51
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Narjala A, Nair A, Tirumalai V, Hari Sundar GV, Shivaprasad PV. A conserved sequence signature is essential for robust plant miRNA biogenesis. Nucleic Acids Res 2020; 48:3103-3118. [PMID: 32025695 PMCID: PMC7102948 DOI: 10.1093/nar/gkaa077] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/23/2020] [Accepted: 01/29/2020] [Indexed: 12/19/2022] Open
Abstract
Micro (mi)RNAs are 20–22nt long non-coding RNA molecules involved in post-transcriptional silencing of targets having high base-pair complementarity. Plant miRNAs are processed from long Pol II-transcripts with specific stem-loop structures by Dicer-like (DCL) 1 protein. Although there were reports indicating how a specific region is selected for miRNA biogenesis, molecular details were unclear. Here, we show that the presence of specific GC-rich sequence signature within miRNA/miRNA* region is required for the precise miRNA biogenesis. The involvement of GC-rich signatures in precise processing and abundance of miRNAs was confirmed through detailed molecular and functional analysis. Consistent with the presence of the miRNA-specific GC signature, target RNAs of miRNAs also possess conserved complementary sequence signatures in their miRNA binding motifs. The selection of these GC signatures was dependent on an RNA binding protein partner of DCL1 named HYL1. Finally, we demonstrate a direct application of this discovery for enhancing the abundance and efficiency of artificial miRNAs that are popular in plant functional genomic studies.
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Affiliation(s)
- Anushree Narjala
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India.,SASTRA University, Thirumalaisamudram, Thanjavur 613401, India
| | - Ashwin Nair
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India.,SASTRA University, Thirumalaisamudram, Thanjavur 613401, India
| | - Varsha Tirumalai
- 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
| | - Padubidri V Shivaprasad
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India
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52
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Ye BB, Zhang K, Wang JW. The role of miR156 in rejuvenation in Arabidopsis thaliana. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:550-555. [PMID: 31305005 DOI: 10.1111/jipb.12855] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Rejuvenation refers to the process enabling plants to regain physiological and molecular characteristics lost after entering the adult phase. The underlying molecular mechanism is poorly understood. Previous studies have revealed that microRNA156 (miR156) is highly accumulated at juvenile stage and maintains juvenile traits by repressing a group of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors. Here, we found that induction of miR156 expression in adult leaves can only restore some aspects of juvenile traits, such as loss of epidermal leaf hairs on the lower side of leaves and absence of serration at the leaf edges, but is incapable of delaying flowering and promoting adventitious root production.
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Affiliation(s)
- Bin-Bin Ye
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), the Chinese Academy of Sciences (CAS), Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, Beijing
| | - Ke Zhang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), the Chinese Academy of Sciences (CAS), Shanghai, 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 200031, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), the Chinese Academy of Sciences (CAS), Shanghai, 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 200031, China
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53
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Zhang LL, Li Y, Zheng YP, Wang H, Yang X, Chen JF, Zhou SX, Wang LF, Li XP, Ma XC, Zhao JQ, Pu M, Feng H, Fan J, Zhang JW, Huang YY, Wang WM. Expressing a Target Mimic of miR156fhl-3p Enhances Rice Blast Disease Resistance Without Yield Penalty by Improving SPL14 Expression. Front Genet 2020; 11:327. [PMID: 32391053 PMCID: PMC7191088 DOI: 10.3389/fgene.2020.00327] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/19/2020] [Indexed: 12/26/2022] Open
Abstract
MicroRNAs (miRNAs) play essential roles in the regulation of plant growth and defense responses. More and more, miRNA-3ps are reported to act in plant development and immunity. miR156 is a conserved miRNA, and most previous studies focus on its roles in plant growth, development, and yield determinacy. Here, we show that expressing a target mimic of miR156fhl-3p led to enhanced rice blast disease resistance without a yield penalty. miR156fhl-3p was differentially responsive to Magnaporthe oryzae in susceptible and resistant accessions. Transgenic lines expressing a target mimic of miR156fhl-3p (MIM156-3p) exhibited enhanced rice blast disease resistance and increased expression of defense-related genes. MIM156-3p also enhanced the mRNA abundance of SPL14 and WRKY45 by down-regulating miR156-5p and pre-miR156. Moreover, MIM156-3p lines displayed a decreased number of second rachis branches per panicle but enlarged grains, leading to unchanged yield per plant. Consistently, overexpressing miR156h (OX156) led to enhanced susceptibility to M. oryzae and decreased the expression of SPL14 and WRKY45. Our results indicate that miR156fhl-3p mounts a regulatory role on miR156-5p, which subsequently regulates the expression of SPL14 and WRKY45 to improve rice blast disease resistance.
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Affiliation(s)
- Ling-Li Zhang
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at Wenjiang, Chengdu, China
| | - Yan Li
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at Wenjiang, Chengdu, China.,State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Wenjiang, Chengdu, China
| | - Ya-Ping Zheng
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at Wenjiang, Chengdu, China
| | - He Wang
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at Wenjiang, Chengdu, China
| | - Xuemei Yang
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at Wenjiang, Chengdu, China
| | - Jin-Feng Chen
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at Wenjiang, Chengdu, China
| | - Shi-Xin Zhou
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at Wenjiang, Chengdu, China
| | - Liang-Fang Wang
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at Wenjiang, Chengdu, China
| | - Xu-Pu Li
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at Wenjiang, Chengdu, China
| | - Xiao-Chun Ma
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at Wenjiang, Chengdu, China
| | - Ji-Qun Zhao
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at Wenjiang, Chengdu, China.,State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Wenjiang, Chengdu, China
| | - Mei Pu
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at Wenjiang, Chengdu, China.,State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Wenjiang, Chengdu, China
| | - Hui Feng
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at Wenjiang, Chengdu, China.,State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Wenjiang, Chengdu, China
| | - Jing Fan
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at Wenjiang, Chengdu, China.,State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Wenjiang, Chengdu, China
| | - Ji-Wei Zhang
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at Wenjiang, Chengdu, China.,State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Wenjiang, Chengdu, China
| | - Yan-Yan Huang
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at Wenjiang, Chengdu, China.,State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Wenjiang, Chengdu, China
| | - Wen-Ming Wang
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at Wenjiang, Chengdu, China.,State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Wenjiang, Chengdu, China
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54
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Waheed S, Zeng L. The Critical Role of miRNAs in Regulation of Flowering Time and Flower Development. Genes (Basel) 2020; 11:genes11030319. [PMID: 32192095 PMCID: PMC7140873 DOI: 10.3390/genes11030319] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 03/02/2020] [Accepted: 03/13/2020] [Indexed: 12/14/2022] Open
Abstract
Flowering is an important biological process for plants that ensures reproductive success. The onset of flowering needs to be coordinated with an appropriate time of year, which requires tight control of gene expression acting in concert to form a regulatory network. MicroRNAs (miRNAs) are non-coding RNAs known as master modulators of gene expression at the post-transcriptional level. Many different miRNA families are involved in flowering-related processes such as the induction of floral competence, floral patterning, and the development of floral organs. This review highlights the diverse roles of miRNAs in controlling the flowering process and flower development, in combination with potential biotechnological applications for miRNAs implicated in flower regulation.
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Affiliation(s)
- Saquib Waheed
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 35002, China;
- Institute of Genetics and Breeding in Horticultural Plants, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lihui Zeng
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 35002, China;
- Institute of Genetics and Breeding in Horticultural Plants, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: or
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55
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Lunardon A, Johnson NR, Hagerott E, Phifer T, Polydore S, Coruh C, Axtell MJ. Integrated annotations and analyses of small RNA-producing loci from 47 diverse plants. Genome Res 2020; 30:497-513. [PMID: 32179590 PMCID: PMC7111516 DOI: 10.1101/gr.256750.119] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 01/27/2020] [Indexed: 01/25/2023]
Abstract
Plant endogenous small RNAs (sRNAs) are important regulators of gene expression. There are two broad categories of plant sRNAs: microRNAs (miRNAs) and endogenous short interfering RNAs (siRNAs). MicroRNA loci are relatively well-annotated but compose only a small minority of the total sRNA pool; siRNA locus annotations have lagged far behind. Here, we used a large data set of published and newly generated sRNA sequencing data (1333 sRNA-seq libraries containing more than 20 billion reads) and a uniform bioinformatic pipeline to produce comprehensive sRNA locus annotations of 47 diverse plants, yielding more than 2.7 million sRNA loci. The two most numerous classes of siRNA loci produced mainly 24- and 21-nucleotide (nt) siRNAs, respectively. Most often, 24-nt-dominated siRNA loci occurred in intergenic regions, especially at the 5′-flanking regions of protein-coding genes. In contrast, 21-nt-dominated siRNA loci were most often derived from double-stranded RNA precursors copied from spliced mRNAs. Genic 21-nt-dominated loci were especially common from disease resistance genes, including from a large number of monocots. Individual siRNA sequences of all types showed very little conservation across species, whereas mature miRNAs were more likely to be conserved. We developed a web server where our data and several search and analysis tools are freely accessible.
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Affiliation(s)
- Alice Lunardon
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Nathan R Johnson
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Emily Hagerott
- Department of Biology, Knox College, Galesburg, Illinois 61401, USA
| | - Tamia Phifer
- Department of Biology, Knox College, Galesburg, Illinois 61401, USA
| | - Seth Polydore
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Ceyda Coruh
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Michael J Axtell
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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56
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Ma J, Zhao P, Liu S, Yang Q, Guo H. The Control of Developmental Phase Transitions by microRNAs and Their Targets in Seed Plants. Int J Mol Sci 2020; 21:E1971. [PMID: 32183075 PMCID: PMC7139601 DOI: 10.3390/ijms21061971] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 02/29/2020] [Accepted: 03/12/2020] [Indexed: 12/18/2022] Open
Abstract
Seed plants usually undergo various developmental phase transitions throughout their lifespan, mainly including juvenile-to-adult and vegetative-to-reproductive transitions, as well as developmental transitions within organ/tissue formation. MicroRNAs (miRNAs), as a class of small endogenous non-coding RNAs, are involved in the developmental phase transitions in plants by negatively regulating the expression of their target genes at the post-transcriptional level. In recent years, cumulative evidence has revealed that five miRNAs, miR156, miR159, miR166, miR172, and miR396, are key regulators of developmental phase transitions in plants. In this review, the advanced progress of the five miRNAs and their targets in regulating plant developmental transitions, especially in storage organ formation, are summarized and discussed, combining our own findings with the literature. In general, the functions of the five miRNAs and their targets are relatively conserved, but their functional divergences also emerge to some extent. In addition, potential research directions of miRNAs in regulating plant developmental phase transitions are prospected.
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Affiliation(s)
- Jingyi Ma
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing 100083, China; (J.M.); (P.Z.); (Q.Y.)
| | - Pan Zhao
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing 100083, China; (J.M.); (P.Z.); (Q.Y.)
| | - Shibiao Liu
- College of Biology and Environmental Sciences, Jishou University, Jishou 416000, China;
| | - Qi Yang
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing 100083, China; (J.M.); (P.Z.); (Q.Y.)
| | - Huihong Guo
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing 100083, China; (J.M.); (P.Z.); (Q.Y.)
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57
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Identification of Grafting-Responsive MicroRNAs Associated with Growth Regulation in Pecan [Carya illinoinensis (Wangenh.) K. Koch]. FORESTS 2020. [DOI: 10.3390/f11020196] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Pecan [Carya illinoinensis (Wangenh.) K. Koch] is an economically important nut tree and grafting is often used for clonal propagation of cultivars. However, there is a lack of research on the effects of rootstocks on scions, which are meaningful targets for directed breeding of pecan grafts. MicroRNAs (miRNAs) play an important role in many biological processes, but the mechanism underlying the involvement of miRNAs in grafting-conferred physiological changes is unclear. To identify the grafting-responsive miRNAs that may be involved in the regulation of growth in grafted pecan, six small RNA libraries were constructed from the phloem of two groups of grafts with significantly different growth performance on short and tall rootstocks. A total of 441 conserved miRNAs belonging to 42 miRNA families and 603 novel miRNAs were identified. Among the identified miRNAs, 24 (seven conserved and 17 novel) were significantly differentially expressed by the different grafts, implying that they might be responsive to grafting and potentially involved in the regulation of graft growth. Ninety-five target genes were predicted for the differentially expressed miRNAs; gene annotation was available for 33 of these. Analysis of their targets suggested that the miRNAs may regulate auxin transport, cell activity, and inorganic phosphate (Pi) acquisition, and thereby, mediate pecan graft growth. Use of the recently-published pecan genome enabled identification of a substantial population of miRNAs, which are now available for further research. We also identified the grafting-responsive miRNAs and their potential roles in pecan graft growth, providing a basis for research on long-distance regulation in grafted pecan.
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58
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Zhang J, Fu XX, Li RQ, Zhao X, Liu Y, Li MH, Zwaenepoel A, Ma H, Goffinet B, Guan YL, Xue JY, Liao YY, Wang QF, Wang QH, Wang JY, Zhang GQ, Wang ZW, Jia Y, Wang MZ, Dong SS, Yang JF, Jiao YN, Guo YL, Kong HZ, Lu AM, Yang HM, Zhang SZ, Van de Peer Y, Liu ZJ, Chen ZD. The hornwort genome and early land plant evolution. NATURE PLANTS 2020; 6:107-118. [PMID: 32042158 PMCID: PMC7027989 DOI: 10.1038/s41477-019-0588-4] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 12/20/2019] [Indexed: 05/10/2023]
Abstract
Hornworts, liverworts and mosses are three early diverging clades of land plants, and together comprise the bryophytes. Here, we report the draft genome sequence of the hornwort Anthoceros angustus. Phylogenomic inferences confirm the monophyly of bryophytes, with hornworts sister to liverworts and mosses. The simple morphology of hornworts correlates with low genetic redundancy in plant body plan, while the basic transcriptional regulation toolkit for plant development has already been established in this early land plant lineage. Although the Anthoceros genome is small and characterized by minimal redundancy, expansions are observed in gene families related to RNA editing, UV protection and desiccation tolerance. The genome of A. angustus bears the signatures of horizontally transferred genes from bacteria and fungi, in particular of genes operating in stress-response and metabolic pathways. Our study provides insight into the unique features of hornworts and their molecular adaptations to live on land.
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Affiliation(s)
- Jian Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xin-Xing Fu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rui-Qi Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiang Zhao
- PubBio-Tech Services Corporation, Wuhan, China
| | - Yang Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
| | - Ming-He Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Arthur Zwaenepoel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Hong Ma
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Yan-Long Guan
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jia-Yu Xue
- Center for Plant Diversity and Systematics, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yi-Ying Liao
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Qing-Feng Wang
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Qing-Hua Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jie-Yu Wang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Guo-Qiang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | | | - Yu Jia
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Mei-Zhi Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Shan-Shan Dong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Jian-Fen Yang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Yuan-Nian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hong-Zhi Kong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - An-Ming Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | | | - Shou-Zhou Zhang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, Pretoria, South Africa.
- College of Horticulture, Nanjing Agricultural University, Nanjing, China.
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China.
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Zhi-Duan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.
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59
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Kang T, Yu CY, Liu Y, Song WM, Bao Y, Guo XT, Li B, Zhang HX. Subtly Manipulated Expression of ZmmiR156 in Tobacco Improves Drought and Salt Tolerance Without Changing the Architecture of Transgenic Plants. FRONTIERS IN PLANT SCIENCE 2020; 10:1664. [PMID: 31998347 PMCID: PMC6965348 DOI: 10.3389/fpls.2019.01664] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 11/26/2019] [Indexed: 05/23/2023]
Abstract
Plants in the juvenile state are more tolerant to adverse conditions. Constitutive expression of MicroRNA156 (miR156) prolonged the juvenile phase and increased resistance to abiotic stress, but also affected the architecture of transgenic plants. In this study, we investigated the possibility of subtle manipulation of miR156 expression in flowering plants, with the goal to increase tolerance to abiotic stress without altering the normal growth and development of transgenic plants. Transgenic tobacco plants expressing ZmmiR156 from maize were generated, driven either by the cauliflower mosaic virus (CaMV) 35S promoter or the stress-inducible ZmRab17 promoter. Expression of ZmmiR156 led to improved drought and salt tolerance in both 35S::MIR156 and Rab17::MIR156 transgenic plants, as shown by more vigorous growth, greater biomass production and higher antioxidant enzyme expression after a long period of drought or salt treatment, when compared to wild type and transgenic vector control plants. However, constitutive expression of ZmmiR156 also resulted in retarded growth, increased branching and delayed flowering of transgenic plants. These undesirable developmental changes could be mitigated by using the stress-inducible ZmRab17 promoter. Furthermore, under drought or salt stress conditions, expression of ZmmiR156 reduced the transcript level of NtSPL2 and NtSPL9, the genes potentially targeted by ZmmiR156, as well as that of CP1, CP2, and SAG12, the senescence-associated genes in tobacco. Collectively, our results indicate that ZmmiR156 can be temporally manipulated for the genetic improvement of plants resistant to various abiotic stresses.
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Affiliation(s)
- Tao Kang
- College of Agriculture, Ludong University, Yantai, China
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chun-Yan Yu
- College of Agriculture, Ludong University, Yantai, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), Yantai, China
| | - Yue Liu
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), Yantai, China
- College of Life Sciences, Qingdao University, Qingdao, China
| | - Wei-Meng Song
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Bao
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Tong Guo
- College of Agriculture, Ludong University, Yantai, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), Yantai, China
| | - Bei Li
- College of Agriculture, Ludong University, Yantai, China
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), Yantai, China
| | - Hong-Xia Zhang
- College of Agriculture, Ludong University, Yantai, China
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), Yantai, China
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Gramzow L, Lobbes D, Innard N, Theißen G. Independent origin of MIRNA genes controlling homologous target genes by partial inverted duplication of antisense-transcribed sequences. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:401-419. [PMID: 31571291 DOI: 10.1111/tpj.14550] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/21/2019] [Accepted: 09/18/2019] [Indexed: 06/10/2023]
Abstract
Some microRNAs (miRNAs) are key regulators of developmental processes, mainly by controlling the accumulation of transcripts encoding transcription factors that are important for morphogenesis. MADS-box genes encode a family of transcription factors which control diverse developmental processes in flowering plants. Here we study the convergent evolution of two MIRNA (MIR) gene families, named MIR444 and MIR824, targeting members of the same clade of MIKCC -group MADS-box genes. We show that these two MIR genes most likely originated independently in monocots (MIR444) and in Brassicales (eudicots, MIR824). We provide evidence that, in both cases, the future target gene was transcribed in antisense prior to the evolution of the MIR genes. Both MIR genes then likely originated by a partial inverted duplication of their target genes, resulting in natural antisense organization of the newly evolved MIR gene and its target gene at birth. We thus propose a model for the origin of MIR genes, MEPIDAS (MicroRNA Evolution by Partial Inverted Duplication of Antisense-transcribed Sequences). MEPIDAS is a refinement of the inverted duplication hypothesis. According to MEPIDAS, a MIR gene evolves at a genomic locus at which the future target gene is also transcribed in the antisense direction. A partial inverted duplication at this locus causes the antisense transcript to fold into a stem-loop structure that is recognized by the miRNA biogenesis machinery to produce a miRNA that regulates the gene at this locus. Our analyses exemplify how to elucidate the origin of conserved miRNAs by comparative genomics and will guide future studies. OPEN RESEARCH BADGE: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://www.ncbi.nlm.nih.gov/genbank/.
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Affiliation(s)
- Lydia Gramzow
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743, Jena, Germany
| | - Dajana Lobbes
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743, Jena, Germany
| | - Nathan Innard
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743, Jena, Germany
| | - Günter Theißen
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743, Jena, Germany
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61
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Li J, Gao X, Sang S, Liu C. Genome-wide identification, phylogeny, and expression analysis of the SBP-box gene family in Euphorbiaceae. BMC Genomics 2019; 20:912. [PMID: 31874634 PMCID: PMC6929338 DOI: 10.1186/s12864-019-6319-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 11/21/2019] [Indexed: 01/19/2023] Open
Abstract
Background Euphorbiaceae is one of the largest families of flowering plants. Due to its exceptional growth form diversity and near-cosmopolitan distribution, it has attracted much interest since ancient times. SBP-box (SBP) genes encode plant-specific transcription factors that play critical roles in numerous biological processes, especially flower development. We performed genome-wide identification and characterization of SBP genes from four economically important Euphorbiaceae species. Results In total, 77 SBP genes were identified in four Euphorbiaceae genomes. The SBP proteins were divided into three length ranges and 10 groups. Group-6 was absent in Arabidopsis thaliana but conserved in Euphorbiaceae. Segmental duplication played the most important role in the expansion processes of Euphorbiaceae SBP genes, and all the duplicated genes were subjected to purify selection. In addition, about two-thirds of the Euphorbiaceae SBP genes are potential targets of miR156, and some miR-regulated SBP genes exhibited high intensity expression and differential expression in different tissues. The expression profiles related to different stress treatments demonstrated broad involvement of Euphorbiaceae SBP genes in response to various abiotic factors and hormonal treatments. Conclusions In this study, 77 SBP genes were identified in four Euphorbiaceae species, and their phylogenetic relationships, protein physicochemical characteristics, duplication, tissue and stress response expression, and potential roles in Euphorbiaceae development were studied. This study lays a foundation for further studies of Euphorbiaceae SBP genes, providing valuable information for future functional exploration of Euphorbiaceae SBP genes.
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Affiliation(s)
- Jing Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoyang Gao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
| | - Shiye Sang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China. .,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China.
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62
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Wei Y, Li F, Zhang S, Zhang S, Zhang H, Sun R. Analysis of small RNA changes in different Brassica napus synthetic allopolyploids. PeerJ 2019; 7:e7621. [PMID: 31565564 PMCID: PMC6746219 DOI: 10.7717/peerj.7621] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 08/05/2019] [Indexed: 11/20/2022] Open
Abstract
Allopolyploidy is an evolutionary and mechanisticaly intriguing process involving the reconciliation of two or more sets of diverged genomes and regulatory interactions, resulting in new phenotypes. In this study, we explored the small RNA changes of eight F2 synthetic B. napus using small RNA sequencing. We found that a part of miRNAs and siRNAs were non-additively expressed in the synthesized B. napus allotetraploid. Differentially expressed miRNAs and siRNAs differed among eight F2 individuals, and the differential expression of miR159 and miR172 was consistent with that of flowering time trait. The GO enrichment analysis of differential expression miRNA target genes found that most of them were concentrated in ATP-related pathways, which might be a potential regulatory process contributing to heterosis. In addition, the number of siRNAs present in the offspring was significantly higher than that of the parent, and the number of high parents was significantly higher than the number of low parents. The results have shown that the differential expression of miRNA lays the foundation for explaining the trait separation phenomenon, and the significant increase of siRNA alleviates the shock of the newly synthesized allopolyploidy. It provides a new perspective between small RNA changes and trait separation in the early stages of allopolyploid polyploid formation.
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Affiliation(s)
- Yunxiao Wei
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fei Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shujiang Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shifan Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hui Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rifei Sun
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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63
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Yang R, Li P, Mei H, Wang D, Sun J, Yang C, Hao L, Cao S, Chu C, Hu S, Song X, Cao X. Fine-Tuning of MiR528 Accumulation Modulates Flowering Time in Rice. MOLECULAR PLANT 2019; 12:1103-1113. [PMID: 31059825 DOI: 10.1016/j.molp.2019.04.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 03/28/2019] [Accepted: 04/25/2019] [Indexed: 05/18/2023]
Abstract
In plants, microRNA (miRNA) functions in the post-transcriptional repression of target mRNAs have been well explored. However, the mechanisms regulating the accumulation of miRNAs remain poorly understood. Here, we report that distinct mechanisms regulate accumulation of a monocot-specific miRNA, rice (Oryza sativa) miR528. At the transcriptional level, miR528 accumulated to higher levels in older plants than in young seedlings and exhibited aging-modulated gradual accumulation and diurnal rhythms in leaves; at the post-transcriptional level, aging also modulated miR528 levels by enhancing pri-miR528 alternative splicing. We found that miR528 promotes rice flowering under long-day conditions by targeting RED AND FAR-RED INSENSITIVE 2 (OsRFI2). Moreover, natural variations in the MIR528 promoter region caused differences in miR528 expression among rice varieties, which are correlated with their different binding affinities with the transcription factor OsSPL9 that activates the expression of miR528. Taken together, our findings reveal rice plants have evolved sophisticated modes fine-tuning miR528 levels and provide insight into the mechanisms that regulate MIRNA expression in plants.
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Affiliation(s)
- Rongxin Yang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Pingchuan Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hailiang Mei
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dong Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Jing Sun
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chao Yang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lili Hao
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shouyun Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Songnian Hu
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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64
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Wang H, Lu Z, Xu Y, Kong L, Shi J, Liu Y, Fu C, Wang X, Wang ZY, Zhou C, Han L. Genome-wide characterization of SPL family in Medicago truncatula reveals the novel roles of miR156/SPL module in spiky pod development. BMC Genomics 2019; 20:552. [PMID: 31277566 PMCID: PMC6612136 DOI: 10.1186/s12864-019-5937-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 06/26/2019] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND SQUAMOSA Promoter Binding Protein-Likes (SPLs) proteins are plant-specific transcription factors that play many crucial roles in plant growth and development. However, there is little information about SPL family in the model legume Medicago truncatula. RESULTS In this study, a total of 23 MtSPL genes were identified in M. truncatula genome, in which 17 of the MtSPLs contained the putative MtmiR156 binding site at the coding or 3' UTR regions. Tissue-specific expression pattern analysis showed that most MtmiR156-targeted MtSPLs were highly expressed in seed and pod. The observation of MtmiR156B-overexpressing plants reveals that MtmiR156/MtSPL modules are not only involved in the development of leaves and branches, but also in the seed pod development, especially the formation of spine on pod. CONCLUSION The spines on pods are developed in many plant species, which allow pods to adhere to the animals, and then be transported on the outside. This study sheds light on the new function of SPL family in seed dispersal by controlling the formation of spiky pod, and provides insights on understanding evolutionary divergence of the members of SPL gene family among plant species.
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Affiliation(s)
- Hongfeng Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266101, China.,School of Life Science, Guangzhou University, Guangzhou, 510006, China
| | - Zhichao Lu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266101, China
| | - Yiteng Xu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266101, China
| | - Lingcui Kong
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266101, China
| | - Jianjun Shi
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266101, China
| | - Yafei Liu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266101, China
| | - Chunxiang Fu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Xiaoshan Wang
- Department of Grassland Science, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Zeng-Yu Wang
- Noble Research Institute, LLC, Ardmore, OK, USA.,Present Address: Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, People's Republic of China
| | - Chuanen Zhou
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266101, China.
| | - Lu Han
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266101, China.
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65
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Chen P, Shi Q, Liang Z, Lu H, Li R. Comparative profile analysis reveals differentially expressed microRNAs regulate anther and pollen development in kenaf cytoplasmic male sterility line. Genome 2019; 62:455-466. [DOI: 10.1139/gen-2018-0207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cytoplasmic male sterility (CMS) is advantageous in extensive crop breeding and represents a perfect model for understanding anther and pollen development research. MicroRNAs (miRNAs) play key roles in regulating various biological processes. However, the miRNA-mediated regulatory network in kenaf CMS occurrence remains largely unknown. In the present study, a comparative deep sequencing approach was used to investigate the miRNAs and their roles in regulating anther and pollen development during CMS occurrence. We identified 283 known and 46 new candidate miRNAs in kenaf anther. A total of 67 differentially expressed miRNAs (DEMs) were discovered between CMS and its maintainer line. Among them, 40 and 27 miRNAs were up- and downregulated, respectively. These 67 DEMs were predicted to target 189 genes. Validation of DEMs and putative target genes were confirmed by using real-time quantitative PCR. In addition, a potential miRNA-mediated regulatory network, which mainly involves the auxin signaling pathway, signal transduction, glycolysis and energy metabolism, gene expression, transmembrane transport, protein modification and metabolism, and floral development, that mediates anther development during CMS occurrence was proposed. Taken together, our findings provide a better understanding of the molecular mechanism of miRNA regulation in pollen development and CMS occurrence in kenaf.
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Affiliation(s)
- Peng Chen
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Qiqi Shi
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Zhichen Liang
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Hai Lu
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Ru Li
- College of Life Science and Technology, Guangxi University, Nanning, China
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66
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Peng X, Wang Q, Zhao Y, Li X, Ma Q. Comparative genome analysis of the SPL gene family reveals novel evolutionary features in maize. Genet Mol Biol 2019; 42:380-394. [PMID: 31271590 PMCID: PMC6726161 DOI: 10.1590/1678-4685-gmb-2017-0144] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/04/2018] [Indexed: 11/21/2022] Open
Abstract
SPLs are plant-specific transcription factors that play important regulatory roles in plant growth and development. Systematic analysis of the SPL family has been performed in numerous plants, such as Arabidopsis, rice, and Populus. However, no comparative analysis has been performed across different species to examine evolutionary features. In this study, we present a comparative analysis of SPLs in different species. The results showed that 84 SPLs of the four species can be divided into six groups according to phylogeny. We found that most of the SPL-containing regions in maize showed extensive conservation with duplicated regions of rice and sorghum. A gene duplication analysis in maize indicated that ZmSPLs showed a significant excess of segmental duplication. The Ka/Ks analysis indicated that 9 out of 18 duplicated pairs in maize experienced positive selection, while SPL gene pairs of rice and sorghum mainly evolved under purifying selection, suggesting novel evolutionary features for ZmSPLs. The 31 ZmSPLs were further analyzed by describing their gene structure, phylogenetic relationships, chromosomal location, and expression, Among the ZmSPLs, 13 were predicated to be targeted by miR156s and involved in drought stress response. These results provide the foundation for future functional analyses of ZmSPLs.
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Affiliation(s)
- Xiaojian Peng
- National Engineering Laboratory of Crop Stress Resistance, Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Qianqian Wang
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yang Zhao
- National Engineering Laboratory of Crop Stress Resistance, Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xiaoyu Li
- National Engineering Laboratory of Crop Stress Resistance, Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Qing Ma
- National Engineering Laboratory of Crop Stress Resistance, Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, China
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67
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Song X, Li Y, Cao X, Qi Y. MicroRNAs and Their Regulatory Roles in Plant-Environment Interactions. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:489-525. [PMID: 30848930 DOI: 10.1146/annurev-arplant-050718-100334] [Citation(s) in RCA: 366] [Impact Index Per Article: 73.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
MicroRNAs (miRNAs) are 20-24 nucleotide noncoding RNAs abundant in plants and animals. The biogenesis of plant miRNAs involves transcription of miRNA genes, processing of primary miRNA transcripts by DICER-LIKE proteins into mature miRNAs, and loading of mature miRNAs into ARGONAUTE proteins to form miRNA-induced silencing complex (miRISC). By targeting complementary sequences, miRISC negatively regulates gene expression, thereby coordinating plant development and plant-environment interactions. In this review, we present and discuss recent updates on the mechanisms and regulation of miRNA biogenesis, miRISC assembly and actions as well as the regulatory roles of miRNAs in plant developmental plasticity, abiotic/biotic responses, and symbiotic/parasitic interactions. Finally, we suggest future directions for plant miRNA research.
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Affiliation(s)
- Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China;
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China;
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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68
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Zhao L, Chen C, Wang Y, Shen J, Ding Z. Conserved MicroRNA Act Boldly During Sprout Development and Quality Formation in Pingyang Tezaocha ( Camellia sinensis). Front Genet 2019; 10:237. [PMID: 31001312 PMCID: PMC6455055 DOI: 10.3389/fgene.2019.00237] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/04/2019] [Indexed: 01/20/2023] Open
Abstract
Tea tree [Camellia sinensis (L.) O. Kuntze] is an important leaf (sometimes tender stem)-using commercial plant with many medicinal uses. The development of newly sprouts would directly affect the yield and quality of tea product, especially significant for Pingyang Tezaocha (PYTZ) which takes up a large percent in the early spring tea market. MicroRNA (miRNA), particularly the conserved miRNAs, often position in the center of subtle and complex gene regulatory systems, precisely control the biological processes together with other factors in a spatio-temporal pattern. Here, quality-determined metabolites catechins, theanine and caffeine in PYTZ sprouts including buds (sBud), different development stages of leaves (sL1, sL2) and stems (sS1, sS2) were quantified. A total of 15 miRNA libraries of the same tissue with three repetitions for each were constructed to explore vital miRNAs during the biological processes of development and quality formation. We analyzed the whole miRNA profiles during the sprout development and defined conserved miRNA families in the tea plant. The differentially expressed miRNAs related to the expression profiles buds, leaves, and stems development stages were described. Twenty one miRNAs and eight miRNA-TF pairs that most likely to participate in regulating development, and at least two miRNA-TF-metabolite triplets that participate in both development and quality formation had been filtered. Our results indicated that conserved miRNA act boldly during important biological processes, they are (i) more likely to be linked with morphological function in primary metabolism during sprout development, and (ii) hold an important position in secondary metabolism during quality formation in tea plant, also (iii) coordinate with transcription factors in forming networks of complex multicellular organism regulation.
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Affiliation(s)
- Lei Zhao
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticultural Plants, College of Horticulture, Qingdao Agricultural University, Qingdao, China.,Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, United States
| | - Changsong Chen
- Tea Research Institute, Fujian Academy of Agricultural Sciences, Fu'an, China
| | - Yu Wang
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticultural Plants, College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Jiazhi Shen
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhaotang Ding
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticultural Plants, College of Horticulture, Qingdao Agricultural University, Qingdao, China
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Wang R, Han X, Xu S, Xia B, Jiang Y, Xue Y, Wang R. Cloning and characterization of a tyrosine decarboxylase involved in the biosynthesis of galanthamine in Lycoris aurea. PeerJ 2019; 7:e6729. [PMID: 31024762 PMCID: PMC6474336 DOI: 10.7717/peerj.6729] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/06/2019] [Indexed: 11/24/2022] Open
Abstract
Background Galanthamine, one kind of Amaryllidaceae alkaloid extracted from the Lycoris species, is used in the treatment of Alzheimer’s disease. In regards to medical and economic importance, the biosynthesis and regulatory mechanism of the secondary metabolites in Lycoris remain uninvestigated. Methods BLAST was used to identify the sequence of tyrosine decarboxylase in the transcriptome of Lycoris aurea (L’Hér) Herb. The enzyme activity of this TYDC was determined by using heterologous expressed protein in the Escherichia coli cells. The related productive contents of tyramine were detected using High Performance Liquid Chromatography (HPLC). According to the available micro RNA sequencing profiles and degradome database of L. aurea, microRNA396 were isolated, which targets to LaTYDC1 and RNA Ligase-Mediated-Rapid Amplification of cDNA Ends (RLM-RACE) were used to confirm the cleavage. The expression levels of miR396 and LaTYDC1 were measured using a quantitative real-time polymerase chain reaction (qRT-PCR). Results LaTYDC1 was mainly expressed in root, bulb, leaf and flower fitting the models for galanthamine accumulation. This decarboxylase efficiently catalyzes tyrosine to tyramine conversion. Under methyl jasmonate (MeJA) treatment, the expression of LaTYDC1 and the content of tyramine sharply increase. The use of RLM-RACE confirms that miR396 promotes the degradation of LaTYDC1 mRNA. Under MeJA treatment, the expression of miR396 was suppressed while the expression level of LaTYDC1 sharply increased. Following the increase of the miR396 transcriptional level, LaTYDC1 was significantly repressed. Conclusion LaTYDC1 participates in the biosynthesis of galanthamine, and is regulated by miR396. This finding also provides genetic strategy for improving the yield of galanthamine in the future.
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Affiliation(s)
- Rong Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Xiaokang Han
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Sheng Xu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Bing Xia
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yumei Jiang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yong Xue
- Eco-environmental Protection Research Institute, Shanghai Environmental Protection Monitoring Station of Agriculture, Shanghai Engineering Research Centre of Low-carbon Agriculture (SERLA), Shanghai Key Laboratory of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Ren Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
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70
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Yin H, Hong G, Li L, Zhang X, Kong Y, Sun Z, Li J, Chen J, He Y. miR156/SPL9 Regulates Reactive Oxygen Species Accumulation and Immune Response in Arabidopsis thaliana. PHYTOPATHOLOGY 2019; 109:632-642. [PMID: 30526361 DOI: 10.1094/phyto-08-18-0306-r] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The functions of microRNA156 (miR156) and its targeted SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factor genes in plant development have been widely investigated. However, the role of the miR156/SPLs regulatory network in plant immune systems remains obscure. Here, we found that the accumulation of reactive oxygen species (ROS) and the transcripts of basal salicylic acid (SA) signaling pathway genes were lower in Arabidopsis Pro35S:MIR156 seedlings (miR156 overexpression mutants) but higher in Pro35S:MIM156 (miR156 repression mutants) and ProSPL9:rSPL9 (SPL9 overexpression mutants) seedlings compared with wild-type Col-0 plants (WT). As a result, Pro35S:MIR156 mutants induced greater susceptibility to Pseudomonas syringae pv. tomato DC3000 following syringe infiltration than WT, while Pro35S:MIM156 and ProSPL9:rSPL9 mutants showed enhanced resistance. In addition, foliar H2O2 application resulted in activation of SA-mediated defense response and ablation of miR156-induced susceptibility to P. syringae pv. tomato DC3000 infection. Collectively, our results provide new insights into the function of the miR156/SPL network in Arabidopsis immune response by regulating ROS accumulation and activating the SA signaling pathway.
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Affiliation(s)
- Hongbiao Yin
- 1 College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China
- 2 State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China
| | - Gaojie Hong
- 2 State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China
| | - Linying Li
- 2 State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China
- 3 School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Xueying Zhang
- 2 State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China
- 4 Department of Tea Science, Zhejiang University, Hangzhou 310058, China; and
| | - Yaze Kong
- 2 State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China
- 5 College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China; and
| | - Zongtao Sun
- 2 State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China
- 6 Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Junmin Li
- 2 State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China
- 6 Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jianping Chen
- 1 College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China
- 2 State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China
- 6 Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Yuqing He
- 2 State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China
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Fridrich A, Hazan Y, Moran Y. Too Many False Targets for MicroRNAs: Challenges and Pitfalls in Prediction of miRNA Targets and Their Gene Ontology in Model and Non-model Organisms. Bioessays 2019; 41:e1800169. [PMID: 30919506 PMCID: PMC6701991 DOI: 10.1002/bies.201800169] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 01/28/2019] [Indexed: 12/20/2022]
Abstract
Short ("seed") or extended base pairing between microRNAs (miRNAs) and their target RNAs enables post-transcriptional silencing in many organisms. These interactions allow the computational prediction of potential targets. In model organisms, predicted targets are frequently validated experimentally; hence meaningful miRNA-regulated processes are reported. However, in non-models, these reports mostly rely on computational prediction alone. Many times, further bioinformatic analyses such as Gene Ontology (GO) enrichment are based on these in silico projections. Here such approaches are reviewed, their caveats are highlighted and the ease of picking false targets from predicted lists is demonstrated. Discoveries that shed new light on how miRNAs evolved to regulate targets in various phyletic groups are discussed, in addition to the pitfalls of target identification in non-model organisms. The goal is to prevent the misuse of bioinformatic tools, as they cannot bypass the biological understanding of miRNA-target regulation.
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Affiliation(s)
- Arie Fridrich
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Yael Hazan
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
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Micromanagement of Developmental and Stress-Induced Senescence: The Emerging Role of MicroRNAs. Genes (Basel) 2019; 10:genes10030210. [PMID: 30871088 PMCID: PMC6470504 DOI: 10.3390/genes10030210] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/22/2019] [Accepted: 03/06/2019] [Indexed: 01/13/2023] Open
Abstract
MicroRNAs are short (19⁻24-nucleotide-long), non-coding RNA molecules. They downregulate gene expression by triggering the cleavage or translational inhibition of complementary mRNAs. Senescence is a stage of development following growth completion and is dependent on the expression of specific genes. MicroRNAs control the gene expression responsible for plant competence to answer senescence signals. Therefore, they coordinate the juvenile-to-adult phase transition of the whole plant, the growth and senescence phase of each leaf, age-related cellular structure changes during vessel formation, and remobilization of resources occurring during senescence. MicroRNAs are also engaged in the ripening and postharvest senescence of agronomically important fruits. Moreover, the hormonal regulation of senescence requires microRNA contribution. Environmental cues, such as darkness or drought, induce senescence-like processes in which microRNAs also play regulatory roles. In this review, we discuss recent findings concerning the role of microRNAs in the senescence of various plant species.
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Comparative genomics reveals origin of MIR159A–MIR159B paralogy, and complexities of PTGS interaction between miR159 and target GA-MYBs in Brassicaceae. Mol Genet Genomics 2019; 294:693-714. [DOI: 10.1007/s00438-019-01540-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 02/23/2019] [Indexed: 10/27/2022]
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Zeng J, Ye Z, He X, Zhang G. Identification of microRNAs and their targets responding to low-potassium stress in two barley genotypes differing in low-K tolerance. JOURNAL OF PLANT PHYSIOLOGY 2019; 234-235:44-53. [PMID: 30665047 DOI: 10.1016/j.jplph.2019.01.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 01/15/2019] [Accepted: 01/15/2019] [Indexed: 05/24/2023]
Abstract
MicroRNAs (miRNAs) have diverse and crucial roles in plant growth and development, including in the response to abiotic stresses. Although plant responses to K deficiency are well documented at the physiological and transcriptional levels, the miRNA-mediated post-transcriptional pathways are still not clearly elucidated. In this study, high-throughput sequencing and degradome analysis were performed using two barley genotypes differing in low-K tolerance (XZ149, tolerant and ZD9, sensitive), to determine the genotypic difference in miRNAs profiling. A total of 270 miRNAs were detected in the roots of XZ149 and ZD9 at 2 d and 10 d after low-K treatment, of which 195 were commonly found in both genotypes. Their targets were further investigated by bioinformatics prediction and degradome sequencing approach. The results showed that ata-miR1432-5p might act as a regulator participating in Ca2+ signaling pathways in response to low-K stress. The difference in the miR444/MADS-box model as well as pathways mediated by miR319/TCP4 and miR396/GRF could be attributed to high tolerance to low-K stress in XZ149. In addition, other conserved and novel miRNAs families associated with low-K tolerance were also detected. The current results provide molecular evidence for understanding the possible involvement of miRNAs in the regulation of low-K tolerance.
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Affiliation(s)
- Jianbin Zeng
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China; College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Zhilan Ye
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| | - Xiaoyan He
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Guoping Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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Lu X, Yin Z, Wang J, Chen X, Wang D, Wang S, Guo L, Fan W, Chen C, Wang X, Cui R, Zhang B, Han M, Yang X, Ye W. Identification and function analysis of drought-specific small RNAs in Gossypium hirsutum L. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 280:187-196. [PMID: 30823997 DOI: 10.1016/j.plantsci.2018.11.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 11/23/2018] [Accepted: 11/23/2018] [Indexed: 05/24/2023]
Abstract
Cotton production is severely constrained by drought, especially if encountered during the seedling stage or the fiber initiation and elongation stage, but the regulatory mechanisms underlying the effects of drought remain unclear. Therefore, characterization and functional analysis of microRNA-mediated stress regulatory networks are critical to deciphering plant drought response. In this study, 357, 379 and 377 miRNAs with annotations were obtained using the drought-resistant cotton variety ZhongH177 under three treatments, CK, drought and re-watering, and divided into 73 miRNA families with varying copy numbers from 1 to 24. 136 differential expressed genes (DEGs) with significant expression changes were found, of which only 33 DEGs were upregulated, while 103 DEGs were downregulated under drought stress. However, most DEGs recovered their initial expression states when the plants were re-watered. In total, 2657 targets were identified and found to be mainly enriched in the pathways plant-pathogen interaction, plant hormone signal transduction and biosynthesis of amino acids. Drought tolerance was significantly enhanced in 2 transgenic Arabidopsis lines, showing that miRNAs were involved in cotton drought response. Analysis of the expression patterns of 2 miRNA precursors and methylation alterations of 2 targets suggested that these miRNAs or miRNA precursors may be involved in the regulation of target methylation states. Our study provides evidence of transcriptional responses to drought stress, which will be helpful for the research of drought-resistance mechanisms in the future.
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Affiliation(s)
- Xuke Lu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, Henan, China.
| | - Zujun Yin
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, Henan, China.
| | - Junjuan Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, Henan, China.
| | - Xiugui Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, Henan, China.
| | - Delong Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, Henan, China.
| | - Shuai Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, Henan, China.
| | - Lixue Guo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, Henan, China.
| | - Weili Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, Henan, China.
| | - Chao Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, Henan, China.
| | - Xiaoge Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, Henan, China.
| | - Ruifeng Cui
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, Henan, China.
| | - Binglei Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, Henan, China.
| | - Mingge Han
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, Henan, China.
| | - Xiaomin Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, Henan, China.
| | - Wuwei Ye
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, Henan, China.
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DeBoer K, Melser S, Sperschneider J, Kamphuis LG, Garg G, Gao LL, Frick K, Singh KB. Identification and profiling of narrow-leafed lupin (Lupinus angustifolius) microRNAs during seed development. BMC Genomics 2019; 20:135. [PMID: 30764773 PMCID: PMC6376761 DOI: 10.1186/s12864-019-5521-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 02/07/2019] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Whilst information regarding small RNAs within agricultural crops is increasing, the miRNA composition of the nutritionally valuable pulse narrow-leafed lupin (Lupinus angustifolius) remains unknown. RESULTS By conducting a genome- and transcriptome-wide survey we identified 7 Dicer-like and 16 Argonaute narrow-leafed lupin genes, which were highly homologous to their legume counterparts. We identified 43 conserved miRNAs belonging to 16 families, and 13 novel narrow-leafed lupin-specific miRNAs using high-throughput sequencing of small RNAs from foliar and root and five seed development stages. We observed up-regulation of members of the miRNA families miR167, miR399, miR156, miR319 and miR164 in narrow-leafed lupin seeds, and confirmed expression of miR156, miR166, miR164, miR1507 and miR396 using quantitative RT-PCR during five narrow-leafed lupin seed development stages. We identified potential targets for the conserved and novel miRNAs and were able to validate targets of miR399 and miR159 using 5' RLM-RACE. The conserved miRNAs are predicted to predominately target transcription factors and 93% of the conserved miRNAs originate from intergenic regions. In contrast, only 43% of the novel miRNAs originate from intergenic regions and their predicted targets were more functionally diverse. CONCLUSION This study provides important insights into the miRNA gene regulatory networks during narrow-leafed lupin seed development.
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Affiliation(s)
- Kathleen DeBoer
- The UWA Institute of Agriculture, University of Western Australia, Crawley, WA 6009 Australia
| | - Su Melser
- CSIRO Agriculture and Food, Private Bag 5, Wembley, WA 6913 Australia
- Present address: INSERM U1215, Neurocentre Magendie, Bordeaux, France
| | - Jana Sperschneider
- Centre for Genomics, Metabolomics and Bioinformatics (CGMB), The Australian National University, Canberra, ACT 2601 Australia
| | - Lars G. Kamphuis
- The UWA Institute of Agriculture, University of Western Australia, Crawley, WA 6009 Australia
- CSIRO Agriculture and Food, Private Bag 5, Wembley, WA 6913 Australia
- Curtin University, Centre for Crop and Disease Management, Department of Environment and Agriculture, Bentley, WA 6102 Australia
| | - Gagan Garg
- CSIRO Agriculture and Food, Private Bag 5, Wembley, WA 6913 Australia
| | - Ling-Ling Gao
- CSIRO Agriculture and Food, Private Bag 5, Wembley, WA 6913 Australia
| | - Karen Frick
- The UWA Institute of Agriculture, University of Western Australia, Crawley, WA 6009 Australia
- CSIRO Agriculture and Food, Private Bag 5, Wembley, WA 6913 Australia
- The School of Plant Biology, University of Western Australia, Crawley, WA 6009 Australia
| | - Karam B. Singh
- The UWA Institute of Agriculture, University of Western Australia, Crawley, WA 6009 Australia
- CSIRO Agriculture and Food, Private Bag 5, Wembley, WA 6913 Australia
- Curtin University, Centre for Crop and Disease Management, Department of Environment and Agriculture, Bentley, WA 6102 Australia
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Yu L, Guo R, Jiang Y, Ye X, Yang Z, Meng Y, Shao C. Genome-wide identification and characterization of novel microRNAs in seed development of soybean. Biosci Biotechnol Biochem 2019; 83:233-242. [PMID: 30355067 DOI: 10.1080/09168451.2018.1536513] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/03/2018] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) are important and ubiquitous regulators of gene expression in eukaryotes. However, the information about miRNAs population and their regulatory functions involving in soybean seed development remains incomplete. Base on the Dicer-like1-mediated cleavage signals during miRNA processing could be employed for novel miRNA discovery, a genome-wide search for miRNA candidates involved in seed development was carried out. As a result, 17 novel miRNAs, 14 isoforms of miRNA (isomiRs) and 31 previously validated miRNAs were discovered. These novel miRNAs and isomiRs represented tissue-specific expression and the isomiRs showed significantly higher abundance than that of their miRNA counterparts in different tissues. After target prediction and degradome sequencing data-based validation, 13 novel miRNA-target pairs were further identified. Besides, five targets of 22-nt iso-gma-miR393h were found to be triggered to produce secondary trans-acting siRNA (ta-siRNAs). Summarily, our results could expand the repertoire of miRNAs with potentially important functions in soybean.
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Affiliation(s)
- Lan Yu
- a College of Life Sciences , Huzhou University , Huzhou P.R. China
| | - Rongkai Guo
- b Shanghai Institute of Plant Physiology and Ecology , Chinese Academy of Sciences , Shanghai China
| | - Yeqin Jiang
- a College of Life Sciences , Huzhou University , Huzhou P.R. China
| | - Xinghuo Ye
- a College of Life Sciences , Huzhou University , Huzhou P.R. China
| | - Zhihong Yang
- a College of Life Sciences , Huzhou University , Huzhou P.R. China
| | - Yijun Meng
- c College of Life and Environmental Sciences , Hangzhou Normal University , Hangzhou P.R. China
| | - Chaogang Shao
- a College of Life Sciences , Huzhou University , Huzhou P.R. China
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78
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Kuo YW, Lin JS, Li YC, Jhu MY, King YC, Jeng ST. MicroR408 regulates defense response upon wounding in sweet potato. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:469-483. [PMID: 30403812 PMCID: PMC6322576 DOI: 10.1093/jxb/ery381] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/02/2018] [Indexed: 05/08/2023]
Abstract
MiRNAs play diverse roles in plant development and defense responses by binding to their mRNA targets based on sequence complementarity. Here, we investigated a wound-related miR408 and its target genes in sweet potato (Ipomoea batatas) by small RNA deep sequencing and transcriptome analysis. The expression patterns of miR408 and the miR408 precursor were significantly repressed by wounding and jasmonate (JA). In contrast, expression of the putative target genes IbKCS (3-ketoacyl-CoA synthase 4), IbPCL (plantacyanin), and IbGAUT (galacturonosyltransferase 7-like) of miR408 was increased following wounding, whereas only IbKCS was increased after JA treatment. Target cleavage site mapping and Agrobacterium-mediated transient assay demonstrated that IbKCS, IbPCL, and IbGAUT were the targets of miR408. The expression of miR408 target genes was repressed in transgenic sweet potatoes overexpressing miR408. These data indicated a relationship between miR408 and its target genes. Notably, miR408-overexpressing plants showed a semi-dwarf phenotype and attenuated resistance to insect feeding, while transgenic plants overexpressing IbKCS exhibited more insect resistance than plants overexpressing only the empty vector. Collectively, sweet potato reduces the abundance of miR408 upon wounding to elevate the expression of IbKCS, IbPCL, and IbGAUT. The expression of IbKCS enhances the defense system against herbivore wounding.
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Affiliation(s)
- Yun-Wei Kuo
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Jeng-Shane Lin
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Chi Li
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Min-Yao Jhu
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yu-Chi King
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Shih-Tong Jeng
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
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79
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Kravchik M, Stav R, Belausov E, Arazi T. Functional Characterization of microRNA171 Family in Tomato. PLANTS (BASEL, SWITZERLAND) 2019; 8:E10. [PMID: 30621201 PMCID: PMC6358981 DOI: 10.3390/plants8010010] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 12/26/2018] [Accepted: 12/28/2018] [Indexed: 02/06/2023]
Abstract
Deeply conserved plant microRNAs (miRNAs) function as pivotal regulators of development. Nevertheless, in the model crop Solanum lycopersicum (tomato) several conserved miRNAs are still poorly annotated and knowledge about their functions is lacking. Here, the tomato miR171 family was functionally analyzed. We found that the tomato genome contains at least 11 SlMIR171 genes that are differentially expressed along tomato development. Downregulation of sly-miR171 in tomato was successfully achieved by transgenic expression of a short tandem target mimic construct (STTM171). Consequently, sly-miR171-targeted mRNAs were upregulated in the silenced plants. Target upregulation was associated with irregular compound leaf development and an increase in the number of axillary branches. A prominent phenotype of STTM171 expressing plants was their male sterility due to a production of a low number of malformed and nonviable pollen. We showed that sly-miR171 was expressed in anthers along microsporogenesis and significantly silenced upon STTM171 expression. Sly-miR171-silenced anthers showed delayed tapetum ontogenesis and reduced callose deposition around the tetrads, both of which together or separately can impair pollen development. Collectively, our results show that sly-miR171 is involved in the regulation of anther development as well as shoot branching and compound leaf morphogenesis.
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Affiliation(s)
- Michael Kravchik
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, P.O. Box 6, Bet Dagan 50250, Israel.
| | - Ran Stav
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, P.O. Box 6, Bet Dagan 50250, Israel.
| | - Eduard Belausov
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, P.O. Box 6, Bet Dagan 50250, Israel.
| | - Tzahi Arazi
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, P.O. Box 6, Bet Dagan 50250, Israel.
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80
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Nadiya F, Anjali N, Thomas J, Gangaprasad A, Sabu KK. Deep sequencing identified potential miRNAs involved in defence response, stress and plant growth characteristics of wild genotypes of cardamom. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:3-14. [PMID: 30098091 DOI: 10.1111/plb.12888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 08/06/2018] [Indexed: 06/08/2023]
Abstract
Cardamom has long been used as a food flavouring agent and in ayurvedic medicines for mouth ulcers, digestive problems and even depression. Extensive occurrence of pests and diseases adversely affect its cultivation and result in substantial reductions in total production and productivity. Numerous studies revealed the significant role of miRNAs in plant biotic stress responses. In the current study, miRNA profiling of cultivar and wild cardamom genotypes was performed using an Ion Proton sequencer. We identified 161 potential miRNAs representing 42 families, including monocot/tissue-specific and 14 novel miRNAs in both genotypes. Significant differences in miRNA family abundance between the libraries were observed in read frequencies. A total of 19 miRNAs (from known miRNAs) displayed a twofold difference in expression between wild and cultivar genotypes. We found 1168 unique potential targets for 40 known miRNA families in wild and 1025 potential targets for 42 known miRNA families in cultivar genotypes. The differential expression analysis revealed that most miRNAs identified were highly expressed in cultivars and, furthermore, lower expression of miR169 and higher expression of miR529 in wild cardamom proved evidence that wild genotypes have stronger drought stress tolerance and floral development than cultivars. Potential targets predicted for the newly identified miRNAs from the miRNA libraries of wild and cultivar cardamom genotypes involved in metabolic and developmental processes and in response to various stimuli. qRT-PCR confirmed miRNAs were differentially expressed between wild and cultivar genotypes. Furthermore, four target genes were validated experimentally to confirm miRNA-mRNA target pairing using RNA ligase-mediated 5' Rapid Amplification of cDNA Ends (5'RLM-RACE) PCR.
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Affiliation(s)
- F Nadiya
- Jawaharlal Nehru Tropical Botanic Garden and Research Institute (JNTBGRI), Palode, Thiruvananthapuram, India
| | - N Anjali
- Jawaharlal Nehru Tropical Botanic Garden and Research Institute (JNTBGRI), Palode, Thiruvananthapuram, India
| | - J Thomas
- Jawaharlal Nehru Tropical Botanic Garden and Research Institute (JNTBGRI), Palode, Thiruvananthapuram, India
| | - A Gangaprasad
- Department of Botany, University of Kerala, Thiruvananthapuram, India
| | - K K Sabu
- Jawaharlal Nehru Tropical Botanic Garden and Research Institute (JNTBGRI), Palode, Thiruvananthapuram, India
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Clearance of maternal barriers by paternal miR159 to initiate endosperm nuclear division in Arabidopsis. Nat Commun 2018; 9:5011. [PMID: 30479343 PMCID: PMC6258693 DOI: 10.1038/s41467-018-07429-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 10/24/2018] [Indexed: 12/17/2022] Open
Abstract
Sperm entry triggers central cell division during seed development, but what factors besides the genome are inherited from sperm, and the mechanism by which paternal factors regulate early division events, are not understood. Here we show that sperm-transmitted miR159 promotes endosperm nuclear division by repressing central cell-transmitted miR159 targets. Disruption of paternal miR159 causes approximately half of the seeds to abort as a result of defective endosperm nuclear divisions. In wild-type plants, MYB33 and MYB65, two miR159 targets, are highly expressed in the central cell before fertilization, but both are rapidly abolished after fertilization. In contrast, loss of paternal miR159 leads to retention of MYB33 and MYB65 in the central cell after fertilization. Furthermore, ectopic expression of a miR159-resistant version of MYB33 (mMYB33) in the endosperm significantly inhibits initiation of endosperm nuclear division. Collectively, these results show that paternal miR159 inhibits its maternal targets to promote endosperm nuclear division, thus uncovering a previously unknown paternal effect on seed development. Seed development in plants is triggered by entry of sperm to the ovule. Here, Zhao et al. uncover miR159 as a paternal-trigger of seed development that is transmitted to the central cell where it represses expression of maternal targets to promote nuclear division in the endosperm.
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82
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Feng G, Xu L, Wang J, Nie G, Bushman BS, Xie W, Yan H, Yang Z, Guan H, Huang L, Zhang X. Integration of small RNAs and transcriptome sequencing uncovers a complex regulatory network during vernalization and heading stages of orchardgrass (Dactylis glomerata L.). BMC Genomics 2018; 19:727. [PMID: 30285619 PMCID: PMC6171228 DOI: 10.1186/s12864-018-5104-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/21/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Flowering is a critical reproductive process in higher plants. Timing of optimal flowering depends upon the coordination among seasonal environmental cues. For cool season grasses, such as Dactylis glomerata, vernalization induced by low temperature provides competence to initiate flowering after prolonged cold. We combined analyses of the transcriptome and microRNAs (miRNAs) to generate a comprehensive resource for regulatory miRNAs and their target circuits during vernalization and heading stages. RESULTS A total of 3,846 differentially expressed genes (DEGs) and 69 differentially expressed miRNAs were identified across five flowering stages. The expression of miR395, miR530, miR167, miR396, miR528, novel_42, novel_72, novel_107, and novel_123 demonstrated significant variations during vernalization. These miRNA targeted genes were involved in phytohormones, transmembrane transport, and plant morphogenesis in response to vernalization. The expression patterns of DEGs related to plant hormones, stress responses, energy metabolism, and signal transduction changed significantly in the transition from vegetative to reproductive phases. CONCLUSIONS Five hub genes, c136110_g1 (BRI1), c131375_g1 (BZR1), c133350_g1 (VRN1), c139830_g1 (VIN3), and c125792_g2 (FT), might play central roles in vernalization response. Our comprehensive analyses have provided a useful platform for investigating consecutive transcriptional and post-transcriptional regulation of critical phases in D. glomerata and provided insights into the genetic engineering of flowering-control in cereal crops.
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Affiliation(s)
- Guangyan Feng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 Sichuan Province China
| | - Lei Xu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 Sichuan Province China
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL 32611 USA
| | - Gang Nie
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 Sichuan Province China
| | | | - Wengang Xie
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020 Gansu Province China
| | - Haidong Yan
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061 USA
| | - Zhongfu Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 Sichuan Province China
| | - Hao Guan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 Sichuan Province China
| | - Linkai Huang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 Sichuan Province China
| | - Xinquan Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 Sichuan Province China
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Microsynteny analysis to understand evolution and impact of polyploidization on MIR319 family within Brassicaceae. Dev Genes Evol 2018; 228:227-242. [PMID: 30242472 DOI: 10.1007/s00427-018-0620-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 09/14/2018] [Indexed: 10/28/2022]
Abstract
The availability of a large number of whole-genome sequences allows comparative genomic analysis to reveal and understand evolution of regulatory regions and elements. The role played by events such as whole-genome and segmental duplications followed by genome fractionation in shaping genomic landscape and in expansion of gene families is crucial toward developing insights into evolutionary trends and consequences such as sequence and functional diversification. Members of Brassicaceae are known to have experienced several rounds of whole-genome duplication (WGD) that have been termed as paleopolyploidy, mesopolyploidy, and neopolyploidy. Such repeated events led to the creation and expansion of a large number of gene families. MIR319 is reported to be one of the most ancient and conserved plant MIRNA families and plays a role in growth and development including leaf development, seedling development, and embryo patterning. We have previously reported functional diversification of members of miR319 in Brassica oleracea affecting leaf architecture; however, the evolutionary history of the MIR319 gene family across Brassicaceae remains unknown and requires investigation. We therefore identified homologous and homeologous segments of ca. 100 kb, with or without MIR319, performed comparative synteny analysis and genome fractionation studies. We detected variable rates of gene retention across members of Brassicaceae when genomic blocks of MIR319a, MIR319b, and MIR319c were compared either between themselves or against Arabidopsis thaliana genome which was taken as the base genome. The highest levels of shared genes were found between A. thaliana and Capsella rubella in both MIR319b- and MIR319c-containing genomic segments, and with the closest species of A. thaliana, A. lyrata, only in MIR319a-containing segment. Synteny analysis across 12 genomes (with 30 sub-genomes) revealed MIR319c to be the most conserved MIRNA loci (present in 27 genomes/sub-genomes) followed by MIR319a (present in 23 genomes/sub-genomes); MIR319b was found to be frequently lost (present in 20 genomes/sub-genomes) and thus is under least selection pressure for retention. Genome fractionation revealed extensive and differential loss of MIRNA homeologous loci and flanking genes from various sub-genomes of Brassica species that is in accordance with their older history of polyploidy when compared to Camelina sativa, a recent neopolyploid, where the effect of genome fractionation was least. Finally, estimation of phylogenetic relationship using precursor sequences of MIR319 reveals MIR319a and MIR319b form sister clades, with MIR319c forming a separate clade. An intra-species synteny analysis between MIR319a-, MIR319b-, and MIR319c-containing genomic segments suggests segmental duplications at the base of Brassicaceae to be responsible for the origin of MIR319a and MIR319b.
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84
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Du F, Guan C, Jiao Y. Molecular Mechanisms of Leaf Morphogenesis. MOLECULAR PLANT 2018; 11:1117-1134. [PMID: 29960106 DOI: 10.1016/j.molp.2018.06.006] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/06/2018] [Accepted: 06/21/2018] [Indexed: 05/17/2023]
Abstract
Plants maintain the ability to form lateral appendages throughout their life cycle and form leaves as the principal lateral appendages of the stem. Leaves initiate at the peripheral zone of the shoot apical meristem and then develop into flattened structures. In most plants, the leaf functions as a solar panel, where photosynthesis converts carbon dioxide and water into carbohydrates and oxygen. To produce structures that can optimally fulfill this function, plants precisely control the initiation, shape, and polarity of leaves. Moreover, leaf development is highly flexible but follows common themes with conserved regulatory mechanisms. Leaves may have evolved from lateral branches that are converted into determinate, flattened structures. Many other plant parts, such as floral organs, are considered specialized leaves, and thus leaf development underlies their morphogenesis. Here, we review recent advances in the understanding of how three-dimensional leaf forms are established. We focus on how genes, phytohormones, and mechanical properties modulate leaf development, and discuss these factors in the context of leaf initiation, polarity establishment and maintenance, leaf flattening, and intercalary growth.
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Affiliation(s)
- Fei Du
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunmei Guan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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85
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Fei Q, Yu Y, Liu L, Zhang Y, Baldrich P, Dai Q, Chen X, Meyers BC. Biogenesis of a 22-nt microRNA in Phaseoleae species by precursor-programmed uridylation. Proc Natl Acad Sci U S A 2018; 115:8037-8042. [PMID: 30012624 PMCID: PMC6077734 DOI: 10.1073/pnas.1807403115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phased, secondary siRNAs (phasiRNAs) represent a class of small RNAs in plants generated via distinct biogenesis pathways, predominantly dependent on the activity of 22-nt miRNAs. Most 22-nt miRNAs are processed by DCL1 from miRNA precursors containing an asymmetric bulge, yielding a 22/21-nt miRNA/miRNA* duplex. Here we show that miR1510, a soybean miRNA capable of triggering phasiRNA production from numerous nucleotide-binding leucine-rich repeat (NB-LRRs), previously described as 21 nt in its mature form, primarily accumulates as a 22-nt isoform via monouridylation. We demonstrate that, in Arabidopsis, this uridylation is performed by HESO1. Biochemical experiments showed that the 3' terminus of miR1510 is only partially 2'-O-methylated because of the terminal mispairing in the miR1510/miR1510* duplex that inhibits HEN1 activity in soybean. miR1510 emerged in the Phaseoleae ∼41-42 million years ago with a conserved precursor structure yielding a 22-nt monouridylated form, yet a variant in mung bean is processed directly in a 22-nt mature form. This analysis of miR1510 yields two observations: (i) plants can utilize postprocessing modification to generate abundant 22-nt miRNA isoforms to more efficiently regulate target mRNA abundances; and (ii) comparative analysis demonstrates an example of selective optimization of precursor processing of a young plant miRNA.
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Affiliation(s)
- Qili Fei
- Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711
- Donald Danforth Plant Science Center, St. Louis, MO 63132
| | - Yu Yu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521
| | - Li Liu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521
| | - Yu Zhang
- Donald Danforth Plant Science Center, St. Louis, MO 63132
| | | | - Qing Dai
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, 518060 Shenzhen, China
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, MO 63132;
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211
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86
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Fei Q, Yu Y, Liu L, Zhang Y, Baldrich P, Dai Q, Chen X, Meyers BC. Biogenesis of a 22-nt microRNA in Phaseoleae species by precursor-programmed uridylation. Proc Natl Acad Sci U S A 2018; 115:8037-8042. [PMID: 30012624 DOI: 10.1101/310920] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023] Open
Abstract
Phased, secondary siRNAs (phasiRNAs) represent a class of small RNAs in plants generated via distinct biogenesis pathways, predominantly dependent on the activity of 22-nt miRNAs. Most 22-nt miRNAs are processed by DCL1 from miRNA precursors containing an asymmetric bulge, yielding a 22/21-nt miRNA/miRNA* duplex. Here we show that miR1510, a soybean miRNA capable of triggering phasiRNA production from numerous nucleotide-binding leucine-rich repeat (NB-LRRs), previously described as 21 nt in its mature form, primarily accumulates as a 22-nt isoform via monouridylation. We demonstrate that, in Arabidopsis, this uridylation is performed by HESO1. Biochemical experiments showed that the 3' terminus of miR1510 is only partially 2'-O-methylated because of the terminal mispairing in the miR1510/miR1510* duplex that inhibits HEN1 activity in soybean. miR1510 emerged in the Phaseoleae ∼41-42 million years ago with a conserved precursor structure yielding a 22-nt monouridylated form, yet a variant in mung bean is processed directly in a 22-nt mature form. This analysis of miR1510 yields two observations: (i) plants can utilize postprocessing modification to generate abundant 22-nt miRNA isoforms to more efficiently regulate target mRNA abundances; and (ii) comparative analysis demonstrates an example of selective optimization of precursor processing of a young plant miRNA.
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Affiliation(s)
- Qili Fei
- Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711
- Donald Danforth Plant Science Center, St. Louis, MO 63132
| | - Yu Yu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521
| | - Li Liu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521
| | - Yu Zhang
- Donald Danforth Plant Science Center, St. Louis, MO 63132
| | | | - Qing Dai
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, 518060 Shenzhen, China
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, MO 63132;
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211
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87
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Lymperopoulos P, Msanne J, Rabara R. Phytochrome and Phytohormones: Working in Tandem for Plant Growth and Development. FRONTIERS IN PLANT SCIENCE 2018; 9:1037. [PMID: 30100912 PMCID: PMC6072860 DOI: 10.3389/fpls.2018.01037] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 06/26/2018] [Indexed: 05/07/2023]
Abstract
Being sessile organisms, plants need to continually adapt and modulate their rate of growth and development in accordance with the changing environmental conditions, a phenomenon referred to as plasticity. Plasticity in plants is a highly complex process that involves a well-coordinated interaction between different signaling pathways, the spatiotemporal involvement of phytohormones and cues from the environment. Though research studies are being carried out over the years to understand how plants perceive the signals from changing environmental conditions and activate plasticity, such remain a mystery to be resolved. Among all environmental cues, the light seems to be the stand out factor influencing plant growth and development. During the course of evolution, plants have developed well-equipped signaling system that enables regulation of both quantitative and qualitative differences in the amount of perceived light. Light influences essential developmental switches in plants ranging from germination or transition to flowering, photomorphogenesis, as well as switches in response to shade avoidances and architectural changes occurring during phototropism. Abscisic acid (ABA) is controlling seed germination and is regulated by light. Furthermore, circadian clock adds another level of regulation to plant growth by integrating light signals with different hormonal pathways. MYB96 has been identified as a regulator of circadian gating of ABA-mediated responses in plants by binding to the TIMING OF CAB EXPRESSION 1(TOC1) promoter. This review will present a representative regulatory model, highlight the successes achieved in employing novel strategies to dissect the levels of interaction and provide perspective for future research on phytochrome-phytohormones relationships toward facilitating plant growth, development, and function under abiotic-biotic stresses.
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Affiliation(s)
| | - Joseph Msanne
- New Mexico Consortium, Los Alamos, NM, United States
| | - Roel Rabara
- New Mexico Consortium, Los Alamos, NM, United States
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88
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89
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Liu H, Yu H, Tang G, Huang T. Small but powerful: function of microRNAs in plant development. PLANT CELL REPORTS 2018; 37:515-528. [PMID: 29318384 DOI: 10.1007/s00299-017-2246-5] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 12/15/2017] [Indexed: 05/02/2023]
Abstract
MicroRNAs (miRNAs) are a group of endogenous noncoding small RNAs frequently 21 nucleotides long. miRNAs act as negative regulators of their target genes through sequence-specific mRNA cleavage, translational repression, or chromatin modifications. Alterations of the expression of a miRNA or its targets often result in a variety of morphological and physiological abnormalities, suggesting the strong impact of miRNAs on plant development. Here, we review the recent advances on the functional studies of plant miRNAs. We will summarize the regulatory networks of miRNAs in a series of developmental processes, including meristem development, establishment of lateral organ polarity and boundaries, vegetative and reproductive organ growth, etc. We will also conclude the conserved and species-specific roles of plant miRNAs in evolution and discuss the strategies for further elucidating the functional mechanisms of miRNAs during plant development.
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Affiliation(s)
- Haiping Liu
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, 49931, USA
| | - Hongyang Yu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Guiliang Tang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, 49931, USA
| | - Tengbo Huang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China.
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90
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Lin WY, Lin YY, Chiang SF, Syu C, Hsieh LC, Chiou TJ. Evolution of microRNA827 targeting in the plant kingdom. THE NEW PHYTOLOGIST 2018; 217:1712-1725. [PMID: 29214636 DOI: 10.1111/nph.14938] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 10/26/2017] [Indexed: 05/08/2023]
Abstract
Unlike most ancient microRNAs, which conservatively target homologous genes across species, microRNA827 (miR827) targets two different types of SPX (SYG1/PHO81/XPR1)-domain-containing genes, NITROGEN LIMITATION ADAPTATION (NLA) and PHOSPHATE TRANSPORTER 5 (PHT5), in Arabidopsis thaliana and Oryza sativa to regulate phosphate (Pi) transport and storage, respectively. However, how miR827 shifted its target preference and its evolutionary history are unknown. Based on target prediction analysis, we found that in most angiosperms, miR827 conservatively targets PHT5 homologs, but in Brassicaceae and Cleomaceae it preferentially targets NLA homologs, and we provide evidence for the transition of target preference during Brassicales evolution. Intriguingly, we found a lineage-specific loss of the miR827-regulatory module in legumes. Analysis of miR827-mediated cleavage efficiency and the expression of PHT5 in A. thaliana indicated that accumulation of mutations in the target site and the exclusion of the target site by alternative transcriptional initiation eliminated PHT5 targeting by miR827. Here, we identified a transition of miR827 target preference during plant evolution and revealed the uniqueness of miR827-mediated regulation among conserved plant miRNAs. Despite the change in its target preference, upregulation of miR827 by Pi starvation and its role in regulating cellular Pi homeostasis were retained.
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Affiliation(s)
- Wei-Yi Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
- Department of Agronomy, National Taiwan University, Taipei, 106, Taiwan
| | - Yen-Yu Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Su-Fen Chiang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Cueihuan Syu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan
| | - Li-Ching Hsieh
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan
| | - Tzyy-Jen Chiou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan
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91
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92
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Kajal M, Singh K. Small RNA profiling for identification of miRNAs involved in regulation of saponins biosynthesis in Chlorophytum borivilianum. BMC PLANT BIOLOGY 2017; 17:265. [PMID: 29281971 PMCID: PMC5745966 DOI: 10.1186/s12870-017-1214-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 12/14/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND MicroRNAs act as molecular regulator of cell signaling, plant growth and development, and regulate various primary and secondary plant metabolic processes. In the present study, deep sequencing of small RNAs was carried out to identify known and novel miRNAs from pharmaceutically important plant, Chlorophytum borivilianum. RESULTS Total 442 known miRNAs and 5 novel miRNAs were identified from young leaf small RNA library. Experimental validation with stem loop RT-PCR confirmed the in silico identification. Based on transcriptome data of root and leaf of C. borivilianum, Oryza sativa, and Arabidopsis thaliana target gene prediction was done using psRNAtarget and mirRanda. BLAST2GO helped in localization of predicted targets and KEGG (Kyoto Encyclopedia for Genes and Genomes) pathway analysis concluded that miR9662, miR894, miR172, and miR166 might be involved in regulating saponin biosynthetic pathway. The correlation between miRNA and its target gene was further validated by RT-qPCR analysis. CONCLUSION This study provides first elaborated glimpse of miRNA pool of C. borivilianum, which can help to understand the miRNA dependent regulation of saponin biosynthesis and to design further metabolic engineering experiment to enhance their contents in the plant.
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Affiliation(s)
- Monika Kajal
- Department of Biotechnology, Panjab University, BMS Block-I, Sector 25, Chandigarh, 160014, India
| | - Kashmir Singh
- Department of Biotechnology, Panjab University, BMS Block-I, Sector 25, Chandigarh, 160014, India.
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93
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Litholdo CG, Eamens AL, Waterhouse PM. The phenotypic and molecular assessment of the non-conserved Arabidopsis MICRORNA163/S-ADENOSYL-METHYLTRANSFERASE regulatory module during biotic stress. Mol Genet Genomics 2017; 293:503-523. [PMID: 29196849 DOI: 10.1007/s00438-017-1399-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 11/22/2017] [Indexed: 10/18/2022]
Abstract
In plants, microRNAs (miRNAs) have evolved in parallel to the protein-coding genes that they target for expression regulation, and miRNA-directed gene expression regulation is central to almost every cellular process. MicroRNA, miR163, is unique to the Arabidopsis genus and is processed into a 24-nucleotide (nt) mature small regulatory RNA (sRNA) from a single precursor transcript transcribed from a single locus, the MIR163 gene. The MIR163 locus is a result of a recent inverted duplication event of one of the five closely related S-ADENOSYL-METHYLTRANSFERASE genes that the mature miR163 sRNA targets for expression regulation. Currently, however, little is known about the role of the miR163/S-ADENOSYL-METHYLTRANSFERASE regulatory module in response to biotic stress. Here, we document the expression domains of MIR163 and the S-ADENOSYL-METHYLTRANSFERASE target genes following fusion of their putative promoter sequences to the β-glucuronidase (GUS) reporter gene and subsequent in planta expression. Further, we report on our phenotypic and molecular assessment of Arabidopsis thaliana plants with altered miR163 accumulation, namely the mir163-1 and mir163-2 insertion knockout mutants and the miR163 overexpression line, the MIR163-OE plant. Finally, we reveal miR163 accumulation and S-ADENOSYL-METHYLTRANSFERASE target gene expression post treatment with the defence elicitors, salicylic acid and jasmonic acid, and following Fusarium oxysporum infection, wounding, and herbivory attack. Together, the work presented here provides a comprehensive new biological insight into the role played by the Arabidopsis genus-specific miR163/S-ADENOSYL-METHYLTRANSFERASE regulatory module in normal A. thaliana development and during the exposure of A. thaliana plants to biotic stress.
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Affiliation(s)
- Celso Gaspar Litholdo
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia. .,Citrus Biotechnology Lab, Centro de Citricultura, Instituto Agronômico de Campinas, Cordeirópolis, SP, 13490-000, Brazil.
| | - Andrew Leigh Eamens
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia.,School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Peter Michael Waterhouse
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia.,Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, 4001, Australia
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94
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D'Ario M, Griffiths-Jones S, Kim M. Small RNAs: Big Impact on Plant Development. TRENDS IN PLANT SCIENCE 2017; 22:1056-1068. [PMID: 29032035 DOI: 10.1016/j.tplants.2017.09.009] [Citation(s) in RCA: 173] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/13/2017] [Accepted: 09/18/2017] [Indexed: 05/19/2023]
Abstract
While the role of proteins in determining cell identity has been extensively studied, the contribution of small noncoding RNA molecules such as miRNAs and siRNAs has been also recognised. miRNAs bind to complementary sites in target mRNA molecules to trigger the degradation or translational inhibition of those targets. Recent studies have revealed that miRNAs play pivotal roles in key developmental processes such as patterning of the embryo, meristem, leaf, and flower. Furthermore, these miRNAs have been recruited throughout plant evolution into pathways that create diverse plant organ forms and shapes. This review focuses on the roles of miRNAs in establishing plant cell identity during key plant development processes and creating morphological diversity during plant evolution.
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Affiliation(s)
- Marco D'Ario
- Faculty of Biology, Medicine, and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Sam Griffiths-Jones
- Faculty of Biology, Medicine, and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK.
| | - Minsung Kim
- Faculty of Biology, Medicine, and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK.
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95
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Xu L, Hu Y, Cao Y, Li J, Ma L, Li Y, Qi Y. An expression atlas of miRNAs in Arabidopsis thaliana. SCIENCE CHINA-LIFE SCIENCES 2017; 61:178-189. [PMID: 29197026 DOI: 10.1007/s11427-017-9199-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 10/16/2017] [Indexed: 01/21/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that regulate a variety of biological processes. MiRNA expression often exhibits spatial and temporal specificity. However, genome-wide miRNA expression patterns in different organs during development of Arabidopsis thaliana have not yet been systemically investigated. In this study, we sequenced small RNA libraries generated from 27 different organ/tissue types, which cover the entire life cycle of Arabidopsis. Analysis of the sequencing data revealed that most miRNAs are ubiquitously expressed, whereas a small set of miRNAs display highly specific expression patterns. In addition, different miRNA members within the same family have distinct spatial and temporal expression patterns. Moreover, we found that some miRNAs are produced from different arms of their hairpin precursors at different developmental stages. This work provides new insights into the regulation of miRNA biogenesis and a rich resource for future investigation of miRNA functions in Arabidopsis.
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Affiliation(s)
- Le Xu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yugang Hu
- College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Ying Cao
- College of Life Sciences-Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Capital Normal University, Beijing, 100048, China
| | - Jingrui Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Ligeng Ma
- College of Life Sciences-Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Capital Normal University, Beijing, 100048, China
| | - Yan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China. .,Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China. .,Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
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96
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Liu Y, El-Kassaby YA. Landscape of Fluid Sets of Hairpin-Derived 21-/24-nt-Long Small RNAs at Seed Set Uncovers Special Epigenetic Features in Picea glauca. Genome Biol Evol 2017; 9:82-92. [PMID: 28082604 PMCID: PMC5381586 DOI: 10.1093/gbe/evw283] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2016] [Indexed: 12/23/2022] Open
Abstract
Conifers’ exceptionally large genome (20–30 Gb) is scattered with 60% retrotransposon (RT) components and we have little knowledge on their origin and evolutionary implications. RTs may impede the expression of flanking genes and provide sources of the formation of novel small RNA (sRNAs) populations to constrain events of transposon (TE) proliferation/transposition. Here we show a declining expression of 24-nt-long sRNAs and low expression levels of their key processing gene, pgRTL2 (RNASE THREE LIKE 2) at seed set in Picea glauca. The sRNAs in 24-nt size class are significantly less enriched in type and read number than 21-nt sRNAs and have not been documented in other species. The architecture of MIR loci generating highly expressed 24-/21-nt sRNAs is featured by long terminal repeat—retrotransposons (LTR-RTs) in families of Ty3/Gypsy and Ty1/Copia elements. This implies that the production of sRNAs may be predominantly originated from TE fragments on chromosomes. Furthermore, a large proportion of highly expressed 24-nt sRNAs does not have predictable targets against unique genes in Picea, suggestive of their potential pathway in DNA methylation modifications on, for instance, TEs. Additionally, the classification of computationally predicted sRNAs suggests that 24-nt sRNA targets may bear particular functions in metabolic processes while 21-nt sRNAs target genes involved in many different biological processes. This study, therefore, directs our attention to a possible extrapolation that lacking of 24-nt sRNAs at the late conifer seed developmental phase may result in less constraints in TE activities, thus contributing to the massive expansion of genome size.
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Affiliation(s)
- Yang Liu
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
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97
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Liu Y, El-Kassaby YA. Global Analysis of Small RNA Dynamics during Seed Development of Picea glauca and Arabidopsis thaliana Populations Reveals Insights on their Evolutionary Trajectories. FRONTIERS IN PLANT SCIENCE 2017; 8:1719. [PMID: 29046688 PMCID: PMC5632664 DOI: 10.3389/fpls.2017.01719] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/20/2017] [Indexed: 06/07/2023]
Abstract
While DNA methylation carries genetic signals and is instrumental in the evolution of organismal complexity, small RNAs (sRNAs), ~18-24 ribonucleotide (nt) sequences, are crucial mediators of methylation as well as gene silencing. However, scant study deals with sRNA evolution via featuring their expression dynamics coupled with species of different evolutionary time. Here we report an atlas of sRNAs and microRNAs (miRNAs, single-stranded sRNAs) produced over time at seed-set of two major spermatophytes represented by populations of Picea glauca and Arabidopsis thaliana with different seed-set duration. We applied diverse profiling methods to examine sRNA and miRNA features, including size distribution, sequence conservation and reproduction-specific regulation, as well as to predict their putative targets. The top 27 most abundant miRNAs were highly overlapped between the two species (e.g., miR166,-319 and-396), but in P. glauca, they were less abundant and significantly less correlated with seed-set phases. The most abundant sRNAs in libraries were deeply conserved miRNAs in the plant kingdom for Arabidopsis but long sRNAs (24-nt) for P. glauca. We also found significant difference in normalized expression between populations for population-specific sRNAs but not for lineage-specific ones. Moreover, lineage-specific sRNAs were enriched in the 21-nt size class. This pattern is consistent in both species and alludes to a specific type of sRNAs (e.g., miRNA, tasiRNA) being selected for. In addition, we deemed 24 and 9 sRNAs in P. glauca and Arabidopsis, respectively, as sRNA candidates targeting known adaptive genes. Temperature had significant influence on selected gene and miRNA expression at seed development in both species. This study increases our integrated understanding of sRNA evolution and its potential link to genomic architecture (e.g., sRNA derivation from genome and sRNA-mediated genomic events) and organismal complexity (e.g., association between different sRNA expression and their functionality).
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98
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Ganie SA, Debnath AB, Gumi AM, Mondal TK. Comprehensive survey and evolutionary analysis of genome-wide miRNA genes from ten diploid Oryza species. BMC Genomics 2017; 18:711. [PMID: 28893199 PMCID: PMC5594537 DOI: 10.1186/s12864-017-4089-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 08/25/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are non-coding RNAs that play versatile roles in post-transcriptional gene regulation. Although much is known about their biogenesis, and gene regulation very little is known about their evolutionary relation among the closely related species. RESULT All the orthologous miRNA genes of Oryza sativa (japonica) from 10 different Oryza species were identified, and the evolutionary changes among these genes were analysed. Significant differences in the expansion of miRNA gene families were observed across the Oryza species. Analysis of the nucleotide substitution rates indicated that the mature sequences show the least substitution rates among the different regions of miRNA genes, and also show a very much less substitution rates as compared to that of all protein-coding genes across the Oryza species. Evolution of miRNA genes was also found to be contributed by transposons. A non-neutral selection was observed at 80 different miRNA loci across Oryza species which were estimated to have lost ~87% of the sequence diversity during the domestication. The phylogenetic analysis revealed that O. longistaminata diverged first among the AA-genomes, whereas O. brachyantha and O. punctata appeared as the eminent out-groups. The miR1861 family organised into nine distinct compact clusters in the studied Oryza species except O. brachyantha. Further, the expression analysis showed that 11 salt-responsive miRNAs were differentially regulated between O. coarctata and O. glaberrima. CONCLUSION Our study provides the evolutionary dynamics in the miRNA genes of 10 different Oryza species which will support more investigations about the structural and functional organization of miRNA genes of Oryza species.
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Affiliation(s)
- Showkat Ahmad Ganie
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, IARI Campus, New Delhi, 110012, India
| | - Ananda Bhusan Debnath
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, IARI Campus, New Delhi, 110012, India
| | - Abubakar Mohammad Gumi
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, IARI Campus, New Delhi, 110012, India
| | - Tapan Kumar Mondal
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, IARI Campus, New Delhi, 110012, India.
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99
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Xie Y, Liu Y, Wang H, Ma X, Wang B, Wu G, Wang H. Phytochrome-interacting factors directly suppress MIR156 expression to enhance shade-avoidance syndrome in Arabidopsis. Nat Commun 2017; 8:348. [PMID: 28839125 PMCID: PMC5570905 DOI: 10.1038/s41467-017-00404-y] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 06/24/2017] [Indexed: 12/22/2022] Open
Abstract
Plants have evolved a repertoire of strategies collectively termed the shade-avoidance syndrome to avoid shade from canopy and compete for light with their neighbors. However, the signaling mechanism governing the adaptive changes of adult plant architecture to shade is not well understood. Here, we show that in Arabidopsis, compared with the wild type, several PHYTOCHROME-INTERACTING FACTORS (PIFS) overexpressors all display constitutive shade-avoidance syndrome under normal high red to far-red light ratio conditions but are less sensitive to the simulated shade, whereas the MIR156 overexpressors exhibit an opposite phenotype. The simulated shade induces rapid accumulation of PIF proteins, reduced expression of multiple MIR156 genes, and concomitant elevated expression of the SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) family genes. Moreover, in vivo and in vitro assays indicate that PIFs bind to the promoters of several MIR156 genes directly and repress their expression. Our results establish a direct functional link between the phytochrome-PIFs and miR156-SPL regulatory modules in mediating shade-avoidance syndrome.Plants employ developmental strategies to avoid shade and compete with neighbors for light. Here, Xie et al. show that phytochrome-interacting factors, which are regulated in a light-dependent manner, directly repress MIR156 genes and promote the expression of SPL genes to enhance shade-avoidance responses.
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Affiliation(s)
- Yurong Xie
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yang Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hai Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaojing Ma
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.,Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Baobao Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guangxia Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Haiyang Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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100
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Xu X, Xu X, Zhou Y, Zeng S, Kong W. Identification of protoplast-isolation responsive microRNAs in Citrus reticulata Blanco by high-throughput sequencing. PLoS One 2017; 12:e0183524. [PMID: 28829800 PMCID: PMC5567906 DOI: 10.1371/journal.pone.0183524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Accepted: 08/04/2017] [Indexed: 01/21/2023] Open
Abstract
Protoplast isolation is a stress-inducing process, during which a variety of physiological and molecular alterations take place. Such stress response affects the expression of totipotency of cultured protoplasts. MicroRNAs (miRNAs) play important roles in plant growth, development and stress responses. However, the underlying mechanism of miRNAs involved in the protoplast totipotency remains unclear. In this study, high-throughput sequencing technology was used to sequence two populations of small RNA from calli and callus-derived protoplasts in Citrus reticulata Blanco. A total of 67 known miRNAs from 35 families and 277 novel miRNAs were identified. Among these miRNAs, 18 known miRNAs and 64 novel miRNAs were identified by differentially expressed miRNAs (DEMs) analysis. The expression patterns of the eight DEMs were verified by qRT-PCR. Target prediction showed most targets of the miRNAs were transcription factors. The expression levels of half targets showed a negative correlation to those of the miRNAs. Furthermore, the physiological analysis showed high levels of antioxidant activities in isolated protoplasts. In short, our results indicated that miRNAs may play important roles in protoplast-isolation response.
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Affiliation(s)
- Xiaoyong Xu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
- * E-mail: (XYX); (WWK)
| | - Xiaoling Xu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Yipeng Zhou
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Shaohua Zeng
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, PR China
| | - Weiwen Kong
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
- * E-mail: (XYX); (WWK)
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