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Khraiwesh B, Qudeimat E, Thimma M, Chaiboonchoe A, Jijakli K, Alzahmi A, Arnoux M, Salehi-Ashtiani K. Genome-wide expression analysis offers new insights into the origin and evolution of Physcomitrella patens stress response. Sci Rep 2015; 5:17434. [PMID: 26615914 PMCID: PMC4663497 DOI: 10.1038/srep17434] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/29/2015] [Indexed: 12/22/2022] Open
Abstract
Changes in the environment, such as those caused by climate change, can exert stress
on plant growth, diversity and ultimately global food security. Thus, focused
efforts to fully understand plant response to stress are urgently needed in order to
develop strategies to cope with the effects of climate change. Because
Physcomitrella patens holds a key evolutionary position bridging the gap
between green algae and higher plants, and because it exhibits a well-developed
stress tolerance, it is an excellent model for such exploration. Here, we have used
Physcomitrella patens to study genome-wide responses to abiotic stress
through transcriptomic analysis by a high-throughput sequencing platform. We report
a comprehensive analysis of transcriptome dynamics, defining profiles of elicited
gene regulation responses to abiotic stress-associated hormone Abscisic Acid (ABA),
cold, drought, and salt treatments. We identified more than 20,000 genes expressed
under each aforementioned stress treatments, of which 9,668 display differential
expression in response to stress. The comparison of Physcomitrella patens
stress regulated genes with unicellular algae, vascular and flowering plants
revealed genomic delineation concomitant with the evolutionary movement to land,
including a general gene family complexity and loss of genes associated with
different functional groups.
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Affiliation(s)
- Basel Khraiwesh
- Laboratory of Algal, Systems, and Synthetic Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE.,Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE.,Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, KSA
| | - Enas Qudeimat
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE.,Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, KSA
| | - Manjula Thimma
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, KSA
| | - Amphun Chaiboonchoe
- Laboratory of Algal, Systems, and Synthetic Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Kenan Jijakli
- Laboratory of Algal, Systems, and Synthetic Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Amnah Alzahmi
- Laboratory of Algal, Systems, and Synthetic Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Marc Arnoux
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Kourosh Salehi-Ashtiani
- Laboratory of Algal, Systems, and Synthetic Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE.,Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
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Khraiwesh B, Pugalenthi G, Fedoroff NV. Identification and analysis of red sea mangrove (Avicennia marina) microRNAs by high-throughput sequencing and their association with stress responses. PLoS One 2013; 8:e60774. [PMID: 23593307 PMCID: PMC3620391 DOI: 10.1371/journal.pone.0060774] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 03/02/2013] [Indexed: 11/18/2022] Open
Abstract
Although RNA silencing has been studied primarily in model plants, advances in high-throughput sequencing technologies have enabled profiling of the small RNA components of many more plant species, providing insights into the ubiquity and conservatism of some miRNA-based regulatory mechanisms. Small RNAs of 20 to 24 nucleotides (nt) are important regulators of gene transcript levels by either transcriptional or by posttranscriptional gene silencing, contributing to genome maintenance and controlling a variety of developmental and physiological processes. Here, we used deep sequencing and molecular methods to create an inventory of the small RNAs in the mangrove species, Avicennia marina. We identified 26 novel mangrove miRNAs and 193 conserved miRNAs belonging to 36 families. We determined that 2 of the novel miRNAs were produced from known miRNA precursors and 4 were likely to be species-specific by the criterion that we found no homologs in other plant species. We used qRT-PCR to analyze the expression of miRNAs and their target genes in different tissue sets and some demonstrated tissue-specific expression. Furthermore, we predicted potential targets of these putative miRNAs based on a sequence homology and experimentally validated through endonucleolytic cleavage assays. Our results suggested that expression profiles of miRNAs and their predicted targets could be useful in exploring the significance of the conservation patterns of plants, particularly in response to abiotic stress. Because of their well-developed abilities in this regard, mangroves and other extremophiles are excellent models for such exploration.
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Affiliation(s)
- Basel Khraiwesh
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.
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Bonhomme S, Nogué F, Rameau C, Schaefer DG. Usefulness of Physcomitrella patens for studying plant organogenesis. Methods Mol Biol 2013; 959:21-43. [PMID: 23299666 DOI: 10.1007/978-1-62703-221-6_2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In this chapter, we review the main organogenesis features and associated regulation processes of the moss Physcomitrella patens (P. patens), the model plant for the Bryophytes. We highlight how the study of this descendant of the earliest plant species that colonized earth, brings useful keys to understand the mechanisms that determine and control both vascular and non vascular plants organogenesis. Despite its simple morphogenesis pattern, P. patens still requires the fine tuning of organogenesis regulators, including hormone signalling, common to the whole plant kingdom, and which study is facilitated by a high number of molecular tools, among which the powerful possibility of gene targeting/replacement. The recent discovery of moss cells reprogramming capacity completes the picture of an excellent model for studying plant organogenesis.
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Affiliation(s)
- Sandrine Bonhomme
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France.
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Tang Y, Lai Y, Liu Y. Virus-induced gene silencing using artificial miRNAs in Nicotiana benthamiana. Methods Mol Biol 2013; 975:99-107. [PMID: 23386298 DOI: 10.1007/978-1-62703-278-0_8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Virus-induced gene silencing using artificial microRNAs (MIR VIGS) is a newly developed technique for plant reverse genetic studies. Traditional virus-induced gene silencing (VIGS) assays introduce a large gene fragment, which is expressed and then converted into small RNAs by the endogenous siRNA-based gene silencing machinery of the plant host. By contrast, MIR VIGS uses well-designed miRNAs to induce RNA-mediated silencing of the target gene. Using a single artificial miRNA can provide greater specificity by reducing off-target effects. Here, we describe a detailed protocol for MIR VIGS in Nicotiana benthamiana using a modified Cabbage leaf curl virus (CaLCuV)-based vector.
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Affiliation(s)
- Yang Tang
- School of Life Sciences, Tsinghua University, Beijing, China
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