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Paim Pinto DL, Brancadoro L, Dal Santo S, De Lorenzis G, Pezzotti M, Meyers BC, Pè ME, Mica E. The Influence of Genotype and Environment on Small RNA Profiles in Grapevine Berry. FRONTIERS IN PLANT SCIENCE 2016; 7:1459. [PMID: 27761135 PMCID: PMC5050227 DOI: 10.3389/fpls.2016.01459] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 09/13/2016] [Indexed: 05/21/2023]
Abstract
Understanding the molecular mechanisms involved in the interaction between the genetic composition and the environment is crucial for modern viticulture. We approached this issue by focusing on the small RNA transcriptome in grapevine berries of the two varieties Cabernet Sauvignon and Sangiovese, growing in adjacent vineyards in three different environments. Four different developmental stages were studied and a total of 48 libraries of small RNAs were produced and sequenced. Using a proximity-based pipeline, we determined the general landscape of small RNAs accumulation in grapevine berries. We also investigated the presence of known and novel miRNAs and analyzed their accumulation profile. The results showed that the distribution of small RNA-producing loci is variable between the two cultivars, and that the level of variation depends on the vineyard. Differently, the profile of miRNA accumulation mainly depends on the developmental stage. The vineyard in Riccione maximizes the differences between the varieties, promoting the production of more than 1000 specific small RNA loci and modulating their expression depending on the cultivar and the maturation stage. In total, 89 known vvi-miRNAs and 33 novel vvi-miRNA candidates were identified in our samples, many of them showing the accumulation profile modulated by at least one of the factors studied. The in silico prediction of miRNA targets suggests their involvement in berry development and in secondary metabolites accumulation such as anthocyanins and polyphenols.
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Affiliation(s)
| | - Lucio Brancadoro
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy, University of MilanMilan, Italy
| | - Silvia Dal Santo
- Laboratory of Plant Genetics, Department of Biotechnology, University of VeronaVerona, Italy
| | - Gabriella De Lorenzis
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy, University of MilanMilan, Italy
| | - Mario Pezzotti
- Laboratory of Plant Genetics, Department of Biotechnology, University of VeronaVerona, Italy
| | - Blake C. Meyers
- Donald Danforth Plant Science CenterSt. Louis, MO, USA
- Division of Plant Sciences, University of Missouri–ColumbiaColumbia, MO, USA
| | - Mario E. Pè
- Institute of Life Sciences, Sant'Anna School of Advanced StudiesPisa, Italy
| | - Erica Mica
- Institute of Life Sciences, Sant'Anna School of Advanced StudiesPisa, Italy
- Genomics Research Centre, Agricultural Research CouncilFiorenzuola d'Arda, Italy
- *Correspondence: Erica Mica
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102
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Curtin SJ, Michno JM, Campbell BW, Gil-Humanes J, Mathioni SM, Hammond R, Gutierrez-Gonzalez JJ, Donohue RC, Kantar MB, Eamens AL, Meyers BC, Voytas DF, Stupar RM. MicroRNA Maturation and MicroRNA Target Gene Expression Regulation Are Severely Disrupted in Soybean dicer-like1 Double Mutants. G3 (BETHESDA, MD.) 2015; 6:423-33. [PMID: 26681515 PMCID: PMC4751560 DOI: 10.1534/g3.115.022137] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/07/2015] [Indexed: 01/06/2023]
Abstract
Small nonprotein-coding microRNAs (miRNAs) are present in most eukaryotes and are central effectors of RNA silencing-mediated mechanisms for gene expression regulation. In plants, DICER-LIKE1 (DCL1) is the founding member of a highly conserved family of RNase III-like endonucleases that function as core machinery proteins to process hairpin-like precursor transcripts into mature miRNAs, small regulatory RNAs, 21-22 nucleotides in length. Zinc finger nucleases (ZFNs) were used to generate single and double-mutants of putative soybean DCL1 homologs, DCL1a and DCL1b, to confirm their functional role(s) in the soybean miRNA pathway. Neither DCL1 single mutant, dcl1a or dcl1b plants, exhibited a pronounced morphological or molecular phenotype. However, the dcl1a/dcl1b double mutant expressed a strong morphological phenotype, characterized by reduced seed size and aborted seedling development, in addition to defective miRNA precursor transcript processing efficiency and deregulated miRNA target gene expression. Together, these findings indicate that the two soybean DCL1 paralogs, DCL1a and DCL1b, largely play functionally redundant roles in the miRNA pathway and are essential for normal plant development.
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Affiliation(s)
- Shaun J Curtin
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, 55108
| | - Jean-Michel Michno
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, 55108
| | - Benjamin W Campbell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, 55108
| | - Javier Gil-Humanes
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455 Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Sandra M Mathioni
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711
| | - Reza Hammond
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711
| | | | - Ryan C Donohue
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, 55108
| | - Michael B Kantar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, 55108
| | - Andrew L Eamens
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Blake C Meyers
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711
| | - Daniel F Voytas
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455 Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, 55108
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103
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Abstract
Plant genomes encode various small RNAs that function in distinct, yet overlapping, genetic and epigenetic silencing pathways. However, the abundance and diversity of small-RNA classes varies among plant species, suggesting coevolution between environmental adaptations and gene-silencing mechanisms. Biogenesis of small RNAs in plants is well understood, but we are just beginning to uncover their intricate regulation and activity. Here, we discuss the biogenesis of plant small RNAs, such as microRNAs, secondary siRNAs and heterochromatic siRNAs, and their diverse cellular and developmental functions, including in reproductive transitions, genomic imprinting and paramutation. We also discuss the diversification of small-RNA-directed silencing pathways through the expansion of RNA-dependent RNA polymerases, DICER proteins and ARGONAUTE proteins.
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104
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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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105
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Xia R, Ye S, Liu Z, Meyers BC, Liu Z. Novel and Recently Evolved MicroRNA Clusters Regulate Expansive F-BOX Gene Networks through Phased Small Interfering RNAs in Wild Diploid Strawberry. PLANT PHYSIOLOGY 2015; 169:594-610. [PMID: 26143249 PMCID: PMC4577376 DOI: 10.1104/pp.15.00253] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 07/01/2015] [Indexed: 05/18/2023]
Abstract
The wild strawberry (Fragaria vesca) has recently emerged as an excellent model for cultivated strawberry (Fragaria × ananassa) as well as other Rosaceae fruit crops due to its short seed-to-fruit cycle, diploidy, and sequenced genome. Deep sequencing and parallel analysis of RNA ends were used to identify F. vesca microRNAs (miRNAs) and their target genes, respectively. Thirty-eight novel and 31 known miRNAs were identified. Many known miRNAs targeted not only conserved mRNA targets but also developed new target genes in F. vesca. Significantly, two new clusters of miRNAs were found to collectively target 94 F-BOX (FBX) genes. One of the miRNAs in the new cluster is 22 nucleotides and triggers phased small interfering RNA production from six FBX genes, which amplifies the silencing to additional FBX genes. Comparative genomics revealed that the main novel miRNA cluster evolved from duplications of FBX genes. Finally, conserved trans-acting siRNA pathways were characterized and confirmed with distinct features. Our work identified novel miRNA-FBX networks in F. vesca and shed light on the evolution of miRNAs/phased small interfering RNA networks that regulate large gene families in higher plants.
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Affiliation(s)
- Rui Xia
- United States Department of Agriculture-Agricultural Research Service-Appalachian Fruit Research Station, Kearneysville, West Virginia 25430 (R.X., Zo.L.);Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711 (R.X., B.C.M.); andDepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (S.Y., Zh.L.)
| | - Songqing Ye
- United States Department of Agriculture-Agricultural Research Service-Appalachian Fruit Research Station, Kearneysville, West Virginia 25430 (R.X., Zo.L.);Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711 (R.X., B.C.M.); andDepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (S.Y., Zh.L.)
| | - Zongrang Liu
- United States Department of Agriculture-Agricultural Research Service-Appalachian Fruit Research Station, Kearneysville, West Virginia 25430 (R.X., Zo.L.);Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711 (R.X., B.C.M.); andDepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (S.Y., Zh.L.)
| | - Blake C Meyers
- United States Department of Agriculture-Agricultural Research Service-Appalachian Fruit Research Station, Kearneysville, West Virginia 25430 (R.X., Zo.L.);Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711 (R.X., B.C.M.); andDepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (S.Y., Zh.L.)
| | - Zhongchi Liu
- United States Department of Agriculture-Agricultural Research Service-Appalachian Fruit Research Station, Kearneysville, West Virginia 25430 (R.X., Zo.L.);Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711 (R.X., B.C.M.); andDepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (S.Y., Zh.L.)
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106
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Fei Q, Li P, Teng C, Meyers BC. Secondary siRNAs from Medicago NB-LRRs modulated via miRNA-target interactions and their abundances. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:451-65. [PMID: 26042408 DOI: 10.1111/tpj.12900] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/23/2015] [Accepted: 05/28/2015] [Indexed: 05/04/2023]
Abstract
Small RNAs are a class of non-coding RNAs that are of great importance in gene expression regulatory networks. Different families of small RNAs are generated via distinct biogenesis pathways. One such family specific to plants is that of phased, secondary siRNAs (phasiRNAs); these require RDR6, DCL4, and (typically) a microRNA (miRNA) trigger for their biogenesis. Protein-encoding genes are an important source of phasi-RNAs. The model legume Medicago truncatula generates phasiRNAs from many PHAS loci, and we aimed to investigate their biogenesis and mechanism by which miRNAs trigger these molecules. We modulated miRNA abundances in transgenic tissues showing that the abundance of phasiRNAs correlates with the levels of both miRNA triggers and the target, precursor transcripts. We identified sets of phasiRNAs or PHAS loci that predominantly and substantially increase in response to miRNA overexpression. In the process of validating targets from miRNA overexpression tissues, we found that in the miRNA-mRNA target pairing, the 3' terminal nucleotide (the 22nd position), but not the 10th position, is important for phasiRNA production. Mutating the single 3' terminal nucleotide dramatically diminishes phasiRNA production. Ectopic expression of Medicago NB-LRR-targeting miRNAs in Arabidopsis showed that only a few NB-LRRs are capable of phasiRNA production; our data indicate that this might be due to target inaccessibility determined by sequences flanking target sites. Our results suggest that target accessibility is an important component in miRNA-target interactions that could be utilized in target prediction, and the evolution of mRNA sequences flanking miRNA-target sites may be impacted.
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Affiliation(s)
- Qili Fei
- Department of Plant & Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA
| | - Pingchuan Li
- Department of Plant & Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA
| | - Chong Teng
- Department of Plant & Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA
| | - Blake C Meyers
- Department of Plant & Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA
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107
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Formey D, Iñiguez LP, Peláez P, Li YF, Sunkar R, Sánchez F, Reyes JL, Hernández G. Genome-wide identification of the Phaseolus vulgaris sRNAome using small RNA and degradome sequencing. BMC Genomics 2015; 16:423. [PMID: 26059339 PMCID: PMC4462009 DOI: 10.1186/s12864-015-1639-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 05/18/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND MiRNAs and phasiRNAs are negative regulators of gene expression. These small RNAs have been extensively studied in plant model species but only 10 mature microRNAs are present in miRBase version 21, the most used miRNA database, and no phasiRNAs have been identified for the model legume Phaseolus vulgaris. Thanks to the recent availability of the first version of the common bean genome, degradome data and small RNA libraries, we are able to present here a catalog of the microRNAs and phasiRNAs for this organism and, particularly, we suggest new protagonists in the symbiotic nodulation events. RESULTS We identified a set of 185 mature miRNAs, including 121 previously unpublished sequences, encoded by 307 precursors and distributed in 98 families. Degradome data allowed us to identify a total of 181 targets for these miRNAs. We reveal two regulatory networks involving conserved miRNAs: those known to play crucial roles in the establishment of nodules, and novel miRNAs present only in common bean, suggesting a specific role for these sequences. In addition, we identified 125 loci that potentially produce phased small RNAs, with 47 of them having all the characteristics of being triggered by a total of 31 miRNAs, including 14 new miRNAs identified in this study. CONCLUSIONS We provide here a set of new small RNAs that contribute to the broader knowledge of the sRNAome of Phaseolus vulgaris. Thanks to the identification of the miRNA targets from degradome analysis and the construction of regulatory networks between the mature microRNAs, we present here the probable functional regulation associated with the sRNAome and, particularly, in N2-fixing symbiotic nodules.
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Affiliation(s)
- Damien Formey
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Av. Universidad 1001, Cuernavaca, 62210, Morelos, Mexico.
| | - Luis Pedro Iñiguez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Av. Universidad 1001, Cuernavaca, 62210, Morelos, Mexico.
| | - Pablo Peláez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología (UNAM), Av. Universidad 2001, Cuernavaca, 62210, Morelos, Mexico.
| | - Yong-Fang Li
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA.
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA.
| | - Federico Sánchez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología (UNAM), Av. Universidad 2001, Cuernavaca, 62210, Morelos, Mexico.
| | - José Luis Reyes
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología (UNAM), Av. Universidad 2001, Cuernavaca, 62210, Morelos, Mexico.
| | - Georgina Hernández
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Av. Universidad 1001, Cuernavaca, 62210, Morelos, Mexico.
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108
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Belli Kullan J, Lopes Paim Pinto D, Bertolini E, Fasoli M, Zenoni S, Tornielli GB, Pezzotti M, Meyers BC, Farina L, Pè ME, Mica E. miRVine: a microRNA expression atlas of grapevine based on small RNA sequencing. BMC Genomics 2015; 16:393. [PMID: 25981679 PMCID: PMC4434875 DOI: 10.1186/s12864-015-1610-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 05/01/2015] [Indexed: 11/10/2022] Open
Abstract
Background miRNAs are the most abundant class of small non-coding RNAs, and they are involved in post-transcriptional regulations, playing a crucial role in the refinement of genetic programming during plant development. Here we present a comprehensive picture of miRNA regulation in Vitis vinifera L. plant during its complete life cycle. Furthering our knowledge about the post-transcriptional regulation of plant development is fundamental to understand the biology of such an important crop. Results We analyzed 70 small RNA libraries, prepared from berries, inflorescences, tendrils, buds, carpels, stamens and other samples at different developmental stages. One-hundred and ten known and 175 novel miRNAs have been identified and a wide grapevine expression atlas has been described. The distribution of miRNA abundance reveals that 22 novel miRNAs are specific to stamen, and two of them are, interestingly, involved in ethylene biosynthesis, while only few miRNAs are highly specific to other organs. Thirty-eight miRNAs are present in all our samples, suggesting a role in key regulatory circuit. On the basis of miRNAs abundance and distribution across samples and on the estimated correlation, we suggest that miRNA expression define organ identity. We performed target prediction analysis and focused on miRNA expression analysis in berries and inflorescence during their development, providing an initial functional description of the identified miRNAs. Conclusions Our findings represent a very extensive miRNA expression atlas in grapevine, allowing the definition of how the spatio-temporal distribution of miRNAs defines organ identity. We describe miRNAs abundance in specific tissues not previously described in grapevine and contribute to future targeted functional analyses. Finally, we present a deep characterization of miRNA involvement in berry and inflorescence development, suggesting a role for miRNA-driven hormonal regulation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1610-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jayakumar Belli Kullan
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.
| | - Daniela Lopes Paim Pinto
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.
| | - Edoardo Bertolini
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.
| | - Marianna Fasoli
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
| | - Sara Zenoni
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
| | | | - Mario Pezzotti
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
| | - Blake C Meyers
- Department of Plant and Soil Sciences, University of Delaware, 15 Innovation Way, 19711, Newark, DE, USA.
| | - Lorenzo Farina
- Department of Computer, Control and Management Engineering, University of Rome "La Sapienza", Via Ariosto 25, 00185, Rome, Italy.
| | - Mario Enrico Pè
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.
| | - Erica Mica
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy. .,Genomics Research Centre, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Via S. Protaso 302, 29017, Fiorenzuola d'Arda (PC), Italy.
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109
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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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110
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Zhao M, Cai C, Zhai J, Lin F, Li L, Shreve J, Thimmapuram J, Hughes TJ, Meyers BC, Ma J. Coordination of MicroRNAs, PhasiRNAs, and NB-LRR Genes in Response to a Plant Pathogen: Insights from Analyses of a Set of Soybean Rps Gene Near-Isogenic Lines. THE PLANT GENOME 2015; 8:eplantgenome2014.09.0044. [PMID: 33228285 DOI: 10.3835/plantgenome2014.09.0044] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 11/14/2014] [Indexed: 06/11/2023]
Abstract
Disease-related genes, particularly the nucleotide binding site (NB)-leucine-rich repeat (LRR) class of R plant genes can be triggered by microRNAs (miRNAs) to generate phased small interfering RNAs (phasiRNAs), which could reduce the transcript levels of their targets. However, how global changes in NB-LRR transcript levels coordinate with changes in miRNA and phasiRNA levels in defense responses remains largely unknown. Here, we investigated changes in the relative abundance of small RNAs (sRNAs), with a focus on miRNAs and phasiRNAs and their potential targets in response to the pathogen Phytophthora sojae in the susceptible soybean [Glycine max (L.) Merr.] 'Williams' and nine resistant near-isogenic lines (NILs), each carrying a unique resistance to P. sojae (Rps) gene. In total, 369 distinct miRNAs, including 78 new ones, were identified in the 10 soybean lines. The majority of miRNAs were downregulated by the pathogen. Of the 525 NB-LRR genes found in the soybean reference genome, 257 were predicted to be the targets of eight abundant miRNA families and 126 (dubbed phasi-NB-LRRs or pNLs) were predicted to have produced phasiRNAs. Upregulation of 15 phasi-NB-LRRs was associated with downregulation of their corresponding phasiRNAs in the NILs; these phasiRNAs were predicted to regulate 75 additional NB-LRRs in trans. In addition, we identified putative 24-nucleotide (nt) phasiRNAs from transposons, possibly representing a novel general epigenetic mechanism for regulation of transposon activity under biotic stresses. Together, these observations suggest that miRNAs and phasiRNAs play an important role in response to plant pathogens through complex, multiple layers of post-transcriptional regulation.
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Affiliation(s)
- Meixia Zhao
- Dep. of Agronomy, Purdue Univ., West Lafayette, IN, 47907
| | - Chunmei Cai
- College of Life Sciences, Qingdao Agricultural Univ., Chengyang District, Qingdao, 266109, China
| | - Jixian Zhai
- Dep. of Plant and Soil Sciences, and Delaware Biotechnology Institute, Univ. of Delaware, Newark, DE, 19716
| | - Feng Lin
- Dep. of Agronomy, Purdue Univ., West Lafayette, IN, 47907
| | - Linghong Li
- College of Life Sciences, Qingdao Agricultural Univ., Chengyang District, Qingdao, 266109, China
| | - Jacob Shreve
- Bioinformatics Core Facility, Purdue Univ., West Lafayette, IN, 47907
| | | | - Teresa J Hughes
- USDA-ARS, Crop Production and Pest Control Research Unit, West Lafayette, IN, 47907
- Monsanto Company, St. Louis, MO, 63167
| | - Blake C Meyers
- Dep. of Plant and Soil Sciences, and Delaware Biotechnology Institute, Univ. of Delaware, Newark, DE, 19716
| | - Jianxin Ma
- Dep. of Agronomy, Purdue Univ., West Lafayette, IN, 47907
- College of Life Sciences, Qingdao Agricultural Univ., Chengyang District, Qingdao, 266109, China
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Zhao M, Meyers BC, Cai C, Xu W, Ma J. Evolutionary patterns and coevolutionary consequences of MIRNA genes and microRNA targets triggered by multiple mechanisms of genomic duplications in soybean. THE PLANT CELL 2015; 27:546-62. [PMID: 25747880 PMCID: PMC4558674 DOI: 10.1105/tpc.15.00048] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 02/07/2015] [Accepted: 02/18/2015] [Indexed: 05/04/2023]
Abstract
The evolutionary dynamics of duplicated protein-encoding genes (PEGs) is well documented. However, the evolutionary patterns and consequences of duplicated MIRNAs and the potential influence on the evolution of their PEG targets are poorly understood. Here, we demonstrate the evolution of plant MIRNAs subsequent to a recent whole-genome duplication. Overall, the retention of MIRNA duplicates was correlated to the retention of adjacent PEG duplicates, and the retained MIRNA duplicates exhibited a higher level of interspecific preservation of orthologs than singletons, suggesting that the retention of MIRNA duplicates is related to their functional constraints and local genomic stability. Nevertheless, duplication status, rather than local genic collinearity, was the primary determinant of levels of nucleotide divergence of MIRNAs. In addition, the retention of duplicated MIRNAs appears to be associated with the retention of their corresponding duplicated PEG targets. Furthermore, we characterized the evolutionary novelty of a legume-specific microRNA (miRNA) family, which resulted from rounds of genomic duplication, and consequent dynamic evolution of its NB-LRR targets, an important gene family with primary roles in plant-pathogen interactions. Together, these observations depict evolutionary patterns and novelty of MIRNAs in the context of genomic duplication and evolutionary interplay between MIRNAs and their PEG targets mediated by miRNAs.
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Affiliation(s)
- Meixia Zhao
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47906
| | - Blake C Meyers
- Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19716
| | - Chunmei Cai
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Wei Xu
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Jianxin Ma
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47906 College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
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Hofmann NR. A world beyond Arabidopsis: updates on small RNAs in plant development. THE PLANT CELL 2014; 26:4564. [PMID: 25465406 PMCID: PMC4311220 DOI: 10.1105/tpc.114.134635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
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