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Wang Q, Yang Y, Lu G, Sun X, Feng Y, Yan S, Zhang H, Jiang Q, Zhang H, Hu Z, Chen R. Genome-wide identification of microRNAs and phased siRNAs in soybean roots under long-term salt stress. Genes Genomics 2020; 42:1239-1249. [PMID: 32939614 DOI: 10.1007/s13258-020-00990-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 08/19/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Salinity stress, as the key limiting factor for agricultural productivity, can activate a series of molecular responses and alter gene expression in plants. Endogenous regulatory small RNAs, such as microRNAs (miRNAs) and phased siRNAs (phasiRNAs), play crucial roles during stress adaptation and prevent the injury from environmental circumstances. OBJECTIVE To identify long-term salt stress responsive miRNAs and phasiRNAs as well as their associated genes and pathways in soybean roots. METHODS Small RNA and degradome sequencing strategies were applied to genome widely investigate miRNAs and phasiRNAs in soybean roots under control and long-term salt stress conditions. RESULTS In this study, stringent bioinformatic analysis led to the identification of 253 conserved and 38 novel miRNA candidates. Results of expression profiling, target and endogenous target mimics predictions provided valuable clues to their functional roles. Furthermore, 156 genes were identified to be capable of generating 21 nt and 24 nt phasiRNAs, in which 37 candidates were confirmed by degradome data for miRNA-directed cleavage. Approximately 90% of these phasiRNA loci were protein coding genes. And GO enrichment analysis pointed to "signal transduction" and "ADP binding" entries and reflected the functional roles of identified phasiRNA genes. CONCLUSION Taken together, our findings extended the knowledge of salt responsive miRNAs and phasiRNAs in soybean roots, and provided valuable information for a better understanding of the regulatory events caused by small RNAs underlying plant adaptations to long-term salt stress.
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Affiliation(s)
- Qian Wang
- Biotechnology Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China
| | - Yingxia Yang
- Biotechnology Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China
| | - Guoqing Lu
- Biotechnology Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China
| | - Xianjun Sun
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Youren Feng
- Tianjin Academy of Agricultural Sciences, Tianjin, 300192, China
| | - Shuangyong Yan
- Tianjin Key Laboratory of Crop Genetics and Breeding, Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, 300384, China
| | - Huiyuan Zhang
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qiyan Jiang
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hui Zhang
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zheng Hu
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Rui Chen
- Biotechnology Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China.
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Fu W, Wang C, Xu W, Zhu P, Lu Y, Wei S, Wu X, Wu Y, Zhao Y, Zhu S. Unintended effects of transgenic rice revealed by transcriptome and metabolism. GM CROPS & FOOD 2019; 10:20-34. [PMID: 30955410 DOI: 10.1080/21645698.2019.1598215] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Genetically modified (GM) organisms have been developed for decades. However, unintended effects are the main concerns of safety assessment that needs to be carefully investigated. Here, eight varieties of GM rice that were developed in China were selected to assess the unintended effects through transcriptome and metabolism. There are 2892-8758 differentially expressed genes (DEGs) and 7-50 metabolites at significant level between GM varieties and their isogenic counterparts, which were far fewer than that between traditional rice varieties. The function enrichment analysis showed altered transcription in stress-related pathway and starch and sucrose metabolism. DEGs shared among eight GM samples constitute less than 1% of the genes in the genome, and none of them is reported more than four times. The insertion effect on the nearby gene expression and the associated metabolism is only restricted to 50 genes. All the results provide a comprehensive analysis of unintended effects and indication of difference in Chinese transgenic rice based on their backgrounds, transformation, and insertion elements.
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Affiliation(s)
- Wei Fu
- a Chinese Academy of Inspection and Quarantine , Beijing , China
| | - Chenguang Wang
- a Chinese Academy of Inspection and Quarantine , Beijing , China.,b Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences , China Agricultural University , Beijing , China.,c College of Plant Protection , China Agricultural University , Beijing , China
| | - Wenjie Xu
- a Chinese Academy of Inspection and Quarantine , Beijing , China.,b Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences , China Agricultural University , Beijing , China.,c College of Plant Protection , China Agricultural University , Beijing , China
| | - Pengyu Zhu
- a Chinese Academy of Inspection and Quarantine , Beijing , China
| | - Yun Lu
- a Chinese Academy of Inspection and Quarantine , Beijing , China
| | - Shuang Wei
- d Guangdong Entry-Exit Inspection and Quarantine Bureau , Guangzhou , China
| | - Xiyang Wu
- e Department of Food Science and Engineering , Jinan University , Guangzhou , China
| | - Yuping Wu
- a Chinese Academy of Inspection and Quarantine , Beijing , China
| | - Yiqiang Zhao
- b Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences , China Agricultural University , Beijing , China
| | - Shuifang Zhu
- a Chinese Academy of Inspection and Quarantine , Beijing , China.,c College of Plant Protection , China Agricultural University , Beijing , China
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Yang K, Wen X, Mudunuri S, Varma GPS, Sablok G. Diff isomiRs: Large-scale detection of differential isomiRs for understanding non-coding regulated stress omics in plants. Sci Rep 2019; 9:1406. [PMID: 30723229 PMCID: PMC6363768 DOI: 10.1038/s41598-019-38932-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 01/14/2019] [Indexed: 11/11/2022] Open
Abstract
Plants have an amazing ability to cope with wide variety of stresses by regulating the expression of genes and thus by altering the physiological status. In the past few years, canonical microRNA variants (isomiRs) have been shown to play pivotal roles by acting as regulators of the transcriptional machinery. In the present research, we present Diff isomiRs, a web-based exploratory repository of differential isomiRs across 16 sequenced plant species representing a total of 433 datasets across 21 different stresses and 158 experimental states. Diff isomiRs provides the high-throughput detection of differential isomiRs using mapping-based and model-based differential analysis revealing a total of 16,157 and 2,028 differential isomiRs, respectively. Easy-to-use and web-based exploration of differential isomiRs provides several features such as browsing of the differential isomiRs according to stress or species, as well as association of the differential isomiRs to targets and plant endogenous target mimics (PeTMs). Diff isomiRs also provides the relationship between the canonical miRNAs, isomiRs and the miRNA-target interactions. This is the first web-based large-scale repository for browsing differential isomiRs and will facilitate better understanding of the regulatory role of the isomiRs with respect to the canonical microRNAs. Diff isomiRs can be accessed at: www.mcr.org.in/diffisomirs.
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Affiliation(s)
- Kun Yang
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Guizhou University), Ministry of Education, Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou Province, P. R. China
| | - Xiaopeng Wen
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Guizhou University), Ministry of Education, Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou Province, P. R. China.
| | - Suresh Mudunuri
- Centre for Bioinformatics Research, SRKR Engineering College, Chinna Amiram, Bhimavaram, West Godavari District, Andhra Pradesh, 534204, India
| | - G P Saradhi Varma
- Centre for Bioinformatics Research, SRKR Engineering College, Chinna Amiram, Bhimavaram, West Godavari District, Andhra Pradesh, 534204, India
| | - Gaurav Sablok
- Finnish Museum of Natural History, Helsinki, Finland. .,Organismal and Evolutionary Biology (OEB) Research Programme, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
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Agapito-Tenfen SZ, Vilperte V, Traavik TI, Nodari RO. Systematic miRNome profiling reveals differential microRNAs in transgenic maize metabolism. ENVIRONMENTAL SCIENCES EUROPE 2018; 30:37. [PMID: 30294516 PMCID: PMC6153861 DOI: 10.1186/s12302-018-0168-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/11/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND While some genetically modified organisms (GMOs) are created to produce new double-stranded RNA molecules (dsRNA), in others, such molecules may occur as an unintended effect of the genetic engineering process. Furthermore, GMOs might produce naturally occurring dsRNA molecules in higher or lower quantities than its non-transgenic counterpart. This study is the first to use high-throughput technology to characterize the miRNome of commercialized GM maize events and to investigate potential alterations in miRNA regulatory networks. RESULTS Thirteen different conserved miRNAs were found to be dys-regulated in GM samples. The insecticide Bt GM variety had the most distinct miRNome. These miRNAs target a range of endogenous transcripts, such as transcription factors and nucleic acid binding domains, which play key molecular functions in basic genetic regulation. In addition, we have identified 20 potential novel miRNAs with target transcripts involved in lipid metabolism in maize. isomiRs were also found in 96 conserved miRNAs sequences, as well as potential transgenic miRNA sequences, which both can be a source of potential off-target effects in the plant genome. We have also provided information on technical limitations and when to carry on additional in vivo experimental testing. CONCLUSIONS These findings do not reveal hazards per se but show that robust and reproducible miRNA profiling technique can strengthen the assessment of risk by detecting any new intended and unintended dsRNA molecules, regardless of the outcome, at any stage of GMO development.
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Affiliation(s)
| | - Vinicius Vilperte
- Departamento de Fitotecnia, Universidade Federal de Santa Catarina, Florianópolis, 88034000 Brazil
- Present Address: Institute for Plant Genetics, Faculty of Natural Sciences, Leibniz University of Hannover, 30419 Hannover, Germany
| | - Terje Ingemar Traavik
- GenØk–Centre for Biosafety, Forskningsparken i Breivika, Sykehusveien 23, 9294 Tromsø, Norway
| | - Rubens Onofre Nodari
- Departamento de Fitotecnia, Universidade Federal de Santa Catarina, Florianópolis, 88034000 Brazil
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Comparative analysis of miRNA expression profiles in transgenic and non-transgenic rice using miRNA-Seq. Sci Rep 2018; 8:338. [PMID: 29321648 PMCID: PMC5762784 DOI: 10.1038/s41598-017-18723-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 12/15/2017] [Indexed: 12/02/2022] Open
Abstract
Safety assessment for genetically modified organisms (GMOs) is required before their release. To date, miRNAs that play important roles in eukaryotic gene regulation have not been considered in the current assessment system. In this study, we identified 6 independent Bt and EPSPS GM rice lines using PCR and immune strip. We analyzed the expression levels of Cry1Ac and EPSPS using quantitative real-time PCR and western blot. Further, miRNAs from the developing seeds of the 6 GM rice lines and the wild-type line were investigated using deep sequencing and bioinformatic approaches. Although these GM lines have different types of integration sites, copy numbers, and levels of gene expression, 21 differentially expressed miRNAs have been found compared to wild type. There is no correlation between transgenic protein expression level and the quantity of differentially expressed miRNAs. This study provides useful data about the miRNA composition of GM plants, and it might be helpful for future risk assessments of miRNA-based GM plants.
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Lu XG, Kang X, Zhan LB, Kang LM, Fan ZW, Bai LZ. Circulating miRNAs as biomarkers for severe acute pancreatitis associated with acute lung injury. World J Gastroenterol 2017; 23:7440-7449. [PMID: 29151698 PMCID: PMC5685850 DOI: 10.3748/wjg.v23.i41.7440] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/23/2017] [Accepted: 09/19/2017] [Indexed: 02/06/2023] Open
Abstract
AIM To identify circulating micro (mi)RNAs as biological markers for prediction of severe acute pancreatitis (SAP) with acute lung injury (ALI).
METHODS Twenty-four serum samples were respectively collected and classified as SAP associated with ALI and SAP without ALI, and the miRNA expression profiles were determined by microarray analysis. These miRNAs were validated by quantitative reverse transcription-polymerase chain reaction, and their putative targets were predicted by the online software TargetScan, miRanda and PicTar database. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (commonly known as KEGG) were used to predict their possible functions and pathways involved.
RESULTS We investigated 287 miRNAs based on microarray data analysis. Twelve miRNAs were differentially expressed in the patients with SAP with ALI and those with SAP without ALI. Hsa-miR-1260b, 762, 22-3p, 23b and 23a were differently up-regulated and hsa-miR-550a*, 324-5p, 484, 331-3p, 140-3p, 342-3p and 150 were differently down-regulated in patients with SAP with ALI compared to those with SAP without ALI. In addition, 85 putative target genes of the significantly dysregulated miRNAs were found by TargetScan, miRanda and PicTar. Finally, GO and pathway network analysis showed that they were mainly enriched in signal transduction, metabolic processes, cytoplasm and cell membranes.
CONCLUSION This is the first study to identify 12 circulating miRNAs in patients with SAP with ALI, which may be biomarkers for prediction of ALI after SAP.
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Affiliation(s)
- Xiao-Guang Lu
- Department of Emergency, Zhongshan Hospital, Dalian University, Dalian 116001, Liaoning Province, China
| | - Xin Kang
- Department of Emergency, Zhongshan Hospital, Dalian University, Dalian 116001, Liaoning Province, China
| | - Li-Bin Zhan
- College of Basic Medicine, Nanjing University of Chinese Medicine, Nanjing 210000, Jiangsu Province, China
| | - Li-Min Kang
- Department of Hepatobiliary and Pancreatic Surgery, Puer People’s Hospital, Puer 665000, Yunnan Province, China
| | - Zhi-Wei Fan
- Department of Emergency, Zhongshan Hospital, Dalian University, Dalian 116001, Liaoning Province, China
| | - Li-Zhi Bai
- Department of Emergency, Zhongshan Hospital, Dalian University, Dalian 116001, Liaoning Province, China
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Tian B, Wang S, Todd TC, Johnson CD, Tang G, Trick HN. Genome-wide identification of soybean microRNA responsive to soybean cyst nematodes infection by deep sequencing. BMC Genomics 2017; 18:572. [PMID: 28768484 PMCID: PMC5541722 DOI: 10.1186/s12864-017-3963-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 07/25/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The soybean cyst nematode (SCN), Heterodera glycines, is one of the most devastating diseases limiting soybean production worldwide. It is known that small RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), play important roles in regulating plant growth and development, defense against pathogens, and responses to environmental changes. RESULTS In order to understand the role of soybean miRNAs during SCN infection, we analyzed 24 small RNA libraries including three biological replicates from two soybean cultivars (SCN susceptible KS4607, and SCN HG Type 7 resistant KS4313N) that were grown under SCN-infested and -noninfested soil at two different time points (SCN feeding establishment and egg production). In total, 537 known and 70 putative novel miRNAs in soybean were identified from a total of 0.3 billion reads (average about 13.5 million reads for each sample) with the programs of Bowtie and miRDeep2 mapper. Differential expression analyses were carried out using edgeR to identify miRNAs involved in the soybean-SCN interaction. Comparative analysis of miRNA profiling indicated a total of 60 miRNAs belonging to 25 families that might be specifically related to cultivar responses to SCN. Quantitative RT-PCR validated similar miRNA interaction patterns as sequencing results. CONCLUSION These findings suggest that miRNAs are likely to play key roles in soybean response to SCN. The present work could provide a framework for miRNA functional identification and the development of novel approaches for improving soybean SCN resistance in future studies.
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Affiliation(s)
- Bin Tian
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, 4024 Throckmorton Plant Sciences Center, Manhattan, KS 66506 USA
| | - Shichen Wang
- Genomics and Bioinformatics Service, Texas A&M AgriLife, College Station, TX 77845 USA
| | - Timothy C. Todd
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, 4024 Throckmorton Plant Sciences Center, Manhattan, KS 66506 USA
| | - Charles D. Johnson
- Genomics and Bioinformatics Service, Texas A&M AgriLife, College Station, TX 77845 USA
| | - Guiliang Tang
- Department of Biological Sciences, Michigan Technological University, Dow Environmental Sciences and Engineering Building - Room 406, 1400 Townsend Drive, Houghton, MI 49931-1295 USA
| | - Harold N. Trick
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, 4024 Throckmorton Plant Sciences Center, Manhattan, KS 66506 USA
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Jiang Q, Sun X, Niu F, Hu Z, Chen R, Zhang H. GmDREB1 overexpression affects the expression of microRNAs in GM wheat seeds. PLoS One 2017; 12:e0175924. [PMID: 28459812 PMCID: PMC5411081 DOI: 10.1371/journal.pone.0175924] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 04/03/2017] [Indexed: 01/07/2023] Open
Abstract
MicroRNAs (miRNAs) are small regulators of gene expression that act on many different molecular and biochemical processes in eukaryotes. To date, miRNAs have not been considered in the current evaluation system for GM crops. In this study, small RNAs from the dry seeds of a GM wheat line overexpressing GmDREB1 and non-GM wheat cultivars were investigated using deep sequencing technology and bioinformatic approaches. As a result, 23 differentially expressed miRNAs in dry seeds were identified and confirmed between GM wheat and a non-GM acceptor. Notably, more differentially expressed tae-miRNAs between non-GM wheat varieties were found, indicating that the degree of variance between non-GM cultivars was considerably higher than that induced by the transgenic event. Most of the target genes of these differentially expressed miRNAs between GM wheat and a non-GM acceptor were associated with abiotic stress, in accordance with the product concept of GM wheat in improving drought and salt tolerance. Our data provided useful information and insights into the evaluation of miRNA expression in edible GM crops.
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Affiliation(s)
- Qiyan Jiang
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xianjun Sun
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fengjuan Niu
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zheng Hu
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rui Chen
- Tianjin Institute of Agricultural Quality Standard and Testing Technology, Tianjin Academy of Agricultural Sciences, Tianjin, China
- * E-mail: (RC); (HZ)
| | - Hui Zhang
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail: (RC); (HZ)
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Zhang J, Xue B, Gai M, Song S, Jia N, Sun H. Small RNA and Transcriptome Sequencing Reveal a Potential miRNA-Mediated Interaction Network That Functions during Somatic Embryogenesis in Lilium pumilum DC. Fisch. FRONTIERS IN PLANT SCIENCE 2017; 8:566. [PMID: 28473835 PMCID: PMC5397531 DOI: 10.3389/fpls.2017.00566] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 03/29/2017] [Indexed: 05/23/2023]
Abstract
Plant somatic embryos are widely used in the fields of germplasm conservation, breeding for genetic engineering and artificial seed production. MicroRNAs (miRNAs) play pivotal roles in somatic embryogenesis (SE) regulation. However, their regulatory roles during various stages of SE remain unclear. In this study, six types of embryogenic samples of Lilium pumilum DC. Fisch., including organogenic callus, embryogenic callus induced for 4 weeks, embryogenic callus induced for 6 weeks, globular embryos, torpedo embryos and cotyledon embryos, were prepared for small RNA sequencing. The results revealed a total of 2,378,760 small RNA reads, among which the most common size was 24 nt. Four hundred and fifty-two known miRNAs, belonging to more than 86 families, 57 novel miRNAs and 40 miRNA*s were identified. The 86 known miRNA families were sorted according to an alignment with their homologs across 24 land plants into the following four categories: 23 highly conserved, 4 moderately conserved, 15 less conserved and 44 species-specific miRNAs. Differentially expressed known miRNAs were identified during various stages of SE. Subsequently, the expression levels of 12 differentially expressed miRNAs and 4 targets were validated using qRT-PCR. In addition, six samples were mixed in equal amounts for transcript sequencing, and the sequencing data were used as transcripts for miRNA target prediction. A total of 66,422 unigenes with an average length of 800 bp were assembled from 56,258,974 raw reads. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment indicated that 38,004 and 15,497 unigenes were successfully assigned to GO terms and KEGG pathways, respectively. Among the unigenes, 2,182 transcripts were predicted to be targets for 396 known miRNAs. The potential targets of the identified miRNAs were mostly classified into the following GO terms: cell, binding and metabolic process. Enriched KEGG analysis demonstrated that carbohydrate metabolism was the predominant pathway in Lilium SE. Thus, we performed systemic characterization, homology comparisons and profiling of miRNA expression, and we constructed an miRNA-target network during Lilium SE for the first time. Our findings establish a foundation for the further exploration of critical genes and elucidation of SE in Lilium.
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Affiliation(s)
| | | | | | | | | | - Hongmei Sun
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, College of Horticulture, Shenyang Agricultural UniversityShenyang, China
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Samad AFA, Sajad M, Nazaruddin N, Fauzi IA, Murad AMA, Zainal Z, Ismail I. MicroRNA and Transcription Factor: Key Players in Plant Regulatory Network. FRONTIERS IN PLANT SCIENCE 2017; 8:565. [PMID: 28446918 PMCID: PMC5388764 DOI: 10.3389/fpls.2017.00565] [Citation(s) in RCA: 185] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/29/2017] [Indexed: 05/14/2023]
Abstract
Recent achievements in plant microRNA (miRNA), a large class of small and non-coding RNAs, are very exciting. A wide array of techniques involving forward genetic, molecular cloning, bioinformatic analysis, and the latest technology, deep sequencing have greatly advanced miRNA discovery. A tiny miRNA sequence has the ability to target single/multiple mRNA targets. Most of the miRNA targets are transcription factors (TFs) which have paramount importance in regulating the plant growth and development. Various families of TFs, which have regulated a range of regulatory networks, may assist plants to grow under normal and stress environmental conditions. This present review focuses on the regulatory relationships between miRNAs and different families of TFs like; NF-Y, MYB, AP2, TCP, WRKY, NAC, GRF, and SPL. For instance NF-Y play important role during drought tolerance and flower development, MYB are involved in signal transduction and biosynthesis of secondary metabolites, AP2 regulate the floral development and nodule formation, TCP direct leaf development and growth hormones signaling. WRKY have known roles in multiple stress tolerances, NAC regulate lateral root formation, GRF are involved in root growth, flower, and seed development, and SPL regulate plant transition from juvenile to adult. We also studied the relation between miRNAs and TFs by consolidating the research findings from different plant species which will help plant scientists in understanding the mechanism of action and interaction between these regulators in the plant growth and development under normal and stress environmental conditions.
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Affiliation(s)
- Abdul F. A. Samad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
| | - Muhammad Sajad
- Department of Plant Breeding and Genetics, University College of Agriculture and Environmental Sciences, The Islamia University of Bahawalpur, PunjabPakistan
- Centre of Plant Biotechnology, Institute of Systems Biology, National University of Malaysia, SelangorMalaysia
| | - Nazaruddin Nazaruddin
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Syiah Kuala University, Darussalam, Banda AcehIndonesia
| | - Izzat A. Fauzi
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
| | - Abdul M. A. Murad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
| | - Zamri Zainal
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
- Centre of Plant Biotechnology, Institute of Systems Biology, National University of Malaysia, SelangorMalaysia
| | - Ismanizan Ismail
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
- Centre of Plant Biotechnology, Institute of Systems Biology, National University of Malaysia, SelangorMalaysia
- *Correspondence: Ismanizan Ismail,
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