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Smith-Ramesh LM. Invasive plant alters community and ecosystem dynamics by promoting native predators. Ecology 2017; 98:751-761. [PMID: 28035682 DOI: 10.1002/ecy.1688] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 11/11/2016] [Accepted: 12/08/2016] [Indexed: 11/06/2022]
Abstract
Placing invasion in a more complete food web context expands our understanding of species invasions to reflect the inherent complexity of ecological networks. Garlic mustard (Alliaria petiolata) has traditionally been predicted to dominate native communities through mechanisms embodied in popular hypotheses such as direct plant-plant interactions (allelopathy) and plant-herbivore interactions (enemy escape). However, garlic mustard also interacts directly with native predators by providing habitat for web-building spiders, which colonize the dry fruit structures (siliques) that garlic mustard leaves behind after it senesces. This interaction may lead to altered food web structure, resulting previously unexamined invasion consequences. This idea was tested in a field experiment including three treatments in which garlic mustard siliques were left intact (S+), removed (S-), or native species dominated and garlic mustard was absent (N). When siliques were intact, estimated insect abundance was locally reduced in invaded plots compared to native plots, but this relationship disappeared when siliques were removed. Phosphorus availability and the growth of one native plant species were both elevated in invaded plots where siliques were intact compared to plots where siliques were removed. Results indicate that garlic mustard's close association with web-building spiders initiates cascading invader impacts on the native community and ecosystem properties. This work supports recent theory suggesting that taking a broader food web perspective may help predict invasion impacts in different environmental contexts.
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Affiliation(s)
- Lauren M Smith-Ramesh
- Yale University School of Forestry and Environmental Studies, 195 Prospect Street, New Haven, Connecticut, 06511, USA
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Cosio C, Ranocha P, Francoz E, Burlat V, Zheng Y, Perry SE, Ripoll JJ, Yanofsky M, Dunand C. The class III peroxidase PRX17 is a direct target of the MADS-box transcription factor AGAMOUS-LIKE15 (AGL15) and participates in lignified tissue formation. New Phytol 2017; 213:250-263. [PMID: 27513887 DOI: 10.1111/nph.14127] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/03/2016] [Indexed: 05/22/2023]
Abstract
Several physiological functions have been attributed to class III peroxidases (PRXs) in plants, but the in planta role of most members of this family still remains undetermined. Here, we report the first functional characterization of PRX17 (At2g22420), one of the 73 members of this family in Arabidopsis thaliana. Localization of PRX17 was examined by transient expression in Nicotiana benthamiana. Loss- and gain-of-function mutants in A. thaliana were studied. Regulation at the gene and protein levels was analyzed using β-glucuronidase (GUS) activity, quantitative reverse transcriptase (qRT)-PCR, zymography, and chromatin immunoprecipitation. Phenotypes were characterized including lignin and xylan contents. PRX17 was expressed in various tissues, including vascular tissues, and PRX17 was localized to the cell wall. In prx17, the lignin content was reduced in the stem and siliques and bolting was delayed, while the opposite phenotype was observed in 35S:PRX17 plants, together with a significant increase of lignin and xylan immunofluorescence signal. Finally, we demonstrated that the transcription factor AGAMOUS-LIKE15 (AGL15) binds to the PRX17 promoter and regulates PRX17 expression level. This converging set of structural, transcriptomic and physiological data suggests that PRX17, under the control of AGL15, contributes to developmental programs by playing an essential role in regulating age-dependent lignified tissue formation, including changes in cell wall properties.
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Affiliation(s)
- Claudia Cosio
- Division of Biological Sciences, Section Cell & Developmental Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Philippe Ranocha
- Laboratoire de Recherche en Sciences Végétales, CNRS, UPS, Université de Toulouse, 24 chemin de Borde Rouge, Auzeville, BP42617, Castanet Tolosan, 31326, France
| | - Edith Francoz
- Laboratoire de Recherche en Sciences Végétales, CNRS, UPS, Université de Toulouse, 24 chemin de Borde Rouge, Auzeville, BP42617, Castanet Tolosan, 31326, France
| | - Vincent Burlat
- Laboratoire de Recherche en Sciences Végétales, CNRS, UPS, Université de Toulouse, 24 chemin de Borde Rouge, Auzeville, BP42617, Castanet Tolosan, 31326, France
| | - Yumei Zheng
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546-0091, USA
| | - Sharyn E Perry
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546-0091, USA
| | - Juan-Jose Ripoll
- Division of Biological Sciences, Section Cell & Developmental Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Martin Yanofsky
- Division of Biological Sciences, Section Cell & Developmental Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Christophe Dunand
- Laboratoire de Recherche en Sciences Végétales, CNRS, UPS, Université de Toulouse, 24 chemin de Borde Rouge, Auzeville, BP42617, Castanet Tolosan, 31326, France
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Sinha S, Raxwal VK, Joshi B, Jagannath A, Katiyar-Agarwal S, Goel S, Kumar A, Agarwal M. De novo transcriptome profiling of cold-stressed siliques during pod filling stages in Indian mustard (Brassica juncea L.). Front Plant Sci 2015; 6:932. [PMID: 26579175 PMCID: PMC4626631 DOI: 10.3389/fpls.2015.00932] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 10/15/2015] [Indexed: 05/07/2023]
Abstract
Low temperature is a major abiotic stress that impedes plant growth and development. Brassica juncea is an economically important oil seed crop and is sensitive to freezing stress during pod filling subsequently leading to abortion of seeds. To understand the cold stress mediated global perturbations in gene expression, whole transcriptome of B. juncea siliques that were exposed to sub-optimal temperature was sequenced. Manually self-pollinated siliques at different stages of development were subjected to either short (6 h) or long (12 h) durations of chilling stress followed by construction of RNA-seq libraries and deep sequencing using Illumina's NGS platform. De-novo assembly of B. juncea transcriptome resulted in 133,641 transcripts, whose combined length was 117 Mb and N50 value was 1428 bp. We identified 13,342 differentially regulated transcripts by pair-wise comparison of 18 transcriptome libraries. Hierarchical clustering along with Spearman correlation analysis identified that the differentially expressed genes segregated in two major clusters representing early (5-15 DAP) and late stages (20-30 DAP) of silique development. Further analysis led to the discovery of sub-clusters having similar patterns of gene expression. Two of the sub-clusters (one each from the early and late stages) comprised of genes that were inducible by both the durations of cold stress. Comparison of transcripts from these clusters led to identification of 283 transcripts that were commonly induced by cold stress, and were referred to as "core cold-inducible" transcripts. Additionally, we found that 689 and 100 transcripts were specifically up-regulated by cold stress in early and late stages, respectively. We further explored the expression patterns of gene families encoding for transcription factors (TFs), transcription regulators (TRs) and kinases, and found that cold stress induced protein kinases only during early silique development. We validated the digital gene expression profiles of selected transcripts by qPCR and found a high degree of concordance between the two analyses. To our knowledge this is the first report of transcriptome sequencing of cold-stressed B. juncea siliques. The data generated in this study would be a valuable resource for not only understanding the cold stress signaling pathway but also for introducing cold hardiness in B. juncea.
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Affiliation(s)
- Somya Sinha
- Department of Botany, University of DelhiNew Delhi, India
| | - Vivek K. Raxwal
- Department of Botany, University of DelhiNew Delhi, India
- Department of Plant Molecular Biology, Central European Institute of TechnologyBrno, Czech Republic
| | - Bharat Joshi
- Department of Botany, University of DelhiNew Delhi, India
| | - Arun Jagannath
- Department of Botany, University of DelhiNew Delhi, India
| | | | | | - Amar Kumar
- Department of Botany, University of DelhiNew Delhi, India
| | - Manu Agarwal
- Department of Botany, University of DelhiNew Delhi, India
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Thatcher SR, Burd S, Wright C, Lers A, Green PJ. Differential expression of miRNAs and their target genes in senescing leaves and siliques: insights from deep sequencing of small RNAs and cleaved target RNAs. Plant Cell Environ 2015; 38:188-200. [PMID: 24965556 PMCID: PMC4304344 DOI: 10.1111/pce.12393] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 06/06/2014] [Indexed: 05/03/2023]
Abstract
MicroRNAs (miRNAs) are a class of small RNAs, which typically function by guiding cleavage of target mRNAs. They are known to play roles in a variety of plant processes including development, responses to environmental stresses and senescence. To identify senescence regulation of miRNAs in Arabidopsis thaliana, eight small RNA libraries were constructed and sequenced at four different stages of development and senescence from both leaves and siliques, resulting in more than 200 million genome-matched sequences. Parallel analysis of RNA ends libraries, which enable the large-scale examination of miRNA-guided cleavage products, were constructed and sequenced, resulting in over 750 million genome-matched sequences. These large datasets led to the identification a new senescence-inducible small RNA locus, as well as new regulation of known miRNAs and their target genes during senescence, many of which have established roles in nutrient responsiveness and cell structural integrity. In keeping with remobilization of nutrients thought to occur during senescence, many miRNAs and targets had opposite expression pattern changes between leaf and silique tissues during the progression of senescence. Taken together, these findings highlight the integral role that miRNAs may play in the remobilization of resources and alteration of cellular structure that is known to occur in senescence.
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Affiliation(s)
- Shawn R Thatcher
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA
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Wang CY, Zhang S, Yu Y, Luo YC, Liu Q, Ju C, Zhang YC, Qu LH, Lucas WJ, Wang X, Chen YQ. MiR397b regulates both lignin content and seed number in Arabidopsis via modulating a laccase involved in lignin biosynthesis. Plant Biotechnol J 2014; 12:1132-42. [PMID: 24975689 DOI: 10.1111/pbi.12222] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 05/29/2014] [Accepted: 05/30/2014] [Indexed: 05/02/2023]
Abstract
Plant laccase (LAC) enzymes belong to the blue copper oxidase family and polymerize monolignols into lignin. Recent studies have established the involvement of microRNAs in this process; however, physiological functions and regulation of plant laccases remain poorly understood. Here, we show that a laccase gene, LAC4, regulated by a microRNA, miR397b, controls both lignin biosynthesis and seed yield in Arabidopsis. In transgenic plants, overexpression of miR397b (OXmiR397b) reduced lignin deposition. The secondary wall thickness of vessels and the fibres was reduced in the OXmiR397b line, and both syringyl and guaiacyl subunits are decreased, leading to weakening of vascular tissues. In contrast, overexpression of miR397b-resistant laccase mRNA results in an opposite phenotype. Plants overexpressing miR397b develop more than two inflorescence shoots and have an increased silique number and silique length, resulting in higher seed numbers. In addition, enlarged seeds and more seeds are formed in these miR397b overexpression plants. The study suggests that miR397-mediated development via regulating laccase genes might be a common mechanism in flowering plants and that the modulation of laccase by miR397 may be potential for engineering plant biomass production with less lignin.
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Affiliation(s)
- Cong-Ying Wang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-Sen University, Guangzhou, China
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Abstract
Fruits of angiosperms can be divided into dry and fleshy fruits, depending on their dispersal strategies. Despite their apparently different developmental programmes, researchers have attempted to compare dry and fleshy fruits to establish analogies of the distinct biochemical and physiological processes that occur. But what are the common and specific phenomena in both biological strategies? Is valve dehiscence and senescence of dry fruits comparable to final ripening of fleshy fruits, when seeds become mature and fruits are competent for seed dispersal, or to over-ripening when advanced senescence occurs? We briefly review current knowledge on dry and fleshy fruit development, which has been extensively reported recently, and is the topic of this special issue. We compare the processes taking place in Arabidopsis (dry) and tomato (fleshy) fruit during final development steps using transcriptome data to establish possible analogies. Interestingly, the transcriptomic programme of Arabidopsis silique shares little similarity in gene number to tomato fruit ripening or over-ripening. In contrast, the biological processes carried out by these common genes from ripening and over-ripening programmes are similar, as most biological processes are shared during both programmes. On the other hand, several biological terms are specific of Arabidopsis and tomato ripening, including senescence, but little or no specific processes occur during Arabidopsis and tomato over-ripening. These suggest a closer analogy between silique senescence and ripening than over-ripening, but a major common biological programme between Arabidopsis silique senescence and the last steps of tomato development, irrespective of its distinction between ripening and over-ripening.
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Affiliation(s)
- María Dolores Gómez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Ciudad Politécnica de la Innovación (CPI), Ed. 8E, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - Francisco Vera-Sirera
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Ciudad Politécnica de la Innovación (CPI), Ed. 8E, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - Miguel A Pérez-Amador
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Ciudad Politécnica de la Innovación (CPI), Ed. 8E, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
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Bates PD, Jewell JB, Browse J. Rapid separation of developing Arabidopsis seeds from siliques for RNA or metabolite analysis. Plant Methods 2013; 9:9. [PMID: 23531158 PMCID: PMC3635905 DOI: 10.1186/1746-4811-9-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 03/20/2013] [Indexed: 05/29/2023]
Abstract
BACKGROUND Protein, starch and oil produced in plant seeds are major renewable sources of food, chemicals and biofuels. Developing Arabidopsis thaliana seeds are commonly utilized as a model for seed crop research. However, due to the very small size of Arabidopsis seeds efficient collection of large amounts of tissue for gene expression or metabolite analysis is very difficult and time consuming. RESULTS/CONCLUSIONS Here we describe a method that allows very rapid separation and collection of large amounts of developing Arabidopsis seeds from their encapsulating silique tissue after flash freezing whole siliques in liquid nitrogen. The efficient popping open of the frozen siliques on dry ice and filtering the seeds away from the silique tissue with liquid nitrogen cooled funnels and sieves allows large amounts of developing seeds to be quickly isolated while remaining frozen. This method increases the speed of developing seed collection approximately 10 fold over methods which dissect individual siliques one at a time.
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Affiliation(s)
- Philip David Bates
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
- Current address: Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Jeremy Burke Jewell
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - John Browse
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
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