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Velasco L, Padilla CV. High-Throughput Sequencing of Small RNAs for the Sanitary Certification of Viruses in Grapevine. FRONTIERS IN PLANT SCIENCE 2021; 12:682879. [PMID: 34367209 PMCID: PMC8336637 DOI: 10.3389/fpls.2021.682879] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Biological indexing is the method generally recognized for the certification of propagative grapevines in many countries, and it is mandatory in the European Union. It consists of the evaluation of the plant material after grafting on indicators that are inspected for symptom development. This is a lengthy process that requires well-trained workers, testing field, etc. Alternative diagnostic methods such as serology and RT-qPCR have been discarded for certification because of their intrinsic drawbacks. In turn, high-throughput sequencing (HTS) of plant RNA has been proposed as a plausible alternative to bioassay, but before it is accepted, different aspects of this process must be evaluated. We have compared the HTS of small RNAs with bioassays and other diagnostic methods from a set of 40 grapevine plants submitted for certification. The results allowed the authors the identification of numerous grapevine viruses in the samples, as well as different variants. Besides, relationships between symptom expression and viromes were investigated, in particular leafroll-associated viruses. We compared HTS results using analytical and bioinformatics approaches in order to define minimum acceptable quality standards for certification schemes, resulting in a pipeline proposal. Finally, the comparison between HTS and bioassay resulted favorable for the former in terms of reliability, cost, and timing.
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Affiliation(s)
- Leonardo Velasco
- Instituto Andaluz de Investigación y Formación Agraria, Málaga, Spain
| | - Carlos V. Padilla
- Instituto Murciano de Investigación y Desarrollo Agrario y Alimentario, Murcia, Spain
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Shannon Entropy to Evaluate Substitution Rate Variation Among Viral Nucleotide Positions in Datasets of Viral siRNAs. Methods Mol Biol 2019; 1746:187-195. [PMID: 29492896 DOI: 10.1007/978-1-4939-7683-6_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Next-generation sequencing has opened the door to the reconstruction of viral populations and examination of the composition of mutant spectra in infected cells, tissues, and host organisms. In this chapter we present details on the use of the Shannon entropy method to estimate the site-specific nucleotide relative variability of turnip crinkle virus, a positive (+) stranded RNA plant virus, in a large dataset of short RNAs of Cicer arietinum L., a natural reservoir of the virus. We propose this method as a viral metagenomics tool to provide a more detailed description of the viral quasispecies in infected plant tissue. Viral replicative fitness relates to an optimal composition of variants that provide the molecular basis of virus behavior in the complex environment of natural infections. A complete description of viral quasispecies may have implications in determining fitness landscapes for host-virus coexistence and help to design specific diagnostic protocols and antiviral strategies.
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Barrero RA, Napier KR, Cunnington J, Liefting L, Keenan S, Frampton RA, Szabo T, Bulman S, Hunter A, Ward L, Whattam M, Bellgard MI. An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids. BMC Bioinformatics 2017; 18:26. [PMID: 28077064 PMCID: PMC5225587 DOI: 10.1186/s12859-016-1428-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 12/15/2016] [Indexed: 01/06/2023] Open
Abstract
Background Detection and preventing entry of exotic viruses and viroids at the border is critical for protecting plant industries trade worldwide. Existing post entry quarantine screening protocols rely on time-consuming biological indicators and/or molecular assays that require knowledge of infecting viral pathogens. Plants have developed the ability to recognise and respond to viral infections through Dicer-like enzymes that cleave viral sequences into specific small RNA products. Many studies reported the use of a broad range of small RNAs encompassing the product sizes of several Dicer enzymes involved in distinct biological pathways. Here we optimise the assembly of viral sequences by using specific small RNA subsets. Results We sequenced the small RNA fractions of 21 plants held at quarantine glasshouse facilities in Australia and New Zealand. Benchmarking of several de novo assembler tools yielded SPAdes using a kmer of 19 to produce the best assembly outcomes. We also found that de novo assembly using 21–25 nt small RNAs can result in chimeric assemblies of viral sequences and plant host sequences. Such non-specific assemblies can be resolved by using 21–22 nt or 24 nt small RNAs subsets. Among the 21 selected samples, we identified contigs with sequence similarity to 18 viruses and 3 viroids in 13 samples. Most of the viruses were assembled using only 21–22 nt long virus-derived siRNAs (viRNAs), except for one Citrus endogenous pararetrovirus that was more efficiently assembled using 24 nt long viRNAs. All three viroids found in this study were fully assembled using either 21–22 nt or 24 nt viRNAs. Optimised analysis workflows were customised within the Yabi web-based analytical environment. We present a fully automated viral surveillance and diagnosis web-based bioinformatics toolkit that provides a flexible, user-friendly, robust and scalable interface for the discovery and diagnosis of viral pathogens. Conclusions We have implemented an automated viral surveillance and diagnosis (VSD) bioinformatics toolkit that produces improved viruses and viroid sequence assemblies. The VSD toolkit provides several optimised and reusable workflows applicable to distinct viral pathogens. We envisage that this resource will facilitate the surveillance and diagnosis viral pathogens in plants, insects and invertebrates. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1428-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roberto A Barrero
- Centre for Comparative Genomics, Murdoch University, Murdoch, WA, 6150, Australia.
| | - Kathryn R Napier
- Centre for Comparative Genomics, Murdoch University, Murdoch, WA, 6150, Australia.,Plant Biosecurity Cooperative Research Centre, Canberra, ACT, 2617, Australia
| | - James Cunnington
- Department of Agriculture and Water Resources, Mickleham, VIC, 3064, Australia
| | - Lia Liefting
- Ministry for Primary Industries, Wellington, New Zealand
| | - Sandi Keenan
- The New Zealand Institute for Plant Food and Research Limited, Better Border Biosecurity, Lincoln, 7608, New Zealand
| | - Rebekah A Frampton
- The New Zealand Institute for Plant Food and Research Limited, Better Border Biosecurity, Lincoln, 7608, New Zealand
| | - Tamas Szabo
- Centre for Comparative Genomics, Murdoch University, Murdoch, WA, 6150, Australia
| | - Simon Bulman
- The New Zealand Institute for Plant Food and Research Limited, Better Border Biosecurity, Lincoln, 7608, New Zealand
| | - Adam Hunter
- Centre for Comparative Genomics, Murdoch University, Murdoch, WA, 6150, Australia
| | - Lisa Ward
- Ministry for Primary Industries, Wellington, New Zealand
| | - Mark Whattam
- Department of Agriculture and Water Resources, Mickleham, VIC, 3064, Australia
| | - Matthew I Bellgard
- Centre for Comparative Genomics, Murdoch University, Murdoch, WA, 6150, Australia.
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Pantaleo V, Vitali M, Boccacci P, Miozzi L, Cuozzo D, Chitarra W, Mannini F, Lovisolo C, Gambino G. Novel functional microRNAs from virus-free and infected Vitis vinifera plants under water stress. Sci Rep 2016; 6:20167. [PMID: 26833264 PMCID: PMC4735847 DOI: 10.1038/srep20167] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 12/22/2015] [Indexed: 02/01/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that regulate the post-transcriptional control of several pathway intermediates, thus playing pivotal roles in plant growth, development and response to biotic and abiotic stresses. In recent years, the grapevine genome release, small(s)-RNAseq and degradome-RNAseq together has allowed the discovery and characterisation of many miRNA species, thus rendering the discovery of additional miRNAs difficult and uncertain. Taking advantage of the miRNA responsiveness to stresses and the availability of virus-free Vitis vinifera plants and those infected only by a latent virus, we have analysed grapevines subjected to drought in greenhouse conditions. The sRNA-seq and other sequence-specific molecular analyses have allowed us to characterise conserved miRNA expression profiles in association with specific eco-physiological parameters. In addition, we here report 12 novel grapevine-specific miRNA candidates and describe their expression profile. We show that latent viral infection can influence the miRNA profiles of V. vinifera in response to drought. Moreover, study of eco-physiological parameters showed that photosynthetic rate, stomatal conductance and hydraulic resistance to water transport were significantly influenced by drought and viral infection. Although no unequivocal cause–effect explanation could be attributed to each miRNA target, their contribution to the drought response is discussed.
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Affiliation(s)
- Vitantonio Pantaleo
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Research Unit of Bari. Via Amendola 165/a, 70126 Bari, Italy
| | - Marco Vitali
- Department of Agricultural, Forest and Food Sciences, University of Torino. Largo P. Braccini 2, 10095 Grugliasco-TO, Italy
| | - Paolo Boccacci
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Grugliasco Unit. Largo P. Braccini 2, 10095 Grugliasco-TO, Italy
| | - Laura Miozzi
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino. Strada delle Cacce 73, 10135 Torino, Italy
| | - Danila Cuozzo
- Department of Agricultural, Forest and Food Sciences, University of Torino. Largo P. Braccini 2, 10095 Grugliasco-TO, Italy
| | - Walter Chitarra
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Grugliasco Unit. Largo P. Braccini 2, 10095 Grugliasco-TO, Italy
| | - Franco Mannini
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Grugliasco Unit. Largo P. Braccini 2, 10095 Grugliasco-TO, Italy
| | - Claudio Lovisolo
- Department of Agricultural, Forest and Food Sciences, University of Torino. Largo P. Braccini 2, 10095 Grugliasco-TO, Italy.,Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Grugliasco Unit. Largo P. Braccini 2, 10095 Grugliasco-TO, Italy
| | - Giorgio Gambino
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Grugliasco Unit. Largo P. Braccini 2, 10095 Grugliasco-TO, Italy
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