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Nili O, Azizi A, Abdollahzadeh J. Development of an efficient Tef-1α RNA hairpin structure to efficient management of Lasiodiplodia theobromae and Neofusicoccum parvum. Sci Rep 2021; 11:9612. [PMID: 33953257 PMCID: PMC8099910 DOI: 10.1038/s41598-021-88422-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/12/2021] [Indexed: 12/05/2022] Open
Abstract
Lasiodiplodia theobromae and Neofusicoccum parvum are serious worldwide-distributed plant pathogenic fungi with a wide host range in tropical and temperate climates. They cause fruit rot, canker, and dieback of twigs in various woody plants. Protection of pruning wounds using fungicides is the prevalent strategy for the management of the diseases caused by these fungi. Chemical control of plant diseases is not environmentally safe and the residues of fungicides are a threat to nature. Furthermore, genetic resources of resistance to plant diseases in woody plants are limited. The aim of this study was to investigate the efficiency of RNA silencing using an efficient hairpin structure based on Tef-1α gene for the management of L. theobromae and N. parvum. Hairpin structure of Tef-1α was cloned in pFGC5941 binary vector and the recombinant construct was named pFGC-TEF-d. Transient expression of pFGC-TEF-d using Agrobacterium LBA4404 in grapevine (Bidaneh Sefid cv.) and strawberry cultivars (Camarosa and Ventana) led to a reduction in disease progress of L. theobromae. The disease reduction in grapevine was estimated by 55% and in strawberries cultivars Camarosa and Ventana by 58% and 93%, respectively. Further analysis of transient expression of pFGC-TEF-d in strawberry (Camarosa) shown disease reduction using Neofusicoccum parvum. Here we introduce RNAi silencing using pFGC-TEF-d construct as an efficient strategy to the management of L. theobromae and N. parvum for the first time.
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Affiliation(s)
- Omid Nili
- Department of Plant Protection, University of Kurdistan, 66177-15175, Sanandaj, Iran
| | - Abdolbaset Azizi
- Department of Plant Protection, University of Kurdistan, 66177-15175, Sanandaj, Iran.
| | - Jafar Abdollahzadeh
- Department of Plant Protection, University of Kurdistan, 66177-15175, Sanandaj, Iran.
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Maurer-Alcalá XX, Nowacki M. Evolutionary origins and impacts of genome architecture in ciliates. Ann N Y Acad Sci 2019; 1447:110-118. [PMID: 31074010 PMCID: PMC6767857 DOI: 10.1111/nyas.14108] [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: 12/15/2018] [Revised: 03/18/2019] [Accepted: 04/03/2019] [Indexed: 01/24/2023]
Abstract
Genome architecture is well diversified among eukaryotes in terms of size and content, with many being radically shaped by ancient and ongoing genome conflicts with transposable elements (e.g., the large transposon‐rich genomes common among plants). In ciliates, a group of microbial eukaryotes with distinct somatic and germ‐line genomes present in a single cell, the consequences of these genome conflicts are most apparent in their developmentally programmed genome rearrangements. This complicated developmental phenomenon has largely overshadowed and outpaced our understanding of how germ‐line and somatic genome architectures have influenced the evolutionary dynamism and potential in these taxa. In our review, we highlight three central concepts: how the evolution of atypical ciliate germ‐line genome architectures is linked to ancient genome conflicts; how the complex, epigenetically guided transformation of germline to soma during development can generate widespread genetic variation; and how these features, coupled with their unusual life cycle, have increased the rate of molecular evolution linked to genome architecture in these taxa.
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Affiliation(s)
| | - Mariusz Nowacki
- Institute of Cell Biology, University of Bern, Bern, Switzerland
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Strain Specific Factors Control Effector Gene Silencing in Phytophthora sojae. PLoS One 2016; 11:e0150530. [PMID: 26930612 PMCID: PMC4773254 DOI: 10.1371/journal.pone.0150530] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 02/15/2016] [Indexed: 12/04/2022] Open
Abstract
The Phytophthora sojae avirulence gene Avr3a encodes an effector that is capable of triggering immunity on soybean plants carrying the resistance gene Rps3a. P. sojae strains that express Avr3a are avirulent to Rps3a plants, while strains that do not are virulent. To study the inheritance of Avr3a expression and virulence towards Rps3a, genetic crosses and self-fertilizations were performed. A cross between P. sojae strains ACR10 X P7076 causes transgenerational gene silencing of Avr3a allele, and this effect is meiotically stable up to the F5 generation. However, test-crosses of F1 progeny (ACR10 X P7076) with strain P6497 result in the release of silencing of Avr3a. Expression of Avr3a in the progeny is variable and correlates with the phenotypic penetrance of the avirulence trait. The F1 progeny from a direct cross of P6497 X ACR10 segregate for inheritance for Avr3a expression, a result that could not be explained by parental imprinting or heterozygosity. Analysis of small RNA arising from the Avr3a gene sequence in the parental strains and hybrid progeny suggests that the presence of small RNA is necessary but not sufficient for gene silencing. Overall, we conclude that inheritance of the Avr3a gene silenced phenotype relies on factors that are variable among P. sojae strains.
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Maurer-Alcalá XX, Katz LA. An epigenetic toolkit allows for diverse genome architectures in eukaryotes. Curr Opin Genet Dev 2015; 35:93-9. [PMID: 26649755 DOI: 10.1016/j.gde.2015.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 10/21/2015] [Accepted: 10/22/2015] [Indexed: 02/04/2023]
Abstract
Genome architecture varies considerably among eukaryotes in terms of both size and structure (e.g. distribution of sequences within the genome, elimination of DNA during formation of somatic nuclei). The diversity in eukaryotic genome architectures and the dynamic processes are only possible due to the well-developed epigenetic toolkit, which probably existed in the Last Eukaryotic Common Ancestor (LECA). This toolkit may have arisen as a means of navigating the genomic conflict that arose from the expansion of transposable elements within the ancestral eukaryotic genome. This toolkit has been coopted to support the dynamic nature of genomes in lineages across the eukaryotic tree of life. Here we highlight how the changes in genome architecture in diverse eukaryotes are regulated by epigenetic processes, such as DNA elimination, genome rearrangements, and adaptive changes to genome architecture. The ability to epigenetically modify and regulate genomes has contributed greatly to the diversity of eukaryotes observed today.
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Affiliation(s)
- Xyrus X Maurer-Alcalá
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA; Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA; Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA 01003, USA.
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Åsman AKM, Vetukuri RR, Jahan SN, Fogelqvist J, Corcoran P, Avrova AO, Whisson SC, Dixelius C. Fragmentation of tRNA in Phytophthora infestans asexual life cycle stages and during host plant infection. BMC Microbiol 2014; 14:308. [PMID: 25492044 PMCID: PMC4272539 DOI: 10.1186/s12866-014-0308-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 11/24/2014] [Indexed: 12/17/2022] Open
Abstract
Background The oomycete Phytophthora infestans possesses active RNA silencing pathways, which presumably enable this plant pathogen to control the large numbers of transposable elements present in its 240 Mb genome. Small RNAs (sRNAs), central molecules in RNA silencing, are known to also play key roles in this organism, notably in regulation of critical effector genes needed for infection of its potato host. Results To identify additional classes of sRNAs in oomycetes, we mapped deep sequencing reads to transfer RNAs (tRNAs) thereby revealing the presence of 19–40 nt tRNA-derived RNA fragments (tRFs). Northern blot analysis identified abundant tRFs corresponding to half tRNA molecules. Some tRFs accumulated differentially during infection, as seen by examining sRNAs sequenced from P. infestans-potato interaction libraries. The putative connection between tRF biogenesis and the canonical RNA silencing pathways was investigated by employing hairpin RNA-mediated RNAi to silence the genes encoding P. infestans Argonaute (PiAgo) and Dicer (PiDcl) endoribonucleases. By sRNA sequencing we show that tRF accumulation is PiDcl1-independent, while Northern hybridizations detected reduced levels of specific tRNA-derived species in the PiAgo1 knockdown line. Conclusions Our findings extend the sRNA diversity in oomycetes to include fragments derived from non-protein-coding RNA transcripts and identify tRFs with elevated levels during infection of potato by P. infestans. Electronic supplementary material The online version of this article (doi:10.1186/s12866-014-0308-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna K M Åsman
- Department of Plant Biology, Uppsala BioCenter, Linnéan Centre for Plant Biology, Swedish University of Agricultural Sciences, PO. Box 7080, SE-75007, Uppsala, Sweden.
| | - Ramesh R Vetukuri
- Department of Plant Biology, Uppsala BioCenter, Linnéan Centre for Plant Biology, Swedish University of Agricultural Sciences, PO. Box 7080, SE-75007, Uppsala, Sweden.
| | - Sultana N Jahan
- Department of Plant Biology, Uppsala BioCenter, Linnéan Centre for Plant Biology, Swedish University of Agricultural Sciences, PO. Box 7080, SE-75007, Uppsala, Sweden.
| | - Johan Fogelqvist
- Department of Plant Biology, Uppsala BioCenter, Linnéan Centre for Plant Biology, Swedish University of Agricultural Sciences, PO. Box 7080, SE-75007, Uppsala, Sweden.
| | - Pádraic Corcoran
- Department of Plant Biology, Uppsala BioCenter, Linnéan Centre for Plant Biology, Swedish University of Agricultural Sciences, PO. Box 7080, SE-75007, Uppsala, Sweden. .,Current affiliation: Department of Evolutionary Biology, Uppsala University, SE-75236, Uppsala, Sweden.
| | - Anna O Avrova
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
| | - Stephen C Whisson
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
| | - Christina Dixelius
- Department of Plant Biology, Uppsala BioCenter, Linnéan Centre for Plant Biology, Swedish University of Agricultural Sciences, PO. Box 7080, SE-75007, Uppsala, Sweden.
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Gijzen M, Ishmael C, Shrestha SD. Epigenetic control of effectors in plant pathogens. FRONTIERS IN PLANT SCIENCE 2014; 5:638. [PMID: 25429296 PMCID: PMC4228847 DOI: 10.3389/fpls.2014.00638] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 10/27/2014] [Indexed: 05/07/2023]
Abstract
Plant pathogens display impressive versatility in adapting to host immune systems. Pathogen effector proteins facilitate disease but can become avirulence (Avr) factors when the host acquires discrete recognition capabilities that trigger immunity. The mechanisms that lead to changes to pathogen Avr factors that enable escape from host immunity are diverse, and include epigenetic switches that allow for reuse or recycling of effectors. This perspective outlines possibilities of how epigenetic control of Avr effector gene expression may have arisen and persisted in filamentous plant pathogens, and how it presents special problems for diagnosis and detection of specific pathogen strains or pathotypes.
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Affiliation(s)
- Mark Gijzen
- Agriculture and Agri-Food CanadaLondon, ON, Canada
- Department of Biology, University of Western OntarioLondon, ON, Canada
- *Correspondence: Mark Gijzen, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada e-mail:
| | - Chelsea Ishmael
- Agriculture and Agri-Food CanadaLondon, ON, Canada
- Department of Biology, University of Western OntarioLondon, ON, Canada
| | - Sirjana D. Shrestha
- Agriculture and Agri-Food CanadaLondon, ON, Canada
- Department of Biology, University of Western OntarioLondon, ON, Canada
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