over-expressing miR172 show a reduction in red coloration and anthocyanin accumulation in various tissue types. This reduction was consistent with decreased expression of APETALA2 homolog MdAP2_1a (a miR172 target gene), MdMYB10, and targets of MdMYB10, as demonstrated by both RNA-seq and qRT-PCR analyses. The positive role of MdAP2_1a in regulating anthocyanin biosynthesis was supported by the enhanced petal anthocyanin accumulation in transgenic tobacco plants overexpressing MdAP2_1a, and by the reduction in anthocyanin accumulation in apple and cherry fruits transfected with an MdAP2_1a virus-induced-gene-silencing construct. We demonstrated that MdAP2_1a could bind directly to the promoter and protein sequences of MdMYB10 in yeast and tobacco, and enhance MdMYB10 promotor activity. In Arabidopsis, over-expression of miR172 reduced flavonoid (including anthocyanins and flavonols) concentration and RNA transcript abundance of flavonoid genes in plantlets cultured on medium containing 7% sucrose. The anthocyanin content and RNA abundance of anthocyanin genes could be partially restored by using a synonymous mutant of MdAP2_1a, which had lost the miR172 target sequences at mRNA level, but not restored by using a WT MdAP2_1a. These results indicate that miR172 inhibits flavonoid biosynthesis through suppressing the expression of an AP2 transcription factor that positively regulates MdMYB10.
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Affiliation(s)
- Tiyu Ding
- Zhengzhou Fruit Research Institute, Chinese Academy of
Agricultural Sciences, 32 Gangwan Road, Zhengzhou 450009, China
| | - Sumathi Tomes
- The New Zealand Institute for Plant & Food Research
Limited, Private Bag 92169, Auckland 1142, New Zealand
| | - Andrew P Gleave
- The New Zealand Institute for Plant & Food Research
Limited, Private Bag 92169, Auckland 1142, New Zealand
| | - Hengtao Zhang
- Zhengzhou Fruit Research Institute, Chinese Academy of
Agricultural Sciences, 32 Gangwan Road, Zhengzhou 450009, China
| | - Andrew P Dare
- The New Zealand Institute for Plant & Food Research
Limited, Private Bag 92169, Auckland 1142, New Zealand
| | - Blue Plunkett
- The New Zealand Institute for Plant & Food Research
Limited, Private Bag 92169, Auckland 1142, New Zealand
| | - Richard V Espley
- The New Zealand Institute for Plant & Food Research
Limited, Private Bag 92169, Auckland 1142, New Zealand
| | - Zhiwei Luo
- The New Zealand Institute for Plant & Food Research
Limited, Private Bag 92169, Auckland 1142, New Zealand
| | - Ruiping Zhang
- Zhengzhou Fruit Research Institute, Chinese Academy of
Agricultural Sciences, 32 Gangwan Road, Zhengzhou 450009, China
| | - Andrew C Allan
- The New Zealand Institute for Plant & Food Research
Limited, Private Bag 92169, Auckland 1142, New Zealand
- School of Biological Sciences, University of
Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Zhe Zhou
- Zhengzhou Fruit Research Institute, Chinese Academy of
Agricultural Sciences, 32 Gangwan Road, Zhengzhou 450009, China
| | - Huan Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of
Agricultural Sciences, 32 Gangwan Road, Zhengzhou 450009, China
| | - Mengmeng Wu
- Zhengzhou Fruit Research Institute, Chinese Academy of
Agricultural Sciences, 32 Gangwan Road, Zhengzhou 450009, China
| | - Haiqing Dong
- Zhengzhou Fruit Research Institute, Chinese Academy of
Agricultural Sciences, 32 Gangwan Road, Zhengzhou 450009, China
| | - Chonghuai Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of
Agricultural Sciences, 32 Gangwan Road, Zhengzhou 450009, China
| | - Jihong Liu
- College of Horticulture and Forestry Sciences, Huazhong
Agricultural University, 1 Shizishan Street Wuhan 430070, China
| | - Zhenli Yan
- Zhengzhou Fruit Research Institute, Chinese Academy of
Agricultural Sciences, 32 Gangwan Road, Zhengzhou 450009, China
| | - Jia-Long Yao
- Zhengzhou Fruit Research Institute, Chinese Academy of
Agricultural Sciences, 32 Gangwan Road, Zhengzhou 450009, China
- The New Zealand Institute for Plant & Food Research
Limited, Private Bag 92169, Auckland 1142, New Zealand
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11
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Ma H, Yang T, Li Y, Zhang J, Wu T, Song T, Yao Y, Tian J. The long noncoding RNA MdLNC499 bridges MdWRKY1 and MdERF109 function to regulate early-stage light-induced anthocyanin accumulation in apple fruit. THE PLANT CELL 2021; 33:3309-3330. [PMID: 34270784 PMCID: PMC8505877 DOI: 10.1093/plcell/koab188] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 07/12/2021] [Indexed: 05/24/2023]
Abstract
Anthocyanin pigments contribute to plant coloration and are valuable sources of antioxidants in the human diet as components of fruits and vegetables. Their production is known to be induced by light in apple fruit (Malus domestica); however, the underlying molecular mechanism responsible for early-stage light-induced anthocyanin biosynthesis remains unclear. Here, we identified an ethylene response factor (ERF) protein, ERF109, involved in light-induced anthocyanin biosynthesis and found that it promotes coloration by directly binding to anthocyanin-related gene promoters. Promoter::β-glucuronidase reporter analysis and Hi-C sequencing showed that a long noncoding RNA, MdLNC499, located nearby MdERF109, induces the expression of MdERF109. A W-box cis-element in the MdLNC499 promoter was found to be regulated by a transcription factor, MdWRKY1. Transient expression in apple fruit and stable transformation of apple calli allowed us to reconstruct a MdWRKY1-MdLNC499-MdERF109 transcriptional cascade in which MdWRKY1 is activated by light to increase the transcription of MdLNC499, which in turn induces MdERF109. The MdERF109 protein induces the expression of anthocyanin-related genes and the accumulation of anthocyanins in the early stages of apple coloration. Our results provide a platform for better understanding the various regulatory mechanisms involved in light-induced apple fruit coloration.
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Affiliation(s)
- Huaying Ma
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- Plant Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Tuo Yang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- Plant Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Yu Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- Plant Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Jie Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- Plant Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing 102206, China
| | - Tingting Song
- Plant Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Yuncong Yao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- Plant Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Ji Tian
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- Plant Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
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12
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Chen Q, Wang J, Danzeng P, Danzeng C, Song S, Wang L, Zhao L, Xu W, Zhang C, Ma C, Wang S. VvMYB114 mediated by miR828 negatively regulates trichome development of Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 309:110936. [PMID: 34134843 DOI: 10.1016/j.plantsci.2021.110936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
Trichome is a specialized structure differentiated during the morphogenesis of plant leaf epidermal cells. In recent years, with the continuous researches on trichome development of Arabidopsis and other plants, more and more genes related to trichome morphogenesis have been discovered, including R2R3-type MYB genes. In this study, we cloned a R2R3-type MYB family gene from grape, VvMYB114, a target gene of vvi-miR828. qRT-PCR showed that VvMYB114 mRNA accumulated during grape fruit ripening, and VvMYB114 protein had transcriptional activation activity. Heterologous overexpression of VvMYB114 in Arabidopsis reduced the number of trichome on leaves and stems. Mutating the miR828-binding site in VvMYB114 without altering amino-acid sequence had no effect on trichome development in Arabidopsis. The results showed a different role of the regulation of miR828 to VvMYB114 in Arabidopsis from in grape, which indicated the functional divergence of miRNA targeting homoeologous genes in different species played an important roles in evolution and useful trait selection.
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Affiliation(s)
- Qiuju Chen
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiyuan Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Pingcuo Danzeng
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ciren Danzeng
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shiren Song
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lei Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liping Zhao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wenping Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Caixi Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chao Ma
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Shiping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China; Institute of Agro-food Science and Technology/Key Laboratory of Agro-products Processing Technology of Shandong, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
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13
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Li C, Wang M, Qiu X, Zhou H, Lu S. Noncoding RNAs in Medicinal Plants and their Regulatory Roles in Bioactive Compound Production. Curr Pharm Biotechnol 2021; 22:341-359. [PMID: 32469697 DOI: 10.2174/1389201021666200529101942] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/14/2020] [Accepted: 03/30/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Noncoding RNAs (ncRNAs), such as microRNAs (miRNAs), small interfering RNAs (siRNAs) and long noncoding RNAs (lncRNAs), play significant regulatory roles in plant development and secondary metabolism and are involved in plant response to biotic and abiotic stresses. They have been intensively studied in model systems and crops for approximately two decades and massive amount of information have been obtained. However, for medicinal plants, ncRNAs, particularly their regulatory roles in bioactive compound biosynthesis, are just emerging as a hot research field. OBJECTIVE This review aims to summarize current knowledge on herbal ncRNAs and their regulatory roles in bioactive compound production. RESULTS So far, scientists have identified thousands of miRNA candidates from over 50 medicinal plant species and 11794 lncRNAs from Salvia miltiorrhiza, Panax ginseng, and Digitalis purpurea. Among them, more than 30 miRNAs and five lncRNAs have been predicted to regulate bioactive compound production. CONCLUSION The regulation may achieve through various regulatory modules and pathways, such as the miR397-LAC module, the miR12112-PPO module, the miR156-SPL module, the miR828-MYB module, the miR858-MYB module, and other siRNA and lncRNA regulatory pathways. Further functional analysis of herbal ncRNAs will provide useful information for quality and quantity improvement of medicinal plants.
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Affiliation(s)
- Caili Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Meizhen Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Xiaoxiao Qiu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Hong Zhou
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
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14
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Liu Y, Teng C, Xia R, Meyers BC. PhasiRNAs in Plants: Their Biogenesis, Genic Sources, and Roles in Stress Responses, Development, and Reproduction. THE PLANT CELL 2020; 32:3059-3080. [PMID: 32817252 PMCID: PMC7534485 DOI: 10.1105/tpc.20.00335] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/29/2020] [Accepted: 08/14/2020] [Indexed: 05/08/2023]
Abstract
Phased secondary small interfering RNAs (phasiRNAs) constitute a major category of small RNAs in plants, but most of their functions are still poorly defined. Some phasiRNAs, known as trans-acting siRNAs, are known to target complementary mRNAs for degradation and to function in development. However, the targets or biological roles of other phasiRNAs remain speculative. New insights into phasiRNA biogenesis, their conservation, and their variation across the flowering plants continue to emerge due to the increased availability of plant genomic sequences, deeper and more sophisticated sequencing approaches, and improvements in computational biology and biochemical/molecular/genetic analyses. In this review, we survey recent progress in phasiRNA biology, with a particular focus on two classes associated with male reproduction: 21-nucleotide (accumulate early in anther ontogeny) and 24-nucloetide (produced in somatic cells during meiosis) phasiRNAs. We describe phasiRNA biogenesis, function, and evolution and define the unanswered questions that represent topics for future research.
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Affiliation(s)
- Yuanlong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510640, China
- College of Horticulture, South China Agricultural University, Guangzhou 510640, Guangdong, China
| | - Chong Teng
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510640, China
- College of Horticulture, South China Agricultural University, Guangzhou 510640, Guangdong, China
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
- Division of Plant Sciences, University of Missouri-Columbia, Columbia, Missouri 65211
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15
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RNA-sequencing based gene expression landscape of guava cv. Allahabad Safeda and comparative analysis to colored cultivars. BMC Genomics 2020; 21:484. [PMID: 32669108 PMCID: PMC7364479 DOI: 10.1186/s12864-020-06883-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 07/06/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Guava (Psidium guajava L.) is an important fruit crop of tropical and subtropical areas of the world. Genomics resources in guava are scanty. RNA-Seq based tissue specific expressed genomic information, de novo transcriptome assembly, functional annotation and differential expression among contrasting genotypes has a potential to set the stage for the functional genomics for traits of commerce like colored flesh and apple color peel. RESULTS Development of fruit from flower involves orchestration of myriad molecular switches. We did comparative transcriptome sequencing on leaf, flower and fruit tissues of cv. Allahabad Safeda to understand important genes and pathways controlling fruit development. Tissue specific RNA sequencing and de novo transcriptome assembly using Trinity pipeline provided us the first reference transcriptome for guava consisting of 84,206 genes comprising 279,792 total transcripts with a N50 of 3603 bp. Blast2GO assigned annotation to 116,629 transcripts and PFam based HMM profile annotated 140,061 transcripts with protein domains. Differential expression with EdgeR identified 3033 genes in Allahabad Safeda tissues. Mapping the differentially expressed transcripts over molecular pathways indicate significant Ethylene and Abscisic acid hormonal changes and secondary metabolites, carbohydrate metabolism and fruit softening related gene transcripts during fruit development, maturation and ripening. Differential expression analysis among colored tissue comparisons in 3 cultivars Allahabad Safeda, Punjab Pink and Apple Color identified 68 candidate genes that might be controlling color development in guava fruit. Comparisons of red vs green peel in Apple Color, white pulp vs red pulp in Punjab Pink and fruit maturation vs ripening in non-colored Allahabad Safeda indicates up-regulation of ethylene biosynthesis accompanied to secondary metabolism like phenylpropanoid and monolignol pathways. CONCLUSIONS Benchmarking Universal Single-Copy Orthologs analysis of de novo transcriptome of guava with eudicots identified 93.7% complete BUSCO genes. In silico differential gene expression among tissue types of Allahabad Safeda and validation of candidate genes with qRT-PCR in contrasting color genotypes promises the utility of this first guava transcriptome for its potential of tapping the genetic elements from germplasm collections for enhancing fruit traits.
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16
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Wei X, Ju Y, Ma T, Zhang J, Fang Y, Sun X. New perspectives on the biosynthesis, transportation, astringency perception and detection methods of grape proanthocyanidins. Crit Rev Food Sci Nutr 2020; 61:2372-2398. [PMID: 32551848 DOI: 10.1080/10408398.2020.1777527] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Proanthocyanidins (PAs) are important secondary metabolites crucial for the quality of grape berry and wine. Despite important advances in our understanding of the structural and regulatory genes involved in the PAs biosynthesis pathway, our knowledge about the details of biosynthetic and regulatory networks, especially the mechanism of polymerization and transportation remains limited. We provided an overview of the latest discoveries related to the mechanisms of grape PAs structure, astringency properties, detection methods, biosynthesis and transportation. We also summarized the environmental influencing factors of PAs synthesis in grape. Future trends were discussed.
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Affiliation(s)
- Xiaofeng Wei
- College of Enology, College of Food Science and Engineering, Viti-viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Northwest A&F University, Yangling, China
| | - Yanlun Ju
- College of Enology, College of Food Science and Engineering, Viti-viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Northwest A&F University, Yangling, China
| | - Tingting Ma
- College of Enology, College of Food Science and Engineering, Viti-viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Northwest A&F University, Yangling, China
| | | | - Yulin Fang
- College of Enology, College of Food Science and Engineering, Viti-viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Northwest A&F University, Yangling, China
| | - Xiangyu Sun
- College of Enology, College of Food Science and Engineering, Viti-viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Northwest A&F University, Yangling, China
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17
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Sunitha S, Rock CD. CRISPR/Cas9-mediated targeted mutagenesis of TAS4 and MYBA7 loci in grapevine rootstock 101-14. Transgenic Res 2020; 29:355-367. [PMID: 32328868 PMCID: PMC7283210 DOI: 10.1007/s11248-020-00196-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 02/21/2020] [Indexed: 02/07/2023]
Abstract
Pierce’s disease (PD) of grapevine (Vitis vinifera) is caused by the bacterium Xylella fastidiosa and is vectored by xylem sap-sucking insects, whereas Grapevine Red Blotch Virus (GRBV) causes Red Blotch Disease and is transmitted in the laboratory by alfalfa leafhopper Spissistilus festinus. The significance of anthocyanin accumulations in distinct tissues of grapevine by these pathogens is unknown, but vector feeding preferences and olfactory cues from host anthocyanins may be important for these disease etiologies. Phosphate, sugar, and UV light are known to regulate anthocyanin accumulation via miR828 and Trans-Acting Small-interfering locus4 (TAS4), specifically in grape by production of phased TAS4a/b/c small-interfering RNAs that are differentially expressed and target MYBA5/6/7 transcription factor transcripts for post-transcriptional slicing and antisense-mediated silencing. To generate materials that can critically test these genes’ functions in PD and GRBV disease symptoms, we produced transgenic grape plants targeting TAS4b and MYBA7 using CRISPR/Cas9 technology. We obtained five MYBA7 lines all with bi-allelic editing events and no off-targets detected at genomic loci with homology to the guide sequence. We obtained two independent edited TAS4b lines; one bi-allelic, the other heterozygous while both had fortuitous evidences of bi-allelic TAS4a off-target editing events at the paralogous locus. No visible anthocyanin accumulation phenotypes were observed in regenerated plants, possibly due to the presence of genetically redundant TAS4c and MYBA5/6 loci or absence of inductive environmental stress conditions. The editing events encompass single base insertions and di/trinucleotide deletions of Vvi-TAS4a/b and Vvi-MYBA7 at expected positions 3 nt upstream from the guideRNA proximal adjacent motifs NGG. We also identified evidences of homologous recombinations of TAS4a with TAS4b at the TAS4a off-target in one of the TAS4b lines, resulting in a chimeric locus with a bi-allelic polymorphism, supporting independent recombination events in transgenic plants associated with apparent high Cas9 activities. The lack of obvious visible pigment phenotypes in edited plants precluded pathogen challenge tests of the role of anthocyanins in host PD and GRBV resistance/tolerance mechanisms. Nonetheless, we demonstrate successful genome-editing of non-coding RNA and MYB transcription factor loci which can serve future characterizations of the functions of TAS4a/b/c and MYBA7 in developmental, physiological, and environmental biotic/abiotic stress response pathways important for value-added nutraceutical synthesis and pathogen responses of winegrape.
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Affiliation(s)
- Sukumaran Sunitha
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409-3131, USA
| | - Christopher D Rock
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409-3131, USA.
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18
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Identification of anthocyanin biosynthesis related microRNAs and total microRNAs in Lonicera edulis by high-throughput sequencing. J Genet 2020. [DOI: 10.1007/s12041-020-01194-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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19
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Tirumalai V, Swetha C, Nair A, Pandit A, Shivaprasad PV. miR828 and miR858 regulate VvMYB114 to promote anthocyanin and flavonol accumulation in grapes. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4775-4792. [PMID: 31145783 PMCID: PMC6760283 DOI: 10.1093/jxb/erz264] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/21/2019] [Indexed: 05/20/2023]
Abstract
MicroRNAs are a class of non-coding small RNAs involved in the negative regulation of gene expression, which play critical roles in developmental and metabolic pathways. Studies in several plants have identified a few microRNAs and other small RNAs that target regulators of the phenylpropanoid metabolic pathway called the MYB transcription factors. However, it is not well understood how sRNA-mediated regulation of MYBs influences the accumulation of specific secondary metabolites. Using sRNA sequencing, degradome analysis, mRNA sequencing, and proteomic analysis, we establish that grape lines with high anthocyanin content express two MYB-targeting microRNAs abundantly, resulting in the differential expression of specific MYB proteins. miR828 and miR858 target coding sequences of specific helix motifs in the mRNA sequences of MYB proteins. Targeting by miR828 caused MYB RNA decay and the production of a cascade of secondary siRNAs that depend on RNA-dependent RNA polymerase 6. MYB suppression and cascade silencing was more robust in grape lines with high anthocyanin content than in a flavonol-rich grape line. We establish that microRNA-mediated silencing targeted the repressor class of MYBs to promote anthocyanin biosynthesis in grape lines with high anthocyanins. We propose that this process regulates the expression of appropriate MYBs in grape lines to produce specific secondary metabolites.
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Affiliation(s)
- Varsha Tirumalai
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
- SASTRA University, Thirumalaisamudram, Thanjavur, India
| | - Chenna Swetha
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
- SASTRA University, Thirumalaisamudram, Thanjavur, India
| | - Ashwin Nair
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
- SASTRA University, Thirumalaisamudram, Thanjavur, India
| | - Awadhesh Pandit
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
| | - Padubidri V Shivaprasad
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
- Correspondence:
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20
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Potnis N, Kandel PP, Merfa MV, Retchless AC, Parker JK, Stenger DC, Almeida RPP, Bergsma-Vlami M, Westenberg M, Cobine PA, De La Fuente L. Patterns of inter- and intrasubspecific homologous recombination inform eco-evolutionary dynamics of Xylella fastidiosa. THE ISME JOURNAL 2019; 13:2319-2333. [PMID: 31110262 PMCID: PMC6776109 DOI: 10.1038/s41396-019-0423-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 04/05/2019] [Accepted: 04/09/2019] [Indexed: 11/09/2022]
Abstract
High rates of homologous recombination (HR) in the bacterial plant pathogen Xylella fastidiosa have been previously detected. This study aimed to determine the extent and explore the ecological significance of HR in the genomes of recombinants experimentally generated by natural transformation and wild-type isolates. Both sets of strains displayed widespread HR and similar average size of recombined fragments consisting of random events (2-10 kb) of inter- and intrasubspecific recombination. A significantly higher proportion and greater lengths (>10 kb, maximum 31.5 kb) of recombined fragments were observed in subsp. morus and in strains isolated in Europe from intercepted coffee plants shipped from the Americas. Such highly recombinant strains pose a serious risk of emergence of novel variants, as genetically distinct and formerly geographically isolated genotypes are brought in close proximity by global trade. Recently recombined regions in wild-type strains included genes involved in regulation and signaling, host colonization, nutrient acquisition, and host evasion, all fundamental traits for X. fastidiosa ecology. Identification of four recombinant loci shared between wild-type and experimentally generated recombinants suggests potential hotspots of recombination in this naturally competent pathogen. These findings provide insights into evolutionary forces possibly affecting the adaptive potential to colonize the host environments of X. fastidiosa.
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Affiliation(s)
- Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, 209 Rouse Life Sciences Bldg, Auburn, AL, USA
| | - Prem P Kandel
- Department of Entomology and Plant Pathology, Auburn University, 209 Rouse Life Sciences Bldg, Auburn, AL, USA
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, USA
| | - Marcus V Merfa
- Department of Entomology and Plant Pathology, Auburn University, 209 Rouse Life Sciences Bldg, Auburn, AL, USA
| | - Adam C Retchless
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
- Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jennifer K Parker
- Department of Entomology and Plant Pathology, Auburn University, 209 Rouse Life Sciences Bldg, Auburn, AL, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Drake C Stenger
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, USA
| | - Rodrigo P P Almeida
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Maria Bergsma-Vlami
- Dutch National Plant Protection Organization (NPPO-NL), P.O. Box. 9102, Wageningen, 6700 HC, The Netherlands
| | - Marcel Westenberg
- Dutch National Plant Protection Organization (NPPO-NL), P.O. Box. 9102, Wageningen, 6700 HC, The Netherlands
| | - Paul A Cobine
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Leonardo De La Fuente
- Department of Entomology and Plant Pathology, Auburn University, 209 Rouse Life Sciences Bldg, Auburn, AL, USA.
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21
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Zhou B, Kang Y, Leng J, Xu Q. Genome-Wide Analysis of the miRNA-mRNAs Network Involved in Cold Tolerance in Populus simonii × P. nigra. Genes (Basel) 2019; 10:genes10060430. [PMID: 31195761 PMCID: PMC6627750 DOI: 10.3390/genes10060430] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/21/2019] [Accepted: 05/31/2019] [Indexed: 12/02/2022] Open
Abstract
Background: Cold tolerance is important for plants’ geographical distribution and survival in extreme seasonal variations of climate. However, Populus simonii × P. nigra shows wide adaptability and strong cold resistance. Transcriptional and post-transcriptional regulation of cold-responsive genes is crucial for cold tolerance in plants. To understand the roles of regulatory RNAs under cold induction in Populus simonii × P. nigra, we constructed cDNA and small RNA libraries from leaf buds treated or not with −4 °C for 8 h for analysis. Results: Through high-throughput sequencing and differential expression analysis, 61 miRNAs and 1229 DEGs were identified under cold induction condition in Populus simonii × P. nigra. The result showed that miR167a, miR1450, miR319a, miR395b, miR393a-5p, miR408-5p, and miR168a-5p were downregulated, whereas transcription level of miR172a increased under the cold treatment. Thirty-one phased-siRNA were also obtained (reads ≥ 4) and some of them proceeded from TAS3 loci. Analysis of the differentially expressed genes (DEGs) showed that transcription factor genes such as Cluster-15451.2 (putative MYB), Cluster-16493.29872 (putative bZIP), Cluster-16493.29175 (putative SBP), and Cluster-1378.1 (putative ARF) were differentially expressed in cold treated and untreated plantlets of Populus simonii × P. nigra. Integrated analysis of miRNAs and transcriptome showed miR319, miR159, miR167, miR395, miR390, and miR172 and their target genes, including MYB, SBP, bZIP, ARF, LHW, and ATL, were predicted to be involved in ARF pathway, SPL pathway, DnaJ related photosystem II, and LRR receptor kinase, and many of them are known to resist chilling injury. Particularly, a sophisticated regulatory model including miRNAs, phasiRNAs, and targets of them was set up. Conclusions: Integrated analysis of miRNAs and transcriptome uncovered the complicated regulation of the tolerance of cold in Populus simonii × P. nigra. MiRNAs, phasiRNAs, and gene-encoded transcription factors were characterized at a whole genome level and their expression patterns were proved to be complementary. This work lays a foundation for further research of the pathway of sRNAs and regulatory factors involved in cold tolerance.
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Affiliation(s)
- Bo Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
- College of Life Science, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
| | - Yutong Kang
- College of Life Science, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
| | - Jingtong Leng
- College of Life Science, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
| | - Qijiang Xu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
- College of Life Science, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
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22
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The Role of UV-B light on Small RNA Activity During Grapevine Berry Development. G3-GENES GENOMES GENETICS 2019; 9:769-787. [PMID: 30647106 PMCID: PMC6404619 DOI: 10.1534/g3.118.200805] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
We explored the effects of ultraviolet B radiation (UV-B) on the developmental dynamics of microRNAs and phased small-interfering-RNA (phasi-RNAs)-producing loci by sequencing small RNAs in vegetative and reproductive organs of grapevine (Vitis vinifera L.). In particular, we tested different UV-B conditions in in vitro-grown plantlets (high-fluence exposition) and in berries from field-grown (radiation filtering) and greenhouse-grown (low- and high-fluence expositions) adult plants throughout fruit development and ripening. The functional significance of the observed UV-coordinated miRNA responses was supported by degradome evidences of ARGONAUTE (AGO)-programmed slicing of mRNAs. Co-expression patterns of the up-regulated miRNAs miR156, miR482, miR530, and miR828 with cognate target gene expressions in response to high-fluence UV-B was tested by q-RT-PCR. The observed UV-response relationships were also interrogated against two published UV-stress and developmental transcriptome datasets. Together, the dynamics observed between miRNAs and targets suggest that changes in target abundance are mediated transcriptionally and, in some cases, modulated post-transcriptionally by miRNAs. Despite the major changes in target abundance are being controlled primarily by those developmental effects that are similar between treatments, we show evidence for novel miRNA-regulatory networks in grape. A model is proposed where high-fluence UV-B increases miR168 and miR530 that target ARGONAUTE 1 (AGO1) and a Plus-3 domain mRNA, respectively, while decreasing miR403 that targets AGO2, thereby coordinating post-transcriptional gene silencing activities by different AGOs. Up-regulation of miR3627/4376 could facilitate anthocyanin accumulation by antagonizing a calcium effector, whereas miR395 and miR399, induced by micronutrient deficiencies known to trigger anthocyanin accumulation, respond positively to UV-B radiation. Finally, increases in the abundance of an anthocyanin-regulatory MYB-bHLH-WD40 complex elucidated in Arabidopsis, mediated by UV-B-induced changes in miR156/miR535, could contribute to the observed up-regulation of miR828. In turn, miR828 would regulate the AtMYB113-ortologues MYBA5, A6 and A7 (and thereby anthocyanins) via a widely conserved and previously validated auto-regulatory loop involving miR828 and phasi TAS4abc RNAs.
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23
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Allan AC, Espley RV. MYBs Drive Novel Consumer Traits in Fruits and Vegetables. TRENDS IN PLANT SCIENCE 2018; 23:693-705. [PMID: 30033210 DOI: 10.1016/j.tplants.2018.06.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/01/2018] [Accepted: 06/05/2018] [Indexed: 05/27/2023]
Abstract
Eating plant-derived compounds can lead to a longer and healthier life and also benefits the environment. Innovation in the fresh food sector, as well as new cultivars, can improve consumption of fruit and vegetables, with MYB transcription factors being a target to drive this novelty. Plant MYB transcription factors are implicated in diverse roles including development, hormone signalling, and metabolite biosynthesis. The reds and blues of fruit and vegetables provided by anthocyanins, phlobaphenes, and betalains are controlled by specific R2R3 MYBs. New studies are now revealing that MYBs also control carotenoid biosynthesis and other quality traits, such as flavour and texture. Future breeding techniques may manipulate or create alleles of key MYB transcription factors.
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Affiliation(s)
- Andrew C Allan
- New Zealand Institute for Plant and Food Research, Mt Albert, Auckland, New Zealand; School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | - Richard V Espley
- New Zealand Institute for Plant and Food Research, Mt Albert, Auckland, New Zealand
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24
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Zhu X, Jiu S, Li X, Zhang K, Wang M, Wang C, Fang J. In silico identification and computational characterization of endogenous small interfering RNAs from diverse grapevine tissues and stages. Genes Genomics 2018; 40:801-817. [PMID: 30047108 DOI: 10.1007/s13258-018-0679-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 02/28/2018] [Indexed: 10/17/2022]
Abstract
Small interfering RNAs (siRNAs) are effectors of regulatory pathways underlying plant development, metabolism, and stress- and nutrient-signaling regulatory networks. The endogenous siRNAs are generally not conserved between plants; consequently, it is necessary and important to identify and characterize siRNAs from various plants. To address the nature and functions of siRNAs, and understand the biological roles of the huge siRNA population in grapevine (Vitis vinifera L.). The high-throughput sequencing technology was used to identify a large set of putative endogenous siRNAs from six grapevine tissues/organs. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was performed to classify the target genes of siRNA. In total, 520,519 candidate siRNAs were identified and their expression profiles exhibited typical temporal characters during grapevine development. In addition, we identified two grapevine trans-acting siRNA (TAS) gene homologs (VvTAS3 and VvTAS4) and the derived trans-acting siRNAs (tasiRNAs) that could target grapevine auxin response factor (ARF) and myeloblastosis (MYB) genes. Furthermore, the GO and KEGG analysis of target genes showed that most of them covered a broad range of functional categories, especially involving in disease-resistance process. The large-scale and completely genome-wide level identification and characterization of grapevine endogenous siRNAs from the diverse tissues by high throughput technology revealed the nature and functions of siRNAs in grapevine.
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Affiliation(s)
- Xudong Zhu
- College of Horticulture, Nanjing Agricultural University, Weigang 1 hao, Nanjing, 210095, China
| | - Songtao Jiu
- College of Horticulture, Nanjing Agricultural University, Weigang 1 hao, Nanjing, 210095, China
| | - Xiaopeng Li
- College of Horticulture, Nanjing Agricultural University, Weigang 1 hao, Nanjing, 210095, China
| | - Kekun Zhang
- College of Horticulture, Nanjing Agricultural University, Weigang 1 hao, Nanjing, 210095, China
| | - Mengqi Wang
- College of Horticulture, Nanjing Agricultural University, Weigang 1 hao, Nanjing, 210095, China
| | - Chen Wang
- College of Horticulture, Nanjing Agricultural University, Weigang 1 hao, Nanjing, 210095, China
| | - Jinggui Fang
- College of Horticulture, Nanjing Agricultural University, Weigang 1 hao, Nanjing, 210095, China.
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25
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Bonar N, Liney M, Zhang R, Austin C, Dessoly J, Davidson D, Stephens J, McDougall G, Taylor M, Bryan GJ, Hornyik C. Potato miR828 Is Associated With Purple Tuber Skin and Flesh Color. FRONTIERS IN PLANT SCIENCE 2018; 9:1742. [PMID: 30619382 PMCID: PMC6297172 DOI: 10.3389/fpls.2018.01742] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/08/2018] [Indexed: 05/10/2023]
Abstract
Anthocyanins are plant pigments responsible for the colors of many flowers, fruits and storage organs and have roles in abiotic and biotic stress resistance. Anthocyanins and polyphenols are bioactive compounds in plants including potato (Solanum tuberosum L.) which is the most important non-cereal crop in the world, cultivated for its tubers rich in starch and nutrients. The genetic regulation of the flavonoid biosynthetic pathway is relatively well known leading to the formation of anthocyanins. However, our knowledge of post-transcriptional regulation of anthocyanin biosynthesis is limited. There is increasing evidence that micro RNAs (miRNAs) and other small RNAs can regulate the expression level of key factors in anthocyanin production. In this study we have found strong associations between the high levels of miR828, TAS4 D4(-) and purple/red color of tuber skin and flesh. This was confirmed not only in different cultivars but in pigmented and non-pigmented sectors of the same tuber. Phytochemical analyses verified the levels of anthocyanins and polyphenols in different tissues. We showed that miR828 is able to direct cleavage of the RNA originating from Trans-acting siRNA gene 4 (TAS4) and initiate the production of phased small interfering RNAs (siRNAs) whose production depends on RNA-dependent RNA polymerase 6 (RDR6). MYB transcription factors were predicted as potential targets of miR828 and TAS4 D4(-) and their expression was characterized. MYB12 and R2R3-MYB genes showed decreased expression levels in purple skin and flesh in contrast with high levels of small RNAs in the same tissues. Moreover, we confirmed that R2R3-MYB and MYB-36284 are direct targets of the small RNAs. Overall, this study sheds light on the small RNA directed anthocyanin regulation in potato, which is an important member of the Solanaceae family.
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Affiliation(s)
- Nicola Bonar
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Michele Liney
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Runxuan Zhang
- Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Ceri Austin
- Environmental and Biochemical Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Jimmy Dessoly
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Diane Davidson
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Jennifer Stephens
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Gordon McDougall
- Environmental and Biochemical Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Mark Taylor
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Glenn J. Bryan
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Csaba Hornyik
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- *Correspondence: Csaba Hornyik,
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26
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Liu Y, Ke L, Wu G, Xu Y, Wu X, Xia R, Deng X, Xu Q. miR3954 is a trigger of phasiRNAs that affects flowering time in citrus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:263-275. [PMID: 28749585 DOI: 10.1111/tpj.13650] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 07/20/2017] [Accepted: 07/25/2017] [Indexed: 05/27/2023]
Abstract
In plant, a few 22-nt miRNAs direct cleavages of their targets and trigger the biogenesis of phased small interfering RNAs (phasiRNAs) in plant. In this study, we characterized a miRNA triggering phasiRNAs generation, miR3954, and explored its downstream target genes and potential function. Our results demonstrated that miR3954 showed specific expression in the flowers of citrus species, and it targeted a NAC transcription factor (Cs7 g22460) and two non-coding RNA transcripts (lncRNAs, Cs1 g09600 and Cs1 g09635). The production of phasiRNAs was detected from transcripts targeted by miR3954, and was further verified in both sequencing data and transient expression experiments. PhasiRNAs derived from the two lncRNAs targeted not only miR3954-targeted NAC gene but also additional NAC homologous genes. No homologous genes of these two lncRNAs were found in plants other than citrus species, implying that this miR3954-lncRNAs-phasiRNAs-NAC pathway is likely citrus-specific. Transgenic analysis indicated that the miR3954-overexpressing lines showed decreased transcripts of lncRNA, elevated abundance of phasiRNAs and reduced expression of NAC genes. Interestingly, the overexpression of miR3954 leads to early flowering in citrus plants. In summary, our results illustrated a model of the regulatory network of miR3954-lncRNA-phasiRNAs-NAC, which may be functionally involved in flowering in citrus.
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Affiliation(s)
- Yuanlong Liu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lili Ke
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guizhi Wu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuantao Xu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaomeng Wu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou, 510642, China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
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27
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Reddy VA, Wang Q, Dhar N, Kumar N, Venkatesh PN, Rajan C, Panicker D, Sridhar V, Mao HZ, Sarojam R. Spearmint R2R3-MYB transcription factor MsMYB negatively regulates monoterpene production and suppresses the expression of geranyl diphosphate synthase large subunit (MsGPPS.LSU). PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1105-1119. [PMID: 28160379 PMCID: PMC5552485 DOI: 10.1111/pbi.12701] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 01/15/2017] [Accepted: 01/27/2017] [Indexed: 05/13/2023]
Abstract
Many aromatic plants, such as spearmint, produce valuable essential oils in specialized structures called peltate glandular trichomes (PGTs). Understanding the regulatory mechanisms behind the production of these important secondary metabolites will help design new approaches to engineer them. Here, we identified a PGT-specific R2R3-MYB gene, MsMYB, from comparative RNA-Seq data of spearmint and functionally characterized it. Analysis of MsMYB-RNAi transgenic lines showed increased levels of monoterpenes, and MsMYB-overexpressing lines exhibited decreased levels of monoterpenes. These results suggest that MsMYB is a novel negative regulator of monoterpene biosynthesis. Ectopic expression of MsMYB, in sweet basil and tobacco, perturbed sesquiterpene- and diterpene-derived metabolite production. In addition, we found that MsMYB binds to cis-elements of MsGPPS.LSU and suppresses its expression. Phylogenetic analysis placed MsMYB in subgroup 7 of R2R3-MYBs whose members govern phenylpropanoid pathway and are regulated by miR858. Analysis of transgenic lines showed that MsMYB is more specific to terpene biosynthesis as it did not affect metabolites derived from phenylpropanoid pathway. Further, our results indicate that MsMYB is probably not regulated by miR858, like other members of subgroup 7.
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Affiliation(s)
- Vaishnavi Amarr Reddy
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Qian Wang
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Niha Dhar
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Nadimuthu Kumar
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | | | - Chakravarthy Rajan
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Deepa Panicker
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Vishweshwaran Sridhar
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Hui-Zhu Mao
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Rajani Sarojam
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
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28
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Alptekin B, Langridge P, Budak H. Abiotic stress miRNomes in the Triticeae. Funct Integr Genomics 2017; 17:145-170. [PMID: 27665284 PMCID: PMC5383695 DOI: 10.1007/s10142-016-0525-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/02/2016] [Accepted: 09/09/2016] [Indexed: 12/14/2022]
Abstract
The continued growth in world population necessitates increases in both the quantity and quality of agricultural production. Triticeae members, particularly wheat and barley, make an important contribution to world food reserves by providing rich sources of carbohydrate and protein. These crops are grown over diverse production environments that are characterized by a range of environmental or abiotic stresses. Abiotic stresses such as drought, heat, salinity, or nutrient deficiencies and toxicities cause large yield losses resulting in economic and environmental damage. The negative effects of abiotic stresses have increased at an alarming rate in recent years and are predicted to further deteriorate due to climate change, land degradation, and declining water supply. New technologies have provided an important tool with great potential for improving crop tolerance to the abiotic stresses: microRNAs (miRNAs). miRNAs are small regulators of gene expression that act on many different molecular and biochemical processes such as development, environmental adaptation, and stress tolerance. miRNAs can act at both the transcriptional and post-transcriptional levels, although post-transcriptional regulation is the most common in plants where miRNAs can inhibit the translation of their mRNA targets via complementary binding and cleavage. To date, expression of several miRNA families such as miR156, miR159, and miR398 has been detected as responsive to environmental conditions to regulate stress-associated molecular mechanisms individually and/or together with their various miRNA partners. Manipulation of these miRNAs and their targets may pave the way to improve crop performance under several abiotic stresses. Here, we summarize the current status of our knowledge on abiotic stress-associated miRNAs in members of the Triticeae tribe, specifically in wheat and barley, and the miRNA-based regulatory mechanisms triggered by stress conditions. Exploration of further miRNA families together with their functions under stress will improve our knowledge and provide opportunities to enhance plant performance to help us meet global food demand.
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Affiliation(s)
- Burcu Alptekin
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Peter Langridge
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, Australia
| | - Hikmet Budak
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA.
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29
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Sharma D, Tiwari M, Pandey A, Bhatia C, Sharma A, Trivedi PK. MicroRNA858 Is a Potential Regulator of Phenylpropanoid Pathway and Plant Development. PLANT PHYSIOLOGY 2016; 171:944-59. [PMID: 27208307 PMCID: PMC4902582 DOI: 10.1104/pp.15.01831] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 04/26/2016] [Indexed: 05/08/2023]
Abstract
MicroRNAs (miRNAs) are endogenous, noncoding small RNAs that function as critical regulators of gene expression. In plants, miRNAs have shown their potential as regulators of growth, development, signal transduction, and stress tolerance. Although the miRNA-mediated regulation of several processes is known, the involvement of miRNAs in regulating secondary plant product biosynthesis is poorly understood. In this study, we functionally characterized Arabidopsis (Arabidopsis thaliana) miR858a, which putatively targets R2R3-MYB transcription factors involved in flavonoid biosynthesis. Overexpression of miR858a in Arabidopsis led to the down-regulation of several MYB transcription factors regulating flavonoid biosynthesis. In contrast to the robust growth and early flowering of miR858OX plants, reduction of plant growth and delayed flowering were observed in Arabidopsis transgenic lines expressing an artificial miRNA target mimic (MIM858). Genome-wide expression analysis using transgenic lines suggested that miR858a targets a number of regulatory factors that modulate the expression of downstream genes involved in plant development and hormonal and stress responses. Furthermore, higher expression of MYBs in MIM858 lines leads to redirection of the metabolic flux towards the synthesis of flavonoids at the cost of lignin synthesis. Altogether, our study has established the potential role of light-regulated miR858a in flavonoid biosynthesis and plant growth and development.
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Affiliation(s)
- Deepika Sharma
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226001, India (D.S., M.T., A.P., C.B., A.S., P.K.T.); andAcademy of Scientific and Innovative Research, Anusandhan Bhawan, New Delhi 110 001, India (D.S., C.B., P.K.T.)
| | - Manish Tiwari
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226001, India (D.S., M.T., A.P., C.B., A.S., P.K.T.); andAcademy of Scientific and Innovative Research, Anusandhan Bhawan, New Delhi 110 001, India (D.S., C.B., P.K.T.)
| | - Ashutosh Pandey
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226001, India (D.S., M.T., A.P., C.B., A.S., P.K.T.); andAcademy of Scientific and Innovative Research, Anusandhan Bhawan, New Delhi 110 001, India (D.S., C.B., P.K.T.)
| | - Chitra Bhatia
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226001, India (D.S., M.T., A.P., C.B., A.S., P.K.T.); andAcademy of Scientific and Innovative Research, Anusandhan Bhawan, New Delhi 110 001, India (D.S., C.B., P.K.T.)
| | - Ashish Sharma
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226001, India (D.S., M.T., A.P., C.B., A.S., P.K.T.); andAcademy of Scientific and Innovative Research, Anusandhan Bhawan, New Delhi 110 001, India (D.S., C.B., P.K.T.)
| | - Prabodh Kumar Trivedi
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226001, India (D.S., M.T., A.P., C.B., A.S., P.K.T.); andAcademy of Scientific and Innovative Research, Anusandhan Bhawan, New Delhi 110 001, India (D.S., C.B., P.K.T.)
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30
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Mittal A, Jiang Y, Ritchie GL, Burke JJ, Rock CD. AtRAV1 and AtRAV2 overexpression in cotton increases fiber length differentially under drought stress and delays flowering. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 241:78-95. [PMID: 26706061 DOI: 10.1016/j.plantsci.2015.09.013] [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: 06/04/2015] [Revised: 09/11/2015] [Accepted: 09/16/2015] [Indexed: 05/23/2023]
Abstract
There is a longstanding problem of an inverse relationship between cotton fiber qualities versus high yields. To better understand drought stress signaling and adaptation in cotton (Gossypium hirsutum) fiber development, we expressed the Arabidopsis transcription factors RELATED_TO_ABA-INSENSITIVE3/VIVIPAROUS1/(RAV1) and AtRAV2, which encode APETALA2-Basic3 domain proteins shown to repress transcription of FLOWERING_LOCUS_T (FT) and to promote stomatal opening cell-autonomously. In three years of field trials, we show that AtRAV1 and AtRAV2-overexpressing cotton had ∼5% significantly longer fibers with only marginal decreases in yields under well-watered or drought stress conditions that resulted in 40-60% yield penalties and 3-7% fiber length penalties in control plants. The longer transgenic fibers from drought-stressed transgenics could be spun into yarn which was measurably stronger and more uniform than that from well-watered control fibers. The transgenic AtRAV1 and AtRAV2 lines flowered later and retained bolls at higher nodes, which correlated with repression of endogenous GhFT-Like (FTL) transcript accumulation. Elevated expression early in development of ovules was observed for GhRAV2L, GhMYB25-Like (MYB25L) involved in fiber initiation, and GhMYB2 and GhMYB25 involved in fiber elongation. Altered expression of RAVs controlling critical nodes in developmental and environmental signaling hierarchies has the potential for phenotypic modification of crops.
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Affiliation(s)
- Amandeep Mittal
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, United States.
| | - Yingwen Jiang
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, United States.
| | - Glen L Ritchie
- Department of Plant and Soils Science, Texas Tech University, Lubbock, TX 79409-2122, United States.
| | - John J Burke
- USDA-ARS Plant Stress and Germplasm Laboratory, Lubbock, TX 79415, United States.
| | - Christopher D Rock
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, United States.
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31
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Xia R, Xu J, Arikit S, Meyers BC. Extensive Families of miRNAs and PHAS Loci in Norway Spruce Demonstrate the Origins of Complex phasiRNA Networks in Seed Plants. Mol Biol Evol 2015; 32:2905-18. [PMID: 26318183 PMCID: PMC4651229 DOI: 10.1093/molbev/msv164] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In eudicot plants, the miR482/miR2118 superfamily regulates and instigates the production of phased secondary small interfering RNAs (siRNAs) from NB-LRR (nucleotide binding leucine-rich repeat) genes that encode disease resistance proteins. In grasses, this miRNA family triggers siRNA production specifically in reproductive tissues from long noncoding RNAs. To understand this functional divergence, we examined the small RNA population in the ancient gymnosperm Norway spruce (Picea abies). As many as 41 miRNA families in spruce were found to trigger phasiRNA (phased, secondary siRNAs) production from diverse PHAS loci, with a remarkable 19 miRNA families capable of targeting over 750 NB-LRR genes to generate phasiRNAs. miR482/miR2118, encoded in spruce by at least 24 precursor loci, targets not only NB-LRR genes to trigger phasiRNA production (as in eudicots) but also noncoding PHAS loci, generating phasiRNAs preferentially in male or female cones, reminiscent of its role in the grasses. These data suggest a dual function of miR482/miR2118 present in gymnosperms that was selectively yet divergently retained in flowering plants. A few MIR482/MIR2118 precursors possess an extremely long stem-loop structure, one arm of which shows significant sequence similarity to spruce NB-LRR genes, suggestive of an evolutionary origin from NB-LRR genes through gene duplication. We also characterized an expanded miR390-TAS3 (TRANS-ACTING SIRNA GENE 3)-ARF (AUXIN RESPONSIVE FACTOR) pathway, comprising 18 TAS3 genes of diverse features. Finally, we annotated spruce miRNAs and their targets. Taken together, these data expand our understanding of phasiRNA network in plants and the evolution of plant miRNAs, particularly miR482/miR2118 and its functional diversification.
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Affiliation(s)
- Rui Xia
- Department of Plant & Soil Sciences, University of Delaware Delaware Biotechnology Institute, University of Delaware
| | - Jing Xu
- Department of Plant & Soil Sciences, University of Delaware Delaware Biotechnology Institute, University of Delaware
| | - Siwaret Arikit
- Delaware Biotechnology Institute, University of Delaware Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen and Rice Science Center, Kasetsart University, Nakhon Pathom, Thailand
| | - Blake C Meyers
- Department of Plant & Soil Sciences, University of Delaware Delaware Biotechnology Institute, University of Delaware
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Zheng Y, Wang Y, Wu J, Ding B, Fei Z. A dynamic evolutionary and functional landscape of plant phased small interfering RNAs. BMC Biol 2015; 13:32. [PMID: 25980406 PMCID: PMC4457045 DOI: 10.1186/s12915-015-0142-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/07/2015] [Indexed: 11/10/2022] Open
Abstract
Background Secondary, phased small interfering RNAs (phasiRNAs) derived from protein-coding or noncoding loci (PHAS) are emerging as a new type of regulators of gene expression in plants. However, the evolution and function of these novel siRNAs in plant species remain largely unexplored. Results We systematically analyzed PHAS loci in 23 plant species covering major phylogenetic groups spanning alga, moss, gymnosperm, basal angiosperm, monocot, and dicot. We identified over 3,300 PHAS loci, among which ~1,600 were protein-coding genes. Most of these PHAS loci were novel and clade- or species-specific and showed distinct expression patterns in association with particular development stages, viral infection, or abiotic stresses. Unexpectedly, numerous PHAS loci produced phasiRNAs from introns or exon–intron junction regions. Our comprehensive analysis suggests that phasiRNAs predominantly regulate protein-coding genes from which they are derived and genes from the same families of the phasiRNA-deriving genes, in contrast to the dominant trans-regulatory mode of miRNAs. The stochastic occurrence of many PHAS loci in the plant kingdom suggests their young evolutionary origins. Conclusions Our study discovered an unprecedented diversity of protein-coding genes that produce phasiRNAs in a wide variety of plants, and set a kingdom-wide foundation for investigating the novel roles of phasiRNAs in shaping phenotype diversities of plants. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0142-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yi Zheng
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA.
| | - Ying Wang
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA. .,The Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA.
| | - Jian Wu
- The Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA. .,Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH, 43210, USA.
| | - Biao Ding
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA. .,The Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA. .,Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH, 43210, USA.
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA. .,USDA Robert W. Holley Center for Agriculture and Health, Tower Road, Ithaca, NY, 14853, USA.
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Xu W, Dubos C, Lepiniec L. Transcriptional control of flavonoid biosynthesis by MYB-bHLH-WDR complexes. TRENDS IN PLANT SCIENCE 2015; 20:176-85. [PMID: 25577424 DOI: 10.1016/j.tplants.2014.12.001] [Citation(s) in RCA: 920] [Impact Index Per Article: 102.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 11/21/2014] [Accepted: 12/10/2014] [Indexed: 05/18/2023]
Abstract
Flavonoids are widely known for the colors they confer to plant tissues, their contribution to plant fitness and health benefits, and impact on food quality. As convenient biological markers, flavonoids have been instrumental in major genetic and epigenetic discoveries. We review recent advances in the characterization of the underlying regulatory mechanisms of flavonoid biosynthesis, with a special focus on the MBW (MYB-bHLH-WDR) protein complexes. These proteins are well conserved in higher plants. They participate in different types of controls ranging from fine-tuned transcriptional regulation by environmental factors to the initiation of the flavonoid biosynthesis pathway by positive regulatory feedback. The MBW protein complexes provide interesting models for investigating developmentally or environmentally controlled transcriptional regulatory networks.
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Affiliation(s)
- Wenjia Xu
- Institut National de la Recherche Agronomique (INRA) Institut Jean-Pierre Bourgin, ERL-CNRS 3559, Saclay Plant Sciences, RD10, 78026 Versailles, France; AgroParisTech, Institut Jean-Pierre Bourgin, ERL-CNRS 3559, Saclay Plant Sciences, RD10, 78026 Versailles, France
| | - Christian Dubos
- INRA and Centre National de la Recherche Scientifique (CNRS) SupAgro-M, Université Montpellier 2 (UM2), Biochimie et Physiologie Moléculaire des Plantes, 2 place Viala, 34060 Montpellier CEDEX 1, France.
| | - Loïc Lepiniec
- Institut National de la Recherche Agronomique (INRA) Institut Jean-Pierre Bourgin, ERL-CNRS 3559, Saclay Plant Sciences, RD10, 78026 Versailles, France; AgroParisTech, Institut Jean-Pierre Bourgin, ERL-CNRS 3559, Saclay Plant Sciences, RD10, 78026 Versailles, France.
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Bustos-Sanmamed P, Hudik E, Laffont C, Reynes C, Sallet E, Wen J, Mysore KS, Camproux AC, Hartmann C, Gouzy J, Frugier F, Crespi M, Lelandais-Brière C. A Medicago truncatula rdr6 allele impairs transgene silencing and endogenous phased siRNA production but not development. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:1308-1318. [PMID: 25060922 DOI: 10.1111/pbi.12230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 06/02/2014] [Accepted: 06/12/2014] [Indexed: 06/03/2023]
Abstract
RNA-dependent RNA polymerase 6 (RDR6) and suppressor of gene silencing 3 (SGS3) act together in post-transcriptional transgene silencing mediated by small interfering RNAs (siRNAs) and in biogenesis of various endogenous siRNAs including the tasiARFs, known regulators of auxin responses and plant development. Legumes, the third major crop family worldwide, has been widely improved through transgenic approaches. Here, we isolated rdr6 and sgs3 mutants in the model legume Medicago truncatula. Two sgs3 and one rdr6 alleles led to strong developmental defects and impaired biogenesis of tasiARFs. In contrast, the rdr6.1 homozygous plants produced sufficient amounts of tasiARFs to ensure proper development. High throughput sequencing of small RNAs from this specific mutant identified 354 potential MtRDR6 substrates, for which siRNA production was significantly reduced in the mutant. Among them, we found a large variety of novel phased loci corresponding to protein-encoding genes or transposable elements. Interestingly, measurement of GFP expression revealed that post-transcriptional transgene silencing was reduced in rdr6.1 roots. Hence, this novel mis-sense mutation, affecting a highly conserved amino acid residue in plant RDR6s, may be an interesting tool both to analyse endogenous pha-siRNA functions and to improve transgene expression, at least in legume species.
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Affiliation(s)
- Pilar Bustos-Sanmamed
- CNRS, Institut des Sciences du Végétal (ISV), UPR2355, Labex SPS Saclay Plant Sciences, Gif-sur-Yvette Cedex, France
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Visser M, van der Walt AP, Maree HJ, Rees DJG, Burger JT. Extending the sRNAome of apple by next-generation sequencing. PLoS One 2014; 9:e95782. [PMID: 24752316 PMCID: PMC3994110 DOI: 10.1371/journal.pone.0095782] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 03/31/2014] [Indexed: 02/07/2023] Open
Abstract
The global importance of apple as a fruit crop necessitates investigations into molecular aspects of the processes that influence fruit quality and yield, including plant development, fruit ripening and disease resistance. In order to study and understand biological processes it is essential to recognise the range of molecules, which influence these processes. Small non-coding RNAs are regulatory agents involved in diverse plant activities, ranging from development to stress response. The occurrence of these molecules in apple leaves was studied by means of next-generation sequencing. 85 novel microRNA (miRNA) gene loci were predicted and characterized along with known miRNA loci. Both cis- and trans-natural antisense transcript pairs were identified. Although the trans-overlapping regions were enriched in small RNA (sRNA) production, cis-overlaps did not seem to agree. More than 150 phased regions were also identified, and for a small subset of these, potential miRNAs that could initiate phasing, were revealed. Repeat-associated siRNAs, which are generated from repetitive genomic regions such as transposons, were also analysed. For this group almost all available repeat sequences, associated with the apple genome and present in Repbase, were found to produce siRNAs. Results from this study extend our current knowledge on apple sRNAs and their precursors significantly. A rich molecular resource has been created and is available to the research community to serve as a baseline for future studies.
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Affiliation(s)
- Marike Visser
- Biotechnology Platform, Agricultural Research Council, Pretoria, Gauteng, South Africa
- Department of Genetics, Stellenbosch University, Stellenbosch, Western Cape, South Africa
| | - Anelda P. van der Walt
- Central Analytical Facilities, Stellenbosch University, Stellenbosch, Western Cape, South Africa
| | - Hans J. Maree
- Department of Genetics, Stellenbosch University, Stellenbosch, Western Cape, South Africa
- Infruitec-Nietvoorbij, Agricultural Research Council, Stellenbosch, Western Cape, South Africa
| | - D. Jasper G. Rees
- Biotechnology Platform, Agricultural Research Council, Pretoria, Gauteng, South Africa
| | - Johan T. Burger
- Department of Genetics, Stellenbosch University, Stellenbosch, Western Cape, South Africa
- * E-mail:
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