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Transcriptome-wide identification of miRNA targets and a TAS3-homologous gene in Populus by degradome sequencing. Genes Genomics 2019; 41:849-861. [PMID: 30912003 DOI: 10.1007/s13258-019-00797-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 02/19/2019] [Indexed: 12/25/2022]
Abstract
BACKGROUND Degradome sequencing has been applied to identify miRNA-directed mRNA cleavage and understand the biological function of miRNAs and their target genes in plants defense to stress. miRNAs involved in the response to cold stress have been identified in Populus, however, there are few reports about the validated targets of miRNAs in Populus under cold stress. OBJECTIVES The primary objective of this investigation was to globally identify and validate the targets of the miRNAs and regulatory components in Populus under cold stress. METHODS Populus plantlets grown in vitro were treated with cold (4 °C for 8 h) and total RNA was extracted using Trizol reagent. Approximately 200 µg total RNA was used for the construction of the degradome library, and degradome sequencing was conducted on an Illumina HiSeq 2000. The sequences were mapped to Populus genome using SOAP 2.0 and then were collected for degradome analysis. Additionally, trans-acting siRNA sequences from transacting siRNA gene 3 sequences and mature miRNAs cleaved from precursor miRNAs of Populus were analyzed. 5' RNA ligase-mediated-RACE (5'-RACE) were further conducted. RESULTS 80 genes were experimentally determined to be the target of 51 unique miRNAs, including three down-regulated miRNAs (pto-miR156k, pto-miR169i-m, and pto-miR394a-5p/b-5p) and two up-regulated miRNAs (pto-miR167a-d and pto-miR167f/g). The specificity and diversity of cleavage sites of miRNA targets were validated through 5'-RACE experiment and the results were similar with that of degradome sequencing, further supporting the empirical cleavage of miRNAs on targets in vivo in Populus. Interestingly, the TAS-homologous gene pto-TAS3 (EF146176.1) was identified and 11 potential ta-siRNAs [D1(+)-D11(+)] and their possible biogenesis sites within the pto-TAS3 transcript sequence were predicted in Populus. In addition, the biosynthesis of miRNA from precursor miRNA (pre-miRNA) was also validated through the detection of a total of 17 pre-miRNAs. CONCLUSION Our investigation expands the application of degradome sequencing for evaluating miRNA regulatory elements and evidence of the miRNA synthesis process, and provides empirical evidence of bona fide cleavage of target genes by miRNAs in Populus, which might be used for the research of miRNA-mediated regulation mechanism and molecular improvement of resistance to cold stress.
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Gorshkov O, Chernova T, Mokshina N, Gogoleva N, Suslov D, Tkachenko A, Gorshkova T. Intrusive Growth of Phloem Fibers in Flax Stem: Integrated Analysis of miRNA and mRNA Expression Profiles. PLANTS (BASEL, SWITZERLAND) 2019; 8:E47. [PMID: 30791461 PMCID: PMC6409982 DOI: 10.3390/plants8020047] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/13/2019] [Accepted: 02/14/2019] [Indexed: 12/21/2022]
Abstract
Phloem fibers are important elements of plant architecture and the target product of many fiber crops. A key stage in fiber development is intrusive elongation, the mechanisms of which are largely unknown. Integrated analysis of miRNA and mRNA expression profiles in intrusivelygrowing fibers obtained by laser microdissection from flax (Linum usitatissimum L.) stem revealed all 124 known flax miRNA from 23 gene families and the potential targets of differentially expressed miRNAs. A comparison of the expression between phloem fibers at different developmental stages, and parenchyma and xylem tissues demonstrated that members of miR159, miR166, miR167, miR319, miR396 families were down-regulated in intrusively growing fibers. Some putative target genes of these miRNA families, such as those putatively encoding growth-regulating factors, an argonaute family protein, and a homeobox-leucine zipper family protein were up-regulated in elongating fibers. miR160, miR169, miR390, and miR394 showed increased expression. Changes in the expression levels of miRNAs and their target genes did not match expectations for the majority of predicted target genes. Taken together, poorly understood intrusive fiber elongation, the key process of phloem fiber development, was characterized from a miRNA-target point of view, giving new insights into its regulation.
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Affiliation(s)
- Oleg Gorshkov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111 Kazan, Russia.
| | - Tatyana Chernova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111 Kazan, Russia.
| | - Natalia Mokshina
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111 Kazan, Russia.
| | - Natalia Gogoleva
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111 Kazan, Russia.
- Laboratory of Extreme Biology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kremlyovskaya Str., 18, 420021 Kazan, Russia.
| | - Dmitry Suslov
- Department of Plant Physiology and Biochemistry, Faculty of Biology, Saint Petersburg State University, Universiteskaya emb., 7/9, 199034 Saint Petersburg, Russia.
| | - Alexander Tkachenko
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, Universiteskaya emb., 7/9, 199034 Saint Petersburg, Russia.
| | - Tatyana Gorshkova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111 Kazan, Russia.
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Mutum RD, Kumar S, Balyan S, Kansal S, Mathur S, Raghuvanshi S. Identification of novel miRNAs from drought tolerant rice variety Nagina 22. Sci Rep 2016; 6:30786. [PMID: 27499088 PMCID: PMC4976344 DOI: 10.1038/srep30786] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 07/11/2016] [Indexed: 11/09/2022] Open
Abstract
MicroRNAs regulate a spectrum of developmental and biochemical processes in plants and animals. Thus, knowledge of the entire miRNome is essential to understand the complete regulatory schema of any organism. The current study attempts to unravel yet undiscovered miRNA genes in rice. Analysis of small RNA libraries from various tissues of drought-tolerant ‘aus’ rice variety Nagina 22 (N22) identified 71 novel miRNAs. These were validated based on precursor hairpin structure, small RNA mapping pattern, ‘star’ sequence, conservation and identification of targets based on degradome data. While some novel miRNAs were conserved in other monocots and dicots, most appear to be lineage-specific. They were segregated into two different classes based on the closeness to the classical miRNA definition. Interestingly, evidence of a miRNA-like cleavage was found even for miRNAs that lie beyond the classical definition. Several novel miRNAs displayed tissue-enriched and/or drought responsive expression. Generation and analysis of the degradome data from N22 along with publicly available degradome identified several high confidence targets implicated in regulation of fundamental processes such as flowering and stress response. Thus, discovery of these novel miRNAs considerably expands the dimension of the miRNA-mediated regulation in rice.
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Affiliation(s)
- Roseeta Devi Mutum
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi - 110021, India
| | - Santosh Kumar
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi - 110021, India
| | - Sonia Balyan
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi - 110021, India
| | - Shivani Kansal
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi - 110021, India
| | - Saloni Mathur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi - 110067, India
| | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi - 110021, India
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Jain A, Das S. Synteny and comparative analysis of miRNA retention, conservation, and structure across Brassicaceae reveals lineage- and sub-genome-specific changes. Funct Integr Genomics 2016; 16:253-68. [PMID: 26873704 DOI: 10.1007/s10142-016-0484-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 02/01/2016] [Accepted: 02/04/2016] [Indexed: 12/22/2022]
Abstract
The recent availability of genome sequences together with syntenic block information for Brassicaceae offers an opportunity to study microRNA (miRNA) evolution across this family. We employed a synteny-based comparative genomics strategy to unambiguously identify miRNA homologs from the genome sequence of members of Brassicaceae. Such an analysis of miRNA across Brassicaceae allowed us to classify miRNAs as conserved, lineage-, karyotype- and sub-genome-specific. The differential loss of miRNA from sub-genomes in polyploid genomes of Brassica rapa and Brassica oleracea shows that miRNA also follows the rules of gene fractionation as observed in the case of protein-coding genes. The study of mature and miR* region of precursors revealed instances of in-dels and SNPs which reflect the evolutionary history of the genomes. High level of conservation in miR* regions in some cases points to their functional relevance which needs to be further investigated. We further show that sequence and length variability in precursor sequences can affect the free energy and foldback structure of miRNA which may ultimately affect their biogenesis and expression in the biological system.
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Affiliation(s)
- Aditi Jain
- Department of Botany, Faculty of Science, University of Delhi, New Delhi, Delhi, 110007, India
| | - Sandip Das
- Department of Botany, Faculty of Science, University of Delhi, New Delhi, Delhi, 110007, India.
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Chen F, Zhang X, Zhang N, Wang S, Yin G, Dong Z, Cui D. Combined Small RNA and Degradome Sequencing Reveals Novel MiRNAs and Their Targets in the High-Yield Mutant Wheat Strain Yunong 3114. PLoS One 2015; 10:e0137773. [PMID: 26372220 PMCID: PMC4570824 DOI: 10.1371/journal.pone.0137773] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 08/20/2015] [Indexed: 01/13/2023] Open
Abstract
Wheat is one of the main food sources worldwide; large amount studies have been conducted to improve wheat production. MicroRNAs (miRNAs) with about 20-30 nucleotide are a class of regulatory small RNAs (sRNAs), which could regulate gene expression through sequence-specific base pairing with target mRNAs, playing important roles in plant growth. An ideal plant architecture (IPA) is crucial to enhance yield in bread wheat. In this study, the high-yield wheat strain Yunong 3114 was EMS-mutagenesis from the wild-type strain Yunong 201, exhibiting a preferable plant structure compared with the wild-type strain. We constructed small RNA and degradome libraries from Yunong 201 and Yunong 3114, and performed small RNA sequencing of these libraries in order identify miRNAs and their targets related to IPA in wheat. Totally, we identified 488 known and 837 novel miRNAs from Yunong 3114 and 391 known and 533 novel miRNAs from Yunong 201. The number of miRNAs in the mutant increased. A total of 37 known and 432 putative novel miRNAs were specifically expressed in the mutant strain; furthermore, 23 known and 159 putative novel miRNAs were specifically expressed in the wild-type strain. A total of 150 known and 100 novel miRNAs were differentially expressed between mutant and wild-type strains. Among these differentially expressed novel miRNAs, 4 and 8 predict novel miRNAs were evidenced by degradome sequencing and showed up-regulated and down-regulated expressions in the mutant strain Yunong 3114, respectively. Targeted gene annotation and previous results indicated that this set of miRNAs is related to plant structure. Our results further suggested that miRNAs may be necessary to obtain an optimal wheat structure.
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Affiliation(s)
- Feng Chen
- Agronomy College/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- * E-mail: (FC); (DC)
| | - Xiangfen Zhang
- Agronomy College/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Ning Zhang
- Agronomy College/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Shasha Wang
- Agronomy College/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Guihong Yin
- Zhoukou Academy of Agricultural Sciences, Zhoukou, China
| | - Zhongdong Dong
- Agronomy College/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Dangqun Cui
- Agronomy College/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- * E-mail: (FC); (DC)
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Transcriptome-Wide Identification of miRNA Targets under Nitrogen Deficiency in Populus tomentosa Using Degradome Sequencing. Int J Mol Sci 2015; 16:13937-58. [PMID: 26096002 PMCID: PMC4490532 DOI: 10.3390/ijms160613937] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 05/21/2015] [Accepted: 06/01/2015] [Indexed: 12/02/2022] Open
Abstract
miRNAs are endogenous non-coding small RNAs with important regulatory roles in stress responses. Nitrogen (N) is an indispensable macronutrient required for plant growth and development. Previous studies have identified a variety of known and novel miRNAs responsive to low N stress in plants, including Populus. However, miRNAs involved in the cleavage of target genes and the corresponding regulatory networks in response to N stress in Populus remain largely unknown. Consequently, degradome sequencing was employed for global detection and validation of N-responsive miRNAs and their targets. A total of 60 unique miRNAs (39 conserved, 13 non-conserved, and eight novel) were experimentally identified to target 64 mRNA transcripts and 21 precursors. Among them, we further verified the cleavage of 11 N-responsive miRNAs identified previously and provided empirical evidence for the cleavage mode of these miRNAs on their target mRNAs. Furthermore, five miRNA stars (miRNA*s) were shown to have cleavage function. The specificity and diversity of cleavage sites on the targets and miRNA precursors in P. tomentosa were further detected. Identification and annotation of miRNA-mediated cleavage of target genes in Populus can increase our understanding of miRNA-mediated molecular mechanisms of woody plants adapted to low N environments.
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Alaba S, Piszczalka P, Pietrykowska H, Pacak AM, Sierocka I, Nuc PW, Singh K, Plewka P, Sulkowska A, Jarmolowski A, Karlowski WM, Szweykowska-Kulinska Z. The liverwort Pellia endiviifolia shares microtranscriptomic traits that are common to green algae and land plants. THE NEW PHYTOLOGIST 2015; 206:352-367. [PMID: 25530158 PMCID: PMC4368373 DOI: 10.1111/nph.13220] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 11/10/2014] [Indexed: 05/03/2023]
Abstract
Liverworts are the most basal group of extant land plants. Nonetheless, the molecular biology of liverworts is poorly understood. Gene expression has been studied in only one species, Marchantia polymorpha. In particular, no microRNA (miRNA) sequences from liverworts have been reported. Here, Illumina-based next-generation sequencing was employed to identify small RNAs, and analyze the transcriptome and the degradome of Pellia endiviifolia. Three hundred and eleven conserved miRNA plant families were identified, and 42 new liverwort-specific miRNAs were discovered. The RNA degradome analysis revealed that target mRNAs of only three miRNAs (miR160, miR166, and miR408) have been conserved between liverworts and other land plants. New targets were identified for the remaining conserved miRNAs. Moreover, the analysis of the degradome permitted the identification of targets for 13 novel liverwort-specific miRNAs. Interestingly, three of the liverwort microRNAs show high similarity to previously reported miRNAs from Chlamydomonas reinhardtii. This is the first observation of miRNAs that exist both in a representative alga and in the liverwort P. endiviifolia but are not present in land plants. The results of the analysis of the P. endivifolia microtranscriptome support the conclusions of previous studies that placed liverworts at the root of the land plant evolutionary tree of life.
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Affiliation(s)
- Sylwia Alaba
- Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University61-614, Poznań, Poland
| | - Pawel Piszczalka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University61-614, Poznań, Poland
| | - Halina Pietrykowska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University61-614, Poznań, Poland
| | - Andrzej M Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University61-614, Poznań, Poland
| | - Izabela Sierocka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University61-614, Poznań, Poland
| | - Przemyslaw W Nuc
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University61-614, Poznań, Poland
| | - Kashmir Singh
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University61-614, Poznań, Poland
| | - Patrycja Plewka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University61-614, Poznań, Poland
| | - Aleksandra Sulkowska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University61-614, Poznań, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University61-614, Poznań, Poland
| | - Wojciech M Karlowski
- Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University61-614, Poznań, Poland
| | - Zofia Szweykowska-Kulinska
- Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University61-614, Poznań, Poland
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University61-614, Poznań, Poland
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Spanudakis E, Jackson S. The role of microRNAs in the control of flowering time. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:365-80. [PMID: 24474808 DOI: 10.1093/jxb/ert453] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The onset of flowering in plants is regulated by complex gene networks that integrate multiple environmental and endogenous cues to ensure that flowering occurs at the appropriate time. This is achieved by precise control of the expression of key flowering genes at both the transcriptional and post-transcriptional level. In recent years, a class of small non-coding RNAs, called microRNAs (miRNAs), has been shown to regulate gene expression in a number of plant developmental processes and stress responses. MiRNA-based biotechnology, which harnesses the regulatory functions of such endogenous or artificial miRNAs, therefore represents a highly promising area of research. In this review, the process of plant miRNA biogenesis, their mode of action, and multiple regulatory functions are summarized. The roles of the miR156, miR172, miR159/319, miR390, and miR399 families in the flowering time regulatory network in Arabidopsis thaliana are discussed in depth.
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Patra D, Fasold M, Langenberger D, Steger G, Grosse I, Stadler PF. plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants. FRONTIERS IN PLANT SCIENCE 2014; 5:708. [PMID: 25566282 PMCID: PMC4274896 DOI: 10.3389/fpls.2014.00708] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 11/26/2014] [Indexed: 05/11/2023]
Abstract
High-throughput sequencing techniques have made it possible to assay an organism's entire repertoire of small non-coding RNAs (ncRNAs) in an efficient and cost-effective manner. The moderate size of small RNA-seq datasets makes it feasible to provide free web services to the research community that provide many basic features of a small RNA-seq analysis, including quality control, read normalization, ncRNA quantification, and the prediction of putative novel ncRNAs. DARIO is one such system that so far has been focussed on animals. Here we introduce an extension of this system to plant short non-coding RNAs (sncRNAs). It includes major modifications to cope with plant-specific sncRNA processing. The current version of plantDARIO covers analyses of mapping files, small RNA-seq quality control, expression analyses of annotated sncRNAs, including the prediction of novel miRNAs and snoRNAs from unknown expressed loci and expression analyses of user-defined loci. At present Arabidopsis thaliana, Beta vulgaris, and Solanum lycopersicum are covered. The web tool links to a plant specific visualization browser to display the read distribution of the analyzed sample. The easy-to-use platform of plantDARIO quantifies RNA expression of annotated sncRNAs from different sncRNA databases together with new sncRNAs, annotated by our group. The plantDARIO website can be accessed at http://plantdario.bioinf.uni-leipzig.de/.
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Affiliation(s)
- Deblina Patra
- Institut für Informatik, Martin-Luther-Universität Halle-WittenbergHalle (Saale), Germany
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University LeipzigLeipzig, Germany
| | - Mario Fasold
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University LeipzigLeipzig, Germany
- ecSeq BioinformaticsLeipzig, Germany
| | - David Langenberger
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University LeipzigLeipzig, Germany
- ecSeq BioinformaticsLeipzig, Germany
| | - Gerhard Steger
- Institut für Pysikalische Biologie, Heinrich-Heine-UniversitätDüsseldorf, Germany
| | - Ivo Grosse
- Institut für Informatik, Martin-Luther-Universität Halle-WittenbergHalle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
| | - Peter F. Stadler
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University LeipzigLeipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
- Max Planck Institute for Mathematics in the SciencesLeipzig, Germany
- Fraunhofer Institute for Cell Therapy and ImmunologyLeipzig, Germany
- Department of Theoretical Chemistry of the University of ViennaVienna, Austria
- Center for RNA in Technology and Health, University of CopenhagenFrederiksberg, Denmark
- Santa Fe InstituteSanta Fe, USA
- *Correspondence: Peter F. Stadler, Bioinformatics Group, Department of Computer Science, University Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany e-mail:
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Shao C, Wu Q, Qiu J, Jin S, Zhang B, Qian J, Chen M, Meng Y. Identification of novel microRNA-like-coding sites on the long-stem microRNA precursors in Arabidopsis. Gene 2013; 527:477-83. [DOI: 10.1016/j.gene.2013.06.070] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 06/14/2013] [Accepted: 06/20/2013] [Indexed: 12/15/2022]
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Guo Q, Tao YL, Chu D. Characterization and comparative profiling of miRNAs in invasive Bemisia tabaci (Gennadius) B and Q. PLoS One 2013; 8:e59884. [PMID: 23527280 PMCID: PMC3603954 DOI: 10.1371/journal.pone.0059884] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 02/19/2013] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are small, conserved, non-coding RNAs that post-transcriptionally regulate gene expression. Bemisia tabaci (Gennadius) B and Q are two invasive and dominant whiteflies, and B. tabaci Q has been displacing B in China. Differences in biological traits (fecundity, host range, resistance to insecticides, etc.) as affected by miRNAs might be involved in the displacement. In this study, we performed high-throughput sequencing to identify miRNAs in B. tabaci B and Q. RESULTS We identified 170 conserved miRNAs and 15 novel candidates, and found significant differences in the expression of miRNAs between B. tabaci B and Q. CONCLUSION Expression levels of miRNAs differ in B. tabaci B vs. Q. Additional research is needed to determine whether these differences are related to differences in the biology of B. tabaci B and Q, and whether these differences help explain why B. tabaci Q is displacing B in China.
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Affiliation(s)
- Qiang Guo
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Yun-Li Tao
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Dong Chu
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao, Shandong Province, China
- * E-mail:
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