1
|
Mostert I, Bester R, Burger JT, Maree HJ. Investigating Protein-Protein Interactions Between Grapevine Leafroll-Associated Virus 3 and Vitis vinifera. PHYTOPATHOLOGY 2023; 113:1994-2005. [PMID: 37311734 DOI: 10.1094/phyto-03-23-0107-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Grapevine leafroll disease (GLD) is a globally important disease that affects the metabolic composition and biomass of grapes, leading to a reduction in grape yield and quality of wine produced. Grapevine leafroll-associated virus 3 (GLRaV-3) is the main causal agent for GLD. This study aimed to identify protein-protein interactions between GLRaV-3 and its host. A yeast two-hybrid (Y2H) library was constructed from Vitis vinifera mRNA and screened against GLRaV-3 open reading frames encoding structural proteins and those potentially involved in systemic spread and silencing of host defense mechanisms. Five interacting protein pairs were identified, three of which were demonstrated in planta. The minor coat protein of GLRaV-3 was shown to interact with 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase 02, a protein involved in primary carbohydrate metabolism and the biosynthesis of aromatic amino acids. Interactions were also identified between GLRaV-3 p20A and an 18.1-kDa class I small heat shock protein, as well as MAP3K epsilon protein kinase 1. Both proteins are involved in the response of plants to various stressors, including pathogen infections. Two additional proteins, chlorophyll a-b binding protein CP26 and a SMAX1-LIKE 6 protein, were identified as interacting with p20A in yeast but these interactions could not be demonstrated in planta. The findings of this study advance our understanding of the functions of GLRaV-3-encoded proteins and how the interaction between these proteins and those of V. vinifera could lead to GLD.
Collapse
Affiliation(s)
- Ilani Mostert
- Department of Genetics, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Rachelle Bester
- Department of Genetics, Stellenbosch University, Stellenbosch 7600, South Africa
- Citrus Research International, Stellenbosch 7600, South Africa
| | - Johan T Burger
- Department of Genetics, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Hans J Maree
- Department of Genetics, Stellenbosch University, Stellenbosch 7600, South Africa
- Citrus Research International, Stellenbosch 7600, South Africa
| |
Collapse
|
2
|
DeMell A, Alvarado V, Scholthof HB. Molecular perspectives on age-related resistance of plants to (viral) pathogens. THE NEW PHYTOLOGIST 2023; 240:80-91. [PMID: 37507820 DOI: 10.1111/nph.19131] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023]
Abstract
Age-related resistance to microbe invasion is a commonly accepted concept in plant pathology. However, the impact of such age-dependent interactive phenomena is perhaps not yet sufficiently recognized by the broader plant science community. Toward cataloging an understanding of underlying mechanisms, this review explores recent molecular studies and their relevance to the concept. Examples describe differences in genetic background, transcriptomics, hormonal balances, protein-mediated events, and the contribution by short RNA-controlled gene silencing events. Throughout, recent findings with viral systems are highlighted as an illustration of the complexity of the interactions. It will become apparent that instead of uncovering a unifying explanation, we unveiled only trends. Nevertheless, with a degree of confidence, we propose that the process of plant age-related defenses is actively regulated at multiple levels. The overarching goal of this control for plants is to avoid a constitutive waste of resources, especially at crucial metabolically draining early developmental stages.
Collapse
Affiliation(s)
- April DeMell
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX, 77843, USA
| | - Veria Alvarado
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX, 77843, USA
| | - Herman B Scholthof
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX, 77843, USA
| |
Collapse
|
3
|
Mostert I, Bester R, Burger JT, Maree HJ. Identification of Interactions between Proteins Encoded by Grapevine Leafroll-Associated Virus 3. Viruses 2023; 15:208. [PMID: 36680248 PMCID: PMC9865355 DOI: 10.3390/v15010208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/06/2023] [Accepted: 01/08/2023] [Indexed: 01/13/2023] Open
Abstract
The roles of proteins encoded by members of the genus Ampelovirus, family Closteroviridae are largely inferred by sequence homology or analogy to similarly located ORFs in related viruses. This study employed yeast two-hybrid and bimolecular fluorescence complementation assays to investigate interactions between proteins of grapevine leafroll-associated virus 3 (GLRaV-3). The p5 movement protein, HSP70 homolog, coat protein, and p20B of GLRaV-3 were all found to self-interact, however, the mechanism by which p5 interacts remains unknown due to the absence of a cysteine residue crucial for the dimerisation of the closterovirus homolog of this protein. Although HSP70h forms part of the virion head of closteroviruses, in GLRaV-3, it interacts with the coat protein that makes up the body of the virion. Silencing suppressor p20B has been shown to interact with HSP70h, as well as the major coat protein and the minor coat protein. The results of this study suggest that the virion assembly of a member of the genus Ampelovirus occurs in a similar but not identical manner to those of other genera in the family Closteroviridae. Identification of interactions of p20B with virus structural proteins provides an avenue for future research to explore the mechanisms behind the suppression of host silencing and suggests possible involvement in other aspects of the viral replication cycle.
Collapse
Affiliation(s)
- Ilani Mostert
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Rachelle Bester
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
- Citrus Research International, P.O. Box 2201, Matieland 7602, South Africa
| | - Johan T. Burger
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Hans J. Maree
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
- Citrus Research International, P.O. Box 2201, Matieland 7602, South Africa
| |
Collapse
|
4
|
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: 3] [Impact Index Per Article: 1.0] [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.
Collapse
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
| |
Collapse
|
5
|
Fabres PJ, Anand L, Sai N, Pederson S, Zheng F, Stewart AA, Clements B, Lampugnani ER, Breen J, Gilliham M, Tricker P, Rodríguez López CM, David R. Tissue and regional expression patterns of dicistronic tRNA-mRNA transcripts in grapevine (Vitis vinifera) and their evolutionary co-appearance with vasculature in land plants. HORTICULTURE RESEARCH 2021; 8:137. [PMID: 34059643 PMCID: PMC8166872 DOI: 10.1038/s41438-021-00572-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 04/13/2021] [Accepted: 04/19/2021] [Indexed: 06/02/2023]
Abstract
Transfer RNAs (tRNA) are crucial adaptor molecules between messenger RNA (mRNA) and amino acids. Recent evidence in plants suggests that dicistronic tRNA-like structures also act as mobile signals for mRNA transcripts to move between distant tissues. Co-transcription is not a common feature in the plant nuclear genome and, in the few cases where polycistronic transcripts have been found, they include non-coding RNA species, such as small nucleolar RNAs and microRNAs. It is not known, however, the extent to which dicistronic transcripts of tRNA and mRNAs are expressed in field-grown plants, or the factors contributing to their expression. We analysed tRNA-mRNA dicistronic transcripts in the major horticultural crop grapevine (Vitis vinifera) using a novel pipeline developed to identify dicistronic transcripts from high-throughput RNA-sequencing data. We identified dicistronic tRNA-mRNA in leaf and berry samples from 22 commercial vineyards. Of the 124 tRNA genes that were expressed in both tissues, 18 tRNA were expressed forming part of 19 dicistronic tRNA-mRNAs. The presence and abundance of dicistronic molecules was tissue and geographic sub-region specific. In leaves, the expression patterns of dicistronic tRNA-mRNAs significantly correlated with tRNA expression, suggesting that their transcriptional regulation might be linked. We also found evidence of syntenic genomic arrangements of tRNAs and protein-coding genes between grapevine and Arabidopsis thaliana, and widespread prevalence of dicistronic tRNA-mRNA transcripts among vascular land plants but no evidence of these transcripts in non-vascular lineages. This suggests that the appearance of plant vasculature and tRNA-mRNA occurred concurrently during the evolution of land plants.
Collapse
Affiliation(s)
- Pastor Jullian Fabres
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | - Lakshay Anand
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | - Na Sai
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
- ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute & School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Stephen Pederson
- Bioinformatics Hub, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Fei Zheng
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
- ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute & School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Alexander A Stewart
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | - Benjamin Clements
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | - Edwin R Lampugnani
- School of Biosciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - James Breen
- Bioinformatics Hub, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Matthew Gilliham
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
- ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute & School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
- ARC Industrial Transformation Training Centre in Innovative Wine Production, Waite Research Institute & School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Penny Tricker
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Carlos M Rodríguez López
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA.
| | - Rakesh David
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
- ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute & School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| |
Collapse
|
6
|
Song Y, Hanner RH, Meng B. Probing into the Effects of Grapevine Leafroll-Associated Viruses on the Physiology, Fruit Quality and Gene Expression of Grapes. Viruses 2021; 13:v13040593. [PMID: 33807294 PMCID: PMC8066071 DOI: 10.3390/v13040593] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 12/19/2022] Open
Abstract
Grapevine leafroll is one of the most widespread and highly destructive grapevine diseases that is responsible for great economic losses to the grape and wine industries throughout the world. Six distinct viruses have been implicated in this disease complex. They belong to three genera, all in the family Closteroviridae. For the sake of convenience, these viruses are named as grapevine leafroll-associated viruses (GLRaV-1, -2, -3, -4, -7, and -13). However, their etiological role in the disease has yet to be established. Furthermore, how infections with each GLRaV induce the characteristic disease symptoms remains unresolved. Here, we first provide a brief overview on each of these GLRaVs with a focus on genome structure, expression strategies and gene functions, where available. We then provide a review on the effects of GLRaV infection on the physiology, fruit quality, fruit chemical composition, and gene expression of grapevine based on the limited information so far reported in the literature. We outline key methodologies that have been used to study how GLRaV infections alter gene expression in the grapevine host at the transcriptomic level. Finally, we present a working model as an initial attempt to explain how infections with GLRaVs lead to the characteristic symptoms of grapevine leafroll disease: leaf discoloration and downward rolling. It is our hope that this review will serve as a starting point for grapevine virology and the related research community to tackle this vastly important and yet virtually uncharted territory in virus-host interactions involving woody and perennial fruit crops.
Collapse
Affiliation(s)
- Yashu Song
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Robert H. Hanner
- Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Baozhong Meng
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada;
- Correspondence: ; Tel.: +1-519-824-4120 (ext. 53876)
| |
Collapse
|
7
|
Abstract
Plant age is a crucial factor in determining the outcome of a host-pathogen interaction. In successive developmental stages throughout their life cycles, plants face dynamic changes in biotic and abiotic conditions that create distinct ecological niches for host-pathogen interactions. As an adaptive strategy, plants have evolved intrinsic regulatory networks that integrate developmental signals with those from pathogen perception and defense activation. As a result, amplitude and timing of defense responses are optimized, so as to balance the cost and benefit of immunity activation. A general term "age-related resistance" refers to a gain of disease resistance against a certain pathogen when plants reach a relatively mature stage. Age-related resistance is a common observation on fruits, vegetables, and row crops for their resistance against viruses, bacteria, fungi, oomycetes pathogens, and insects. This review focuses on the recent advances in understanding the molecular mechanisms of how plants coordinate developmental timing and immune response.
Collapse
Affiliation(s)
- Lanxi Hu
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
| | - Li Yang
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
| |
Collapse
|
8
|
The Role of UV-B light on Small RNA Activity During Grapevine Berry Development. G3-GENES GENOMES GENETICS 2019; 9:769-787. [PMID: 30647106 PMCID: PMC6404619 DOI: 10.1534/g3.118.200805] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
We explored the effects of ultraviolet B radiation (UV-B) on the developmental dynamics of microRNAs and phased small-interfering-RNA (phasi-RNAs)-producing loci by sequencing small RNAs in vegetative and reproductive organs of grapevine (Vitis vinifera L.). In particular, we tested different UV-B conditions in in vitro-grown plantlets (high-fluence exposition) and in berries from field-grown (radiation filtering) and greenhouse-grown (low- and high-fluence expositions) adult plants throughout fruit development and ripening. The functional significance of the observed UV-coordinated miRNA responses was supported by degradome evidences of ARGONAUTE (AGO)-programmed slicing of mRNAs. Co-expression patterns of the up-regulated miRNAs miR156, miR482, miR530, and miR828 with cognate target gene expressions in response to high-fluence UV-B was tested by q-RT-PCR. The observed UV-response relationships were also interrogated against two published UV-stress and developmental transcriptome datasets. Together, the dynamics observed between miRNAs and targets suggest that changes in target abundance are mediated transcriptionally and, in some cases, modulated post-transcriptionally by miRNAs. Despite the major changes in target abundance are being controlled primarily by those developmental effects that are similar between treatments, we show evidence for novel miRNA-regulatory networks in grape. A model is proposed where high-fluence UV-B increases miR168 and miR530 that target ARGONAUTE 1 (AGO1) and a Plus-3 domain mRNA, respectively, while decreasing miR403 that targets AGO2, thereby coordinating post-transcriptional gene silencing activities by different AGOs. Up-regulation of miR3627/4376 could facilitate anthocyanin accumulation by antagonizing a calcium effector, whereas miR395 and miR399, induced by micronutrient deficiencies known to trigger anthocyanin accumulation, respond positively to UV-B radiation. Finally, increases in the abundance of an anthocyanin-regulatory MYB-bHLH-WD40 complex elucidated in Arabidopsis, mediated by UV-B-induced changes in miR156/miR535, could contribute to the observed up-regulation of miR828. In turn, miR828 would regulate the AtMYB113-ortologues MYBA5, A6 and A7 (and thereby anthocyanins) via a widely conserved and previously validated auto-regulatory loop involving miR828 and phasi TAS4abc RNAs.
Collapse
|
9
|
Hadidi A. Next-Generation Sequencing and CRISPR/Cas13 Editing in Viroid Research and Molecular Diagnostics. Viruses 2019; 11:E120. [PMID: 30699972 PMCID: PMC6409718 DOI: 10.3390/v11020120] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 01/24/2019] [Accepted: 01/25/2019] [Indexed: 12/12/2022] Open
Abstract
Viroid discovery as well as the economic significance of viroids and biological properties are presented. Next-generation sequencing (NGS) technologies combined with informatics have been applied to viroid research and diagnostics for almost a decade. NGS provides highly efficient, rapid, low-cost high-throughput sequencing of viroid genomes and of the 21⁻24 nt vd-sRNAs generated by the RNA silencing defense of the host. NGS has been utilized in various viroid studies which are presented. The discovery during the last few years that prokaryotes have heritable adaptive immunity mediated through clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated Cas proteins, have led to transformative advances in molecular biology, notably genome engineering and most recently molecular diagnostics. The potential application of the CRISPR-Cas13a system for engineering viroid interference in plants is suggested by targeting specific motifs of three economically important viroids. The CRISPR-Cas13 system has been utilized recently for the accurate detection of human RNA viruses by visual read out in 90 min or less and by paper-based assay. Multitarget RNA tests by this technology have a good potential for application as a rapid and accurate diagnostic assay for known viroids. The CRISPR/Cas system will work only for known viroids in contrast to NGS, but it should be much faster.
Collapse
Affiliation(s)
- Ahmed Hadidi
- United States Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA.
| |
Collapse
|
10
|
Lan Y, Yan Z, Guo Y, Duan T, Li C, Gao P, Christensen MJ. RETRACTED ARTICLE: Albinism and mosaicism in Apocynum venetum associated with viral infections in China. Arch Virol 2019; 164:333. [DOI: 10.1007/s00705-018-4059-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 09/18/2018] [Indexed: 10/28/2022]
|
11
|
Pooggin MM. Small RNA-Omics for Plant Virus Identification, Virome Reconstruction, and Antiviral Defense Characterization. Front Microbiol 2018; 9:2779. [PMID: 30524398 PMCID: PMC6256188 DOI: 10.3389/fmicb.2018.02779] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/30/2018] [Indexed: 11/13/2022] Open
Abstract
RNA interference (RNAi)-based antiviral defense generates small interfering RNAs that represent the entire genome sequences of both RNA and DNA viruses as well as viroids and viral satellites. Therefore, deep sequencing and bioinformatics analysis of small RNA population (small RNA-ome) allows not only for universal virus detection and genome reconstruction but also for complete virome reconstruction in mixed infections. Viral infections (like other stress factors) can also perturb the RNAi and gene silencing pathways regulating endogenous gene expression and repressing transposons and host genome-integrated endogenous viral elements which can potentially be released from the genome and contribute to disease. This review describes the application of small RNA-omics for virus detection, virome reconstruction and antiviral defense characterization in cultivated and non-cultivated plants. Reviewing available evidence from a large and ever growing number of studies of naturally or experimentally infected hosts revealed that all families of land plant viruses, their satellites and viroids spawn characteristic small RNAs which can be assembled into contigs of sufficient length for virus, satellite or viroid identification and for exhaustive reconstruction of complex viromes. Moreover, the small RNA size, polarity and hotspot profiles reflect virome interactions with the plant RNAi machinery and allow to distinguish between silent endogenous viral elements and their replicating episomal counterparts. Models for the biogenesis and functions of small interfering RNAs derived from all types of RNA and DNA viruses, satellites and viroids as well as endogenous viral elements are presented and discussed.
Collapse
Affiliation(s)
- Mikhail M. Pooggin
- Institut National de la Recherche Agronomique, UMR BGPI, Montpellier, France
| |
Collapse
|
12
|
Zarreen F, Kumar G, Johnson AMA, Dasgupta I. Small RNA-based interactions between rice and the viruses which cause the tungro disease. Virology 2018; 523:64-73. [PMID: 30081310 DOI: 10.1016/j.virol.2018.07.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 07/20/2018] [Accepted: 07/20/2018] [Indexed: 10/28/2022]
Abstract
Rice tungro disease is caused by a complex of two viruses, Rice tungro bacilliform virus (RTBV) and Rice tungro spherical virus (RTSV). To examine the RNAi-based defence response in rice during tungro disease, we characterized the virus-derived small RNAs and miRNAs by Deep Sequencing. We found that, while 21 nt/22 nt (nucleotide) siRNAs are predominantly produced in a continuous, overlapping and asymmetrical manner from RTBV, siRNA accumulation from RTSV were negligible. Additionally, 54 previously known miRNAs from rice, predicted to be regulating genes involved in plant defence, hormone signaling and developmental pathways were differentially expressed in the infected samples, compared to the healthy ones. This is the first study of sRNA profile of tungro virus complex from infected rice plants. The biased response of the host antiviral machinery against the two viruses and the differentially-expressed miRNAs are novel observations, which entail further studies.
Collapse
Affiliation(s)
- Fauzia Zarreen
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Gaurav Kumar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - A M Anthony Johnson
- Department of Botany, Sri Krishnadevaraya University, Anantapur 515003, Andhra Pradesh, India
| | - Indranil Dasgupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India.
| |
Collapse
|
13
|
Chitarra W, Pagliarani C, Abbà S, Boccacci P, Birello G, Rossi M, Palmano S, Marzachì C, Perrone I, Gambino G. miRVIT: A Novel miRNA Database and Its Application to Uncover Vitis Responses to Flavescence dorée Infection. FRONTIERS IN PLANT SCIENCE 2018; 9:1034. [PMID: 30065744 PMCID: PMC6057443 DOI: 10.3389/fpls.2018.01034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 06/26/2018] [Indexed: 05/08/2023]
Abstract
Micro(mi)RNAs play crucial roles in plant developmental processes and in defense responses to biotic and abiotic stresses. In the last years, many works on small RNAs in grapevine (Vitis spp.) were published, and several conserved and putative novel grapevine-specific miRNAs were identified. In order to reorganize the high quantity of available data, we produced "miRVIT," the first database of all novel grapevine miRNA candidates characterized so far, and still not deposited in miRBase. To this aim, each miRNA accession was renamed, repositioned in the last version of the grapevine genome, and compared with all the novel and conserved miRNAs detected in grapevine. Conserved and novel miRNAs cataloged in miRVIT were then used for analyzing Vitis vinifera plants infected by Flavescence dorée (FD), one of the most severe phytoplasma diseases affecting grapevine. The analysis of small RNAs from healthy, recovered (plants showing spontaneous and stable remission of symptoms), and FD-infected "Barbera" grapevines showed that FD altered the expression profiles of several miRNAs, including those involved in cell development and photosynthesis, jasmonate signaling, and disease resistance response. The application of miRVIT in a biological context confirmed the effectiveness of the followed approach, especially for the identification of novel miRNA candidates in grapevine. miRVIT database is available at http://mirvit.ipsp.cnr.it. Highlights: The application of the newly produced database of grapevine novel miRNAs to the analysis of plants infected by Flavescence dorée reveals key roles of miRNAs in photosynthesis and jasmonate signaling.
Collapse
Affiliation(s)
- Walter Chitarra
- Institute for Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
- Viticultural and Enology Research Centre, Council for Agricultural Research and Economics, Conegliano, Italy
| | - Chiara Pagliarani
- Institute for Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
| | - Simona Abbà
- Institute for Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
| | - Paolo Boccacci
- Institute for Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
| | - Giancarlo Birello
- Research Institute on Sustainable Economic Growth, National Research Council of Italy, Turin, Italy
| | - Marika Rossi
- Institute for Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
| | - Sabrina Palmano
- Institute for Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
| | - Cristina Marzachì
- Institute for Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
| | - Irene Perrone
- Institute for Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
| | - Giorgio Gambino
- Institute for Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
| |
Collapse
|
14
|
Luan Y, Cui J, Li J, Jiang N, Liu P, Meng J. Effective enhancement of resistance to Phytophthora infestans by overexpression of miR172a and b in Solanum lycopersicum. PLANTA 2018; 247:127-138. [PMID: 28884358 DOI: 10.1007/s00425-017-2773-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 09/03/2017] [Indexed: 05/22/2023]
Abstract
Overexpression of miR172a and b in tomato ( Solanum lycopersicum ) Zaofen No. 2 increased resistance to Phytophthora infestans infection by suppressing of an AP2/ERF transcription factor. The miR172 family has been shown to participate in the growth phase transition, flowering time control, abiotic and biotic stresses by regulating the expression of a small group of AP2/ERF transcription factors. In this study, the precursors of miR172a and b were cloned from tomato, Solanum pimpinellifolium L3708. We used the degradome sequencing to determine the cleavage site of miR172 to a member of the AP2/ERF transcription factor family (Solyc11g072600.1.1). qRT-PCR results showed that the expression of AP2/ERF was negatively correlated with the expression of miR172 in S. pimpinellifolium L3708 infected with Phytophthora infestans. Overexpression of miR172a and b in S. lycopersicum Zaofen No. 2 conferred greater resistance to P. infestans infection, as evidenced by decreased disease index, lesion sizes, and P. infestans abundance. The SOD and POD play important roles in scavenging late massive ROS in plant-pathogen interaction. Malonaldehyde (MDA) is widely recognized as an indicator of lipid peroxidation. Membrane damage in plants can be estimated by measuring leakage of electrolytes, which is evaluated by determining relative electrolyte leakage (REL). Less H2O2 and O2-, higher activities of POD and SOD, less MDA content and REL, and higher chlorophyll content and photosynthetic rate were also shown in transgenic plants after inoculation with P. infestans. Our results constitute the first step towards further investigations into the biological function and molecular mechanism of miR172-mediated silencing of AP2/ERF transcription factors in S. lycopersicum-P. infestans interaction and provide a candidate gene for breeding to enhance biotic stress-resistance in S. lycopersicum.
Collapse
Affiliation(s)
- Yushi Luan
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Jun Cui
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Jie Li
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Ning Jiang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Ping Liu
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China.
| |
Collapse
|
15
|
Cui ZH, Bi WL, Hao XY, Li PM, Duan Y, Walker MA, Xu Y, Wang QC. Drought Stress Enhances Up-Regulation of Anthocyanin Biosynthesis in Grapevine leafroll-associated virus 3-Infected in vitro Grapevine (Vitis vinifera) Leaves. PLANT DISEASE 2017; 101:1606-1615. [PMID: 30677332 DOI: 10.1094/pdis-01-17-0104-re] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Reddish-purple coloration on the leaf blades and downward rolling of leaf margins are typical symptoms of grapevine leafroll disease (GLD) in red-fruited grapevine cultivars. These typical symptoms are attributed to the expression of genes encoding enzymes for anthocyanins synthesis, and the accumulation of flavonoids in diseased leaves. Drought has been proven to accelerate development of GLD symptoms in virus-infected leaves of grapevine. However, it is not known how drought affects GLD expression nor how anthocyanin biosynthesis in virus-infected leaves is altered. The present study used HPLC to determine the types and levels of anthocyanins, and applied reverse transcription quantitative polymerase chain reaction (RT-qPCR) to analyze the expression of genes encoding enzymes for anthocyanin synthesis. Plantlets of Grapevine leafroll-associated virus 3 (GLRaV-3)-infected Vitis vinifera 'Cabernet Sauvignon' were grown in vitro under PEG-induced drought stress. HPLC found no anthocyanin-related peaks in the healthy plantlets with or without PEG-induced stress, while 11 peaks were detected in the infected plantlets with or without PEG-induced drought stress, but the peaks were significantly higher in infected drought-stressed plantlets. Increased accumulation of total anthocyanin compounds was related to the development of GLD symptoms in the infected plantlets under PEG stress. The highest level of up-regulated gene expression was found in GLRaV-3-infected leaves with PEG-induced drought stress. Analyses of variance and correlation of anthocyanin accumulation with related gene expression levels found that GLRaV-3-infection was the key factor in increased anthocyanin accumulation. This accumulation involved the up-regulation of two key genes, MYBA1 and UFGT, and their expression levels were further enhanced by drought stress.
Collapse
Affiliation(s)
- Zhen-Hua Cui
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Genetic Improvement of Horticultural Crops of Northwest China, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, P.R. China; and Department of Viticulture and Enology, University of California, Davis, 95616-3014
| | - Wen-Lu Bi
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Genetic Improvement of Horticultural Crops of Northwest China, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, P.R. China
| | - Xin-Yi Hao
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Genetic Improvement of Horticultural Crops of Northwest China, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, P.R. China
| | - Peng-Min Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Genetic Improvement of Horticultural Crops of Northwest China, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, P.R. China
| | - Ying Duan
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Genetic Improvement of Horticultural Crops of Northwest China, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, P.R. China
| | - M Andrew Walker
- Department of Viticulture and Enology, University of California, Davis, 95616-3014
| | - Yan Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Genetic Improvement of Horticultural Crops of Northwest China, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, P.R. China
| | - Qiao-Chun Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Genetic Improvement of Horticultural Crops of Northwest China, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, P.R. China
| |
Collapse
|
16
|
Snyman MC, Solofoharivelo MC, Souza-Richards R, Stephan D, Murray S, Burger JT. The use of high-throughput small RNA sequencing reveals differentially expressed microRNAs in response to aster yellows phytoplasma-infection in Vitis vinifera cv. 'Chardonnay'. PLoS One 2017; 12:e0182629. [PMID: 28813447 PMCID: PMC5558978 DOI: 10.1371/journal.pone.0182629] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 07/22/2017] [Indexed: 11/19/2022] Open
Abstract
Phytoplasmas are cell wall-less plant pathogenic bacteria responsible for major crop losses throughout the world. In grapevine they cause grapevine yellows, a detrimental disease associated with a variety of symptoms. The high economic impact of this disease has sparked considerable interest among researchers to understand molecular mechanisms related to pathogenesis. Increasing evidence exist that a class of small non-coding endogenous RNAs, known as microRNAs (miRNAs), play an important role in post-transcriptional gene regulation during plant development and responses to biotic and abiotic stresses. Thus, we aimed to dissect complex high-throughput small RNA sequencing data for the genome-wide identification of known and novel differentially expressed miRNAs, using read libraries constructed from healthy and phytoplasma-infected Chardonnay leaf material. Furthermore, we utilised computational resources to predict putative miRNA targets to explore the involvement of possible pathogen response pathways. We identified multiple known miRNA sequence variants (isomiRs), likely generated through post-transcriptional modifications. Sequences of 13 known, canonical miRNAs were shown to be differentially expressed. A total of 175 novel miRNA precursor sequences, each derived from a unique genomic location, were predicted, of which 23 were differentially expressed. A homology search revealed that some of these novel miRNAs shared high sequence similarity with conserved miRNAs from other plant species, as well as known grapevine miRNAs. The relative expression of randomly selected known and novel miRNAs was determined with real-time RT-qPCR analysis, thereby validating the trend of expression seen in the normalised small RNA sequencing read count data. Among the putative miRNA targets, we identified genes involved in plant morphology, hormone signalling, nutrient homeostasis, as well as plant stress. Our results may assist in understanding the role that miRNA pathways play during plant pathogenesis, and may be crucial in understanding disease symptom development in aster yellows phytoplasma-infected grapevines.
Collapse
Affiliation(s)
- Marius C. Snyman
- The Vitis Laboratory, Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | | | - Rose Souza-Richards
- The Vitis Laboratory, Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Dirk Stephan
- The Vitis Laboratory, Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Shane Murray
- Centre for Proteomic and Genomic Research, Observatory, Cape Town, South Africa
| | - Johan T. Burger
- The Vitis Laboratory, Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| |
Collapse
|
17
|
Matoušek J, Siglová K, Jakše J, Radišek S, Brass JRJ, Tsushima T, Guček T, Duraisamy GS, Sano T, Steger G. Propagation and some physiological effects of Citrus bark cracking viroid and Apple fruit crinkle viroid in multiple infected hop (Humulus lupulus L.). JOURNAL OF PLANT PHYSIOLOGY 2017; 213:166-177. [PMID: 28395198 DOI: 10.1016/j.jplph.2017.02.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/28/2017] [Accepted: 02/28/2017] [Indexed: 06/07/2023]
Abstract
The hop metabolome important for the brewing industry and for medical purposes is endangered worldwide due to multiple viroid infections affecting hop physiology. Combinatorial biolistic hop inoculation with Citrus bark cracking viroid (CBCVd), Apple fruit crinkle viroid (AFCVd), Hop latent viroid, and Hop stunt viroid (HSVd) showed a low CBCVd compatibility with HSVd, while all other viroid combinations were highly compatible. Unlike to other viroids, single CBCVd propagation showed a significant excess of (-) over (+) strands in hop, tomato, and Nicotiana benthamiana, but not in citruses. Inoculation of hop with all viroids led to multiple infections with unstable viroid levels in individual plants in the pre- and post-dormancy periods, and to high plant mortality and morphological disorders. Hop isolates of CBCVd and AFCVd were highly stable, only minor quasispecies were detected. CBCVd caused a strong suppression of some crucial mRNAs related to the hop prenylflavonoid biosynthesis pathway, while AFCVd-caused effects were moderate. According to mRNA degradome analysis, this suppression was not caused by a direct viroid-specific small RNA-mediated degradation. CBCVd infection led to a strong induction of two hop transcription factors from WRKY family and to a disbalance of WRKY/WDR1 complexes important for activation of lupulin genes.
Collapse
Affiliation(s)
- J Matoušek
- Biology Centre ASCR v.v.i, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice 370 05, Czech Republic
| | - K Siglová
- Biology Centre ASCR v.v.i, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice 370 05, Czech Republic; University of South Bohemia, Faculty of Science, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - J Jakše
- University of Ljubljana, Biotechnical Faculty, Department of Agronomy, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - S Radišek
- Slovenian Institute of Hop Research and Brewing, Cesta Žalskega tabora 2, SI-3310 Žalec, Slovenia
| | - Joseph R J Brass
- Institute of Physical Biology, Heinrich-Heine-Universität Düsseldorf, D-40204 Düsseldorf, Germany
| | - T Tsushima
- Faculty of Agriculture and Life Science, Hirosaki University, Bubkyo-cho, Hirosaki 036-8561, Japan
| | - T Guček
- Slovenian Institute of Hop Research and Brewing, Cesta Žalskega tabora 2, SI-3310 Žalec, Slovenia
| | - G S Duraisamy
- Biology Centre ASCR v.v.i, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice 370 05, Czech Republic
| | - T Sano
- Faculty of Agriculture and Life Science, Hirosaki University, Bubkyo-cho, Hirosaki 036-8561, Japan
| | - G Steger
- Institute of Physical Biology, Heinrich-Heine-Universität Düsseldorf, D-40204 Düsseldorf, Germany.
| |
Collapse
|
18
|
Differential expression of miRNAs and associated gene targets in grapevine leafroll-associated virus 3-infected plants. Arch Virol 2016; 162:987-996. [PMID: 28025711 DOI: 10.1007/s00705-016-3197-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/23/2016] [Indexed: 10/20/2022]
Abstract
MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs (sRNA) that play an essential role in the regulation of target mRNAs expressed during plant development and in response to stress. MicroRNA expression profiling has helped to identify miRNAs that regulate a range of processes, including the plant's defence response to pathogens. In this study, differential miRNA expression in own-rooted Vitis vinifera cv. Cabernet Sauvignon plants infected with grapevine leafroll-associated virus 3 was investigated with microarrays and next-generation sequencing (NGS) of sRNA and mRNA. These high-throughput approaches identified several differentially expressed miRNAs. Four miRNAs, identified by both approaches, were validated by stemloop RT-PCRs. Three of the predicted targets of the differentially expressed miRNAs were also differentially expressed in the transcriptome data of infected plants, and were validated by RT-qPCR. Identification of these miRNAs and their targets can lead to a better understanding of host-pathogen interactions involved in grapevine leafroll disease and the identification of possible targets for virus resistance.
Collapse
|
19
|
Mascia T, Gallitelli D. Synergies and antagonisms in virus interactions. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 252:176-192. [PMID: 27717453 DOI: 10.1016/j.plantsci.2016.07.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 07/22/2016] [Accepted: 07/27/2016] [Indexed: 05/25/2023]
Abstract
Metagenomic surveys and data from next generation sequencing revealed that mixed infections among plant viruses are probably a rule rather than an exception in natural pathosystems. The documented cases may range from synergism to antagonism, which may depend from the spatiotemporal order of arrival of the viruses on the host and upon the host itself. In synergistic interactions, the measurable differences in replication, phenotypic and cytopathological changes, cellular tropism, within host movement, and transmission rate of one of the two viruses or both are increased. Conversely, a decrease in replication, or inhibition of one or more of the above functions by one virus against the other, leads to an antagonistic interaction. Viruses may interact directly and by transcomplementation of defective functions or indirectly, through responses mediated by the host like the defense mechanism based on RNA silencing. Outcomes of these interactions can be applied to the risk assessment of transgenic crops expressing viral proteins, or cross-protected crops for the identification of potential hazards. Prior to experimental evidence, mathematical models may help in forecasting challenges deriving from the great variety of pathways of synergistic and antagonistic interactions. Actually, it seems that such predictions do not receive sufficient credit in the framework of agriculture.
Collapse
Affiliation(s)
- Tiziana Mascia
- Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; Istituto del CNR per la Protezione sostenibile delle Piante, Unità Operativa di Supporto di Bari, Via Amendola 165/A, 70126 Bari, Italy
| | - Donato Gallitelli
- Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; Istituto del CNR per la Protezione sostenibile delle Piante, Unità Operativa di Supporto di Bari, Via Amendola 165/A, 70126 Bari, Italy.
| |
Collapse
|
20
|
Liu J, Zhang X, Yang Y, Hong N, Wang G, Wang A, Wang L. Characterization of virus-derived small interfering RNAs in Apple stem grooving virus-infected in vitro-cultured Pyrus pyrifolia shoot tips in response to high temperature treatment. Virol J 2016; 13:166. [PMID: 27716257 PMCID: PMC5053029 DOI: 10.1186/s12985-016-0625-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 09/27/2016] [Indexed: 11/10/2022] Open
Abstract
Background Heat treatment (known as thermotherapy) together with in vitro culture of shoot meristem tips is a commonly used technology to obtain virus-free germplasm for the effective control of virus diseases in fruit trees. RNA silencing as an antiviral defense mechanism has been implicated in this process. To understand if high temperature-mediated acceleration of the host antiviral gene silencing system in the meristem tip facilitates virus-derived small interfering RNAs (vsiRNA) accumulation to reduce the viral RNA titer in the fruit tree meristem tip cells, we used the Apple stem grooving virus (ASGV)–Pyrus pyrifolia pathosystem to explore the possible roles of vsiRNA in thermotherapy. Results At first we determined the full-length genome sequence of the ASGV-Js2 isolate and then profiled vsiRNAs in the meristem tip of in vitro-grown pear (cv. ‘Jinshui no. 2’) shoots infected by ASGV-Js2 and cultured at 24 and 37 °C. A total of 7,495 and 7,949 small RNA reads were obtained from the tips of pear shoots cultured at 24 and 37 °C, respectively. Mapping of the vsiRNAs to the ASGV-Js2 genome revealed that they were unevenly distributed along the ASGV-Js2 genome, and that 21- and 22-nt vsiRNAs preferentially accumulated at both temperatures. The 5′-terminal nucleotides of ASGV-specific siRNAs in the tips cultured under different temperatures had a similar distribution pattern, and the nucleotide U was the most frequent. RT-qPCR analyses suggested that viral genome accumulation was drastically compromised at 37 °C compared to 24 °C, which was accompanied with the elevated levels of vsiRNAs at 37 °C. As plant Dicer-like proteins (DCLs), Argonaute proteins (AGOs), and RNA-dependent RNA polymerases (RDRs) are implicated in vsiRNA biogenesis, we also cloned the partial sequences of PpDCL2,4, PpAGO1,2,4 and PpRDR1 genes, and found their expression levels were up-regulated in the ASGV-infected pear shoots at 37 °C. Conclusions Collectively, these results showed that upon high temperature treatment, the ASGV-infected meristem shoot tips up-regulated the expression of key genes in the RNA silencing pathway, induced the biogenesis of vsiRNAs and inhibited viral RNA accumulation. This study represents the first report on the characterization of the vsiRNA population in pear plants infected by ASGV-Js2, in response to high temperature treatment. Electronic supplementary material The online version of this article (doi:10.1186/s12985-016-0625-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Juan Liu
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei, 430070, People's Republic of China.,Laboratory of Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei, 430070, People's Republic of China
| | - XueJiao Zhang
- Shihezi University, Shihezi City, Xinjiang Uyghur Autonomous Region, 832003, People's Republic of China
| | - YueKun Yang
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei, 430070, People's Republic of China.,Laboratory of Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei, 430070, People's Republic of China
| | - Ni Hong
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei, 430070, People's Republic of China.,Laboratory of Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei, 430070, People's Republic of China
| | - GuoPing Wang
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei, 430070, People's Republic of China.,Laboratory of Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei, 430070, People's Republic of China
| | - Aiming Wang
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, N5V 4 T3, Canada
| | - LiPing Wang
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei, 430070, People's Republic of China. .,Laboratory of Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei, 430070, People's Republic of China.
| |
Collapse
|
21
|
Hadidi A, Flores R, Candresse T, Barba M. Next-Generation Sequencing and Genome Editing in Plant Virology. Front Microbiol 2016; 7:1325. [PMID: 27617007 PMCID: PMC4999435 DOI: 10.3389/fmicb.2016.01325] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 08/11/2016] [Indexed: 01/18/2023] Open
Abstract
Next-generation sequencing (NGS) has been applied to plant virology since 2009. NGS provides highly efficient, rapid, low cost DNA, or RNA high-throughput sequencing of the genomes of plant viruses and viroids and of the specific small RNAs generated during the infection process. These small RNAs, which cover frequently the whole genome of the infectious agent, are 21-24 nt long and are known as vsRNAs for viruses and vd-sRNAs for viroids. NGS has been used in a number of studies in plant virology including, but not limited to, discovery of novel viruses and viroids as well as detection and identification of those pathogens already known, analysis of genome diversity and evolution, and study of pathogen epidemiology. The genome engineering editing method, clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system has been successfully used recently to engineer resistance to DNA geminiviruses (family, Geminiviridae) by targeting different viral genome sequences in infected Nicotiana benthamiana or Arabidopsis plants. The DNA viruses targeted include tomato yellow leaf curl virus and merremia mosaic virus (begomovirus); beet curly top virus and beet severe curly top virus (curtovirus); and bean yellow dwarf virus (mastrevirus). The technique has also been used against the RNA viruses zucchini yellow mosaic virus, papaya ringspot virus and turnip mosaic virus (potyvirus) and cucumber vein yellowing virus (ipomovirus, family, Potyviridae) by targeting the translation initiation genes eIF4E in cucumber or Arabidopsis plants. From these recent advances of major importance, it is expected that NGS and CRISPR-Cas technologies will play a significant role in the very near future in advancing the field of plant virology and connecting it with other related fields of biology.
Collapse
Affiliation(s)
- Ahmed Hadidi
- United States Department of Agriculture – Agricultural Research ServiceBeltsville, MD, USA
| | - Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia–Consejo Superior de Investigaciones CientíficasValencia, Spain
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Université de BordeauxBordeaux, France
| | - Marina Barba
- Consiglio per la Ricerca in Agricoltura e l’analisi dell’Economia Agraria, Centro di Ricerca per la Patologia VegetaleRome, Italy
| |
Collapse
|
22
|
Alabi OJ, Casassa LF, Gutha LR, Larsen RC, Henick-Kling T, Harbertson JF, Naidu RA. Impacts of Grapevine Leafroll Disease on Fruit Yield and Grape and Wine Chemistry in a Wine Grape (Vitis vinifera L.) Cultivar. PLoS One 2016; 11:e0149666. [PMID: 26919614 PMCID: PMC4769264 DOI: 10.1371/journal.pone.0149666] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 01/17/2016] [Indexed: 12/26/2022] Open
Abstract
Grapevine leafroll disease (GLD) is an economically important virus disease affecting wine grapes (Vitis vinifera L.), but little is known about its effect on wine chemistry and sensory composition of wines. In this study, impacts of GLD on fruit yield, berry quality and wine chemistry and sensory features were investigated in a red wine grape cultivar planted in a commercial vineyard. Own-rooted Merlot vines showing GLD symptoms and tested positive for Grapevine leafroll-associated virus 3 and adjacent non-symptomatic vines that tested negative for the virus were compared during three consecutive seasons. Number and total weight of clusters per vine were significantly less in symptomatic relative to non-symptomatic vines. In contrast to previous studies, a time-course analysis of juice from grapes harvested at different stages of berry development from symptomatic and non-symptomatic vines indicated more prominent negative impacts of GLD on total soluble solids (TSS) and berry skin anthocyanins than in juice pH and titratable acidity. Differences in TSS between grapes of symptomatic and non-symptomatic vines were more pronounced after the onset of véraison, with significantly lower concentrations of TSS in grapes from symptomatic vines throughout berry ripening until harvest. Wines made from grapes of GLD-affected vines had significantly lower alcohol, polymeric pigments, and anthocyanins compared to corresponding wines from grapes of non-symptomatic vines. Sensory descriptive analysis of 2010 wines indicated significant differences in color, aroma and astringency between wines made from grapes harvested from GLD-affected and unaffected vines. The impacts of GLD on yield and fruit and wine quality traits were variable between the seasons, with greater impacts observed during a cooler season, suggesting the influence of host plant × environment interactions on overall impacts of the disease.
Collapse
Affiliation(s)
- Olufemi J. Alabi
- Department of Plant Pathology, Washington State University, Irrigated Agriculture Research and Extension Center, Prosser, Washington, United States of America
| | - L. Federico Casassa
- Viticulture and Enology Program, Washington State University, Wine Science Center, 2710 Crimson Way, Richland, Washington, United States of America
| | - Linga R. Gutha
- Department of Plant Pathology, Washington State University, Irrigated Agriculture Research and Extension Center, Prosser, Washington, United States of America
| | - Richard C. Larsen
- Viticulture and Enology Program, Washington State University, Wine Science Center, 2710 Crimson Way, Richland, Washington, United States of America
| | - Thomas Henick-Kling
- Viticulture and Enology Program, Washington State University, Wine Science Center, 2710 Crimson Way, Richland, Washington, United States of America
| | - James F. Harbertson
- Viticulture and Enology Program, Washington State University, Wine Science Center, 2710 Crimson Way, Richland, Washington, United States of America
| | - Rayapati A. Naidu
- Department of Plant Pathology, Washington State University, Irrigated Agriculture Research and Extension Center, Prosser, Washington, United States of America
- * E-mail:
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Han L, Weng K, Ma H, Xiang G, Li Z, Wang Y, Liu G, Xu Y. Identification and Characterization of Erysiphe necator-Responsive MicroRNAs in Chinese Wild Vitis pseudoreticulata by High-Throughput Sequencing. FRONTIERS IN PLANT SCIENCE 2016; 7:621. [PMID: 27303408 PMCID: PMC4885880 DOI: 10.3389/fpls.2016.00621] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 04/22/2016] [Indexed: 05/21/2023]
Abstract
Grapevine powdery mildew is one of the most damaging fungal diseases. Therefore, a precise understanding of the grapevine disease resistance system becomes a subject of significant importance. Plant microRNAs(miRNAs) have been implicated to play regulatory roles in plant biotic stress responses. In this study, high-throughput sequencing and miRDeep-P were employed to identify miRNAs in Chinese wild Vitis pseudoreticulata leaves following inoculation with Erysiphe necator. Altogether, 126 previously identified microRNAs and 124 novel candidates of miRNA genes were detected. Among them, 43 conserved miRNAs belong to 20 families and 23 non-conserved but previously-known miRNAs belong to 15 families. Following E. necator inoculation, 119 miRNAs were down-regulated and 131 were up-regulated. Furthermore, the expression changes occurring in 32 miRNAs were significant. The expression patterns of some miRNAs were validated by semi-quantitative RT-PCR and qRT-PCR. A total of 485 target genes were predicted and categorized by Gene Ontology (GO). In addition, 14 vvi-miRNAs were screened with 36 targets which may be involved in powdery mildew resistance in grape. Highly accumulated vvi-NewmiR2118 was detected from accession "Baihe-35-1," whose targets were mostly NBS-LRR resistance genes. It was down-regulated rapidly and strongly in "Baihe-35-1" leaves after inoculated with E. necator, indicating its involvement in grape powdery mildew resistance. Finally, the study verified interaction between vvi-NewmiR2118 and RPP13 by histochemical staining and GUS fluorescence quantitative assay.
Collapse
Affiliation(s)
- Lijuan Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, China
- College of Horticulture, Northwest A&F UniversityYangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A& F UniversityYangling, China
| | - Kai Weng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, China
- College of Horticulture, Northwest A&F UniversityYangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A& F UniversityYangling, China
| | - Hui Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, China
- College of Horticulture, Northwest A&F UniversityYangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A& F UniversityYangling, China
| | - Gaoqing Xiang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, China
- College of Horticulture, Northwest A&F UniversityYangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A& F UniversityYangling, China
| | - Zhiqian Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, China
- College of Horticulture, Northwest A&F UniversityYangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A& F UniversityYangling, China
| | - Yuejin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, China
- College of Horticulture, Northwest A&F UniversityYangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A& F UniversityYangling, China
| | - Guotian Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, China
- College of Horticulture, Northwest A&F UniversityYangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A& F UniversityYangling, China
| | - Yan Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, China
- College of Horticulture, Northwest A&F UniversityYangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A& F UniversityYangling, China
- *Correspondence: Yan Xu
| |
Collapse
|
25
|
Paim Pinto DL, Brancadoro L, Dal Santo S, De Lorenzis G, Pezzotti M, Meyers BC, Pè ME, Mica E. The Influence of Genotype and Environment on Small RNA Profiles in Grapevine Berry. FRONTIERS IN PLANT SCIENCE 2016; 7:1459. [PMID: 27761135 PMCID: PMC5050227 DOI: 10.3389/fpls.2016.01459] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 09/13/2016] [Indexed: 05/21/2023]
Abstract
Understanding the molecular mechanisms involved in the interaction between the genetic composition and the environment is crucial for modern viticulture. We approached this issue by focusing on the small RNA transcriptome in grapevine berries of the two varieties Cabernet Sauvignon and Sangiovese, growing in adjacent vineyards in three different environments. Four different developmental stages were studied and a total of 48 libraries of small RNAs were produced and sequenced. Using a proximity-based pipeline, we determined the general landscape of small RNAs accumulation in grapevine berries. We also investigated the presence of known and novel miRNAs and analyzed their accumulation profile. The results showed that the distribution of small RNA-producing loci is variable between the two cultivars, and that the level of variation depends on the vineyard. Differently, the profile of miRNA accumulation mainly depends on the developmental stage. The vineyard in Riccione maximizes the differences between the varieties, promoting the production of more than 1000 specific small RNA loci and modulating their expression depending on the cultivar and the maturation stage. In total, 89 known vvi-miRNAs and 33 novel vvi-miRNA candidates were identified in our samples, many of them showing the accumulation profile modulated by at least one of the factors studied. The in silico prediction of miRNA targets suggests their involvement in berry development and in secondary metabolites accumulation such as anthocyanins and polyphenols.
Collapse
Affiliation(s)
| | - Lucio Brancadoro
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy, University of MilanMilan, Italy
| | - Silvia Dal Santo
- Laboratory of Plant Genetics, Department of Biotechnology, University of VeronaVerona, Italy
| | - Gabriella De Lorenzis
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy, University of MilanMilan, Italy
| | - Mario Pezzotti
- Laboratory of Plant Genetics, Department of Biotechnology, University of VeronaVerona, Italy
| | - Blake C. Meyers
- Donald Danforth Plant Science CenterSt. Louis, MO, USA
- Division of Plant Sciences, University of Missouri–ColumbiaColumbia, MO, USA
| | - Mario E. Pè
- Institute of Life Sciences, Sant'Anna School of Advanced StudiesPisa, Italy
| | - Erica Mica
- Institute of Life Sciences, Sant'Anna School of Advanced StudiesPisa, Italy
- Genomics Research Centre, Agricultural Research CouncilFiorenzuola d'Arda, Italy
- *Correspondence: Erica Mica
| |
Collapse
|
26
|
Jo Y, Choi H, Kyong Cho J, Yoon JY, Choi SK, Kyong Cho W. In silico approach to reveal viral populations in grapevine cultivar Tannat using transcriptome data. Sci Rep 2015; 5:15841. [PMID: 26508692 PMCID: PMC4623741 DOI: 10.1038/srep15841] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/01/2015] [Indexed: 11/09/2022] Open
Abstract
Viruses are ubiquitous and present in a wide range of settings, from living organisms to various environments. Although viruses are regarded as important pathogens in higher plants, viral populations in specific host plants have not yet been fully examined. This study revealed viral populations in grape berries obtained from a cultivar from a single vineyard using currently available grapevine transcriptomes. Eight viruses and two viroids were identified using 11 grapevine libraries. Virus-associated sequences in each transcriptome ranged from 0.2% (seed) to 8.8% (skin). The amount of viral RNAs and virus copy numbers was quantified, thus revealing the dominant virus or viroid in each individual library. In addition, five viral genomes were successfully assembled de novo using transcriptome data. Phylogenetic analyses revealed that the viruses and viroids might have originated from Europe, along with the host. Single nucleotide variation studies revealed the quasispecies of RNA viruses. Taken together, this study defines complex viral populations in three different grape tissues from a single vineyard.
Collapse
Affiliation(s)
- Yeonhwa Jo
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Hoseong Choi
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Jin Kyong Cho
- Department of Fruit Tree, Korea National College of Agriculture and Fisheries, Jeonju, 560-500, Republic of Korea
| | - Ju-Yeon Yoon
- Virology Unit, Department of Horticultural Environment, National Institute of Horticultural and Herbal Science, RDA, Wan-Ju, 565-852, Republic of Korea
| | - Seung-Kook Choi
- Virology Unit, Department of Horticultural Environment, National Institute of Horticultural and Herbal Science, RDA, Wan-Ju, 565-852, Republic of Korea
| | - Won Kyong Cho
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| |
Collapse
|
27
|
Belli Kullan J, Lopes Paim Pinto D, Bertolini E, Fasoli M, Zenoni S, Tornielli GB, Pezzotti M, Meyers BC, Farina L, Pè ME, Mica E. miRVine: a microRNA expression atlas of grapevine based on small RNA sequencing. BMC Genomics 2015; 16:393. [PMID: 25981679 PMCID: PMC4434875 DOI: 10.1186/s12864-015-1610-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 05/01/2015] [Indexed: 11/10/2022] Open
Abstract
Background miRNAs are the most abundant class of small non-coding RNAs, and they are involved in post-transcriptional regulations, playing a crucial role in the refinement of genetic programming during plant development. Here we present a comprehensive picture of miRNA regulation in Vitis vinifera L. plant during its complete life cycle. Furthering our knowledge about the post-transcriptional regulation of plant development is fundamental to understand the biology of such an important crop. Results We analyzed 70 small RNA libraries, prepared from berries, inflorescences, tendrils, buds, carpels, stamens and other samples at different developmental stages. One-hundred and ten known and 175 novel miRNAs have been identified and a wide grapevine expression atlas has been described. The distribution of miRNA abundance reveals that 22 novel miRNAs are specific to stamen, and two of them are, interestingly, involved in ethylene biosynthesis, while only few miRNAs are highly specific to other organs. Thirty-eight miRNAs are present in all our samples, suggesting a role in key regulatory circuit. On the basis of miRNAs abundance and distribution across samples and on the estimated correlation, we suggest that miRNA expression define organ identity. We performed target prediction analysis and focused on miRNA expression analysis in berries and inflorescence during their development, providing an initial functional description of the identified miRNAs. Conclusions Our findings represent a very extensive miRNA expression atlas in grapevine, allowing the definition of how the spatio-temporal distribution of miRNAs defines organ identity. We describe miRNAs abundance in specific tissues not previously described in grapevine and contribute to future targeted functional analyses. Finally, we present a deep characterization of miRNA involvement in berry and inflorescence development, suggesting a role for miRNA-driven hormonal regulation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1610-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jayakumar Belli Kullan
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.
| | - Daniela Lopes Paim Pinto
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.
| | - Edoardo Bertolini
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.
| | - Marianna Fasoli
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
| | - Sara Zenoni
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
| | | | - Mario Pezzotti
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
| | - Blake C Meyers
- Department of Plant and Soil Sciences, University of Delaware, 15 Innovation Way, 19711, Newark, DE, USA.
| | - Lorenzo Farina
- Department of Computer, Control and Management Engineering, University of Rome "La Sapienza", Via Ariosto 25, 00185, Rome, Italy.
| | - Mario Enrico Pè
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.
| | - Erica Mica
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy. .,Genomics Research Centre, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Via S. Protaso 302, 29017, Fiorenzuola d'Arda (PC), Italy.
| |
Collapse
|
28
|
Maliogka VI, Olmos A, Pappi PG, Lotos L, Efthimiou K, Grammatikaki G, Candresse T, Katis NI, Avgelis AD. A novel grapevine badnavirus is associated with the Roditis leaf discoloration disease. Virus Res 2015; 203:47-55. [PMID: 25791736 DOI: 10.1016/j.virusres.2015.03.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 03/04/2015] [Accepted: 03/08/2015] [Indexed: 01/15/2023]
Abstract
Roditis leaf discoloration (RLD), a graft-transmissible disease of grapevine, was first reported in Greece in the 1980s. Even though various native grapevine viruses were identified in the affected vines, the etiology of the disease remained unknown. In the present study, we used an NGS platform for sequencing siRNAs from a twenty-year old Roditis vine showing typical RLD symptoms. Analysis of the NGS data revealed the presence of various known grapevine viruses and viroids as well as a hitherto uncharacterized DNA virus. The circular genome of the new virus was fully reassembled. It is 6988 nts long and includes 4 open reading frames (ORFs). ORF1, ORF2 and ORF4 code for proteins with unknown functions while ORF3 encodes a polyprotein with motifs related to the replication, encapsidation and movement of the virus. Phylogenetic analysis classified the novel virus within the genus Badnavirus, with closest relationship to Fig badnavirus 1. Further studies showed that the new badnavirus is closely related with the RLD disease and the provisional name grapevine Roditis leaf discoloration-associated virus (GRLDaV) is proposed. Our findings extend the number of DNA viruses identified in grapevine, further drawing attention to the potential importance of this virus group on grapevine pathology.
Collapse
Affiliation(s)
- Varvara I Maliogka
- Lab of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, 54124 Thessaloniki, Greece.
| | - Antonio Olmos
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Plant Protection and Biotechnology Center, 46113 Moncada, Valencia, Spain
| | - Polyxeni G Pappi
- Lab of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, 54124 Thessaloniki, Greece
| | - Leonidas Lotos
- Lab of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, 54124 Thessaloniki, Greece
| | - Konstantinos Efthimiou
- Lab of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, 54124 Thessaloniki, Greece
| | - Garyfalia Grammatikaki
- Faculty of Agriculture & Food Technology, Technological Education Institute of Crete, 71 004 Heraklion, Crete, Greece
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, CS20032, F-33882 Villenave d'Ornon cedex, France; UMR 1332 Biologie du Fruit et Pathologie, Université de Bordeaux, CS20032, F-33882 Villenave d'Ornon cedex, France
| | - Nikolaos I Katis
- Lab of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, 54124 Thessaloniki, Greece
| | - Apostolos D Avgelis
- Institute of Viticulture of Heraklion, Hellenic Agricultural Organization-Demeter, 71 307 Heraklion, Crete, Greece
| |
Collapse
|
29
|
Abstract
Next-generation sequencing (NGS) technologies, for the first time, provide a truly "complete" representation of the viral (and other) pathogens present in a host organism. This is achieved in an unbiased way, and without any prior biological or molecular knowledge of these pathogen(s). During recent years a number of broad approaches, for most of the popular NGS platforms, have been developed. Here we describe such a protocol-one that accurately and reliably analyze viruses (and viroids) infecting grapevine. Our strategy relies on the synthesis of cDNA sequencing libraries from dsRNA, extracted from diseased grapevine tissues; the sequencing of these on an Illumina platform, and a streamlined bioinformatics pipeline to analyze the NGS data, yielding the virus composition (virome) of a specific grapevine tissue type, organ, entire plant, or even a vineyard.
Collapse
Affiliation(s)
- Johan T Burger
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa,
| | | |
Collapse
|
30
|
Naidu RA, Maree HJ, Burger JT. Grapevine leafroll disease and associated viruses: a unique pathosystem. ANNUAL REVIEW OF PHYTOPATHOLOGY 2015; 53:613-34. [PMID: 26243729 DOI: 10.1146/annurev-phyto-102313-045946] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Grapevine leafroll is the most complex and intriguing viral disease of grapevine (Vitis spp.). Several monopartite closteroviruses (family Closteroviridae) from grapevines have been molecularly characterized, yet their role in disease etiology is not completely resolved. Hence, these viruses are currently designated under the umbrella term of Grapevine leafroll-associated viruses (GLRaVs). This review examines our current understanding of the genetically divergent GLRaVs and highlights the emerging picture of several unique aspects of the leafroll disease pathosystem. A systems biology approach using contemporary technologies in molecular biology, -omics, and cell biology aids in exploring the comparative molecular biology of GLRaVs and deciphering the complex network of host-virus-vector interactions to bridge the gap between genomics and phenomics of leafroll disease. In addition, grapevine-infecting closteroviruses have a great potential as designer viruses to pursue functional genomics and for the rational design of novel disease intervention strategies in this agriculturally important perennial fruit crop.
Collapse
Affiliation(s)
- Rayapati A Naidu
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, Washington 99350;
| | | | | |
Collapse
|
31
|
Stewart LR, Teplier R, Todd JC, Jones MW, Cassone BJ, Wijeratne S, Wijeratne A, Redinbaugh MG. Viruses in maize and Johnsongrass in southern Ohio. PHYTOPATHOLOGY 2014; 104:1360-9. [PMID: 24918609 DOI: 10.1094/phyto-08-13-0221-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The two major U.S. maize viruses, Maize dwarf mosaic virus (MDMV) and Maize chlorotic dwarf virus (MCDV), emerged in southern Ohio and surrounding regions in the 1960s and caused significant losses. Planting resistant varieties and changing cultural practices has dramatically reduced virus impact in subsequent decades. Current information on the distribution, diversity, and impact of known and potential U.S. maize disease-causing viruses is lacking. To assess the current reservoir of viruses present at the sites of past disease emergence, we used a combination of serological testing and next-generation RNA sequencing approaches. Here, we report enzyme-linked immunosorbent assay and RNA-Seq data from samples collected over 2 years to assess the presence of viruses in cultivated maize and an important weedy reservoir, Johnsongrass (Sorghum halepense). Results revealed a persistent reservoir of MDMV and two strains of MCDV in Ohio Johnsongrass. We identified sequences of several other grass-infecting viruses and confirmed the presence of Wheat mosaic virus in Ohio maize. Together, these results provide important data for managing virus disease in field corn and sweet corn maize crops, and identifying potential future virus threats.
Collapse
|
32
|
Montes C, Castro Á, Barba P, Rubio J, Sánchez E, Carvajal D, Aguirre C, Tapia E, DelÍ Orto P, Decroocq V, Prieto H. Differential RNAi responses of Nicotiana benthamiana individuals transformed with a hairpin-inducing construct during Plum pox virus challenge. Virus Genes 2014; 49:325-38. [PMID: 24964777 DOI: 10.1007/s11262-014-1093-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 05/30/2014] [Indexed: 10/25/2022]
Abstract
Gene silencing and large-scale small RNA analysis can be used to develop RNA interference (RNAi)-based resistance strategies for Plum pox virus (PPV), a high impact disease of Prunus spp. In this study, a pPPViRNA hairpin-inducing vector harboring two silencing motif-rich regions of the PPV coat protein (CP) gene was evaluated in transgenic Nicotiana benthamiana (NB) plants. Wild-type NB plants infected with a chimeric PPV virus (PPV::GFP) exhibited affected leaves with mosaic chlorosis congruent to GFP fluorescence at 21 day post-inoculation; transgenic lines depicted a range of phenotypes from fully resistant to susceptible. ELISA values and GFP fluorescence intensities were used to select transgenic-resistant (TG-R) and transgenic-susceptible (TG-S) lines for further characterization of small interfering RNAs (siRNAs) by large-scale small RNA sequencing. In infected TG-S and untransformed (WT) plants, the observed siRNAs were nearly exclusively 21- and 22-nt siRNAs that targeted the whole PPV::GFP genome; 24-nt siRNAs were absent in these individuals. Challenged TG-R plants accumulated a full set of 21- to 24-nt siRNAs that were primarily associated with the selected motif-rich regions, indicating that a trans-acting siRNAs process prevented viral multiplication. BLAST analysis identified 13 common siRNA clusters targeting the CP gene. 21-nt siRNA sequences were associated with the 22-nt siRNAs and the scarce 23- and 24-nt molecules in TG-S plants and with most of the observed 22-, 23-, and 24-nt siRNAs in TG-R individuals. These results validate the use of a multi-hot spot silencing vector against PPV and elucidate the molecules by which hairpin-inducing vectors initiate RNAi in vivo.
Collapse
Affiliation(s)
- Christian Montes
- Biotechnology Laboratory, Instituto de Investigaciones Agropecuarias, La Platina Research Station, Avenida Santa Rosa 11610, La Pintana, 8831314, Santiago, Chile
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Solofoharivelo MC, van der Walt AP, Stephan D, Burger JT, Murray SL. MicroRNAs in fruit trees: discovery, diversity and future research directions. PLANT BIOLOGY (STUTTGART, GERMANY) 2014; 16:856-65. [PMID: 24750383 DOI: 10.1111/plb.12153] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 12/14/2013] [Indexed: 05/04/2023]
Abstract
Since the first description of microRNAs (miRNAs) 20 years ago, the number of miRNAs identified in different eukaryotic organisms has exploded, largely due to the recent advances in DNA sequencing technologies. Functional studies, mostly from model species, have revealed that miRNAs are major post-transcriptional regulators of gene expression in eukaryotes. In plants, they are implicated in fundamental biological processes, from plant development and morphogenesis, to regulation of plant pathogen and abiotic stress responses. Although a substantial number of miRNAs have been identified in fruit trees to date, their functions remain largely uncharacterised. The present review aims to summarise the progress made in miRNA research in fruit trees, focusing specifically on the economically important species Prunus persica, Malus domestica, Citrus spp, and Vitis vinifera. We also discuss future miRNA research prospects in these plants and highlight potential applications of miRNAs in the on-going improvement of fruit trees.
Collapse
Affiliation(s)
- M C Solofoharivelo
- Vitis Lab, Department of Genetics, Stellenbosch University, Matieland, South Africa
| | | | | | | | | |
Collapse
|
34
|
What has been happening with viroids? Virus Genes 2014; 49:175-84. [DOI: 10.1007/s11262-014-1110-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 08/18/2014] [Indexed: 12/18/2022]
|
35
|
Massart S, Olmos A, Jijakli H, Candresse T. Current impact and future directions of high throughput sequencing in plant virus diagnostics. Virus Res 2014; 188:90-6. [PMID: 24717426 DOI: 10.1016/j.virusres.2014.03.029] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 03/27/2014] [Accepted: 03/28/2014] [Indexed: 12/17/2022]
Abstract
The ability to provide a fast, inexpensive and reliable diagnostic for any given viral infection is a key parameter in efforts to fight and control these ubiquitous pathogens. The recent developments of high-throughput sequencing (also called Next Generation Sequencing - NGS) technologies and bioinformatics have drastically changed the research on viral pathogens. It is now raising a growing interest for virus diagnostics. This review provides a snapshot vision on the current use and impact of high throughput sequencing approaches in plant virus characterization. More specifically, this review highlights the potential of these new technologies and their interplay with current protocols in the future of molecular diagnostic of plant viruses. The current limitations that will need to be addressed for a wider adoption of high-throughput sequencing in plant virus diagnostics are thoroughly discussed.
Collapse
Affiliation(s)
- Sebastien Massart
- Laboratory of Phytopathology, University of Liège, Gembloux Agro-BioTech, Passage des déportés, 2, 5030 Gembloux, Belgium.
| | - Antonio Olmos
- Centro de Protección Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Apartado Oficial, 46113 Moncada, Valencia, Spain
| | - Haissam Jijakli
- Laboratory of Phytopathology, University of Liège, Gembloux Agro-BioTech, Passage des déportés, 2, 5030 Gembloux, Belgium
| | - Thierry Candresse
- UMR 1332 de Biologie du fruit et Pathologie, INRA, CS20032, 33882 Villenave d'Ornon cedex, France; UMR 1332 de Biologie du fruit et Pathologie, Université de Bordeaux, CS20032, 33882 Villenave d'Ornon cedex, France
| |
Collapse
|
36
|
Identification and characterization of a viroid resembling apple dimple fruit viroid in fig (Ficus carica L.) by next generation sequencing of small RNAs. Virus Res 2014; 188:54-9. [PMID: 24704673 DOI: 10.1016/j.virusres.2014.03.026] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/20/2014] [Accepted: 03/24/2014] [Indexed: 01/16/2023]
Abstract
Viroids are small (246-401 nt) circular and non coding RNAs infecting higher plants. They are targeted by host Dicer-like enzymes (DCLs) that generate small RNAs of 21-24 nt (sRNAs), which are involved in the host RNA silencing pathways. The accumulation in plant tissues of such viroid-derived small RNAs (vd-sRNAs) is a clear sign of an ongoing viroid infection. In this study, next generation sequencing of a sRNAs library and assembling of the sequenced vd-sRNAs were instrumental for the identification of a viroid resembling apple dimple fruit viroid (ADFVd) in a fig accession. After confirming by molecular methods the presence of this viroid in the fig tree, its population was characterized, showing that the ADFVd master sequence from fig diverges from that of the ADFVd reference variant from apple. Moreover, since this viroid accumulates at a low level in fig, a semi-nested RT-PCR assay was developed for detecting it in other fig accessions. ADFVd seems to have a wider host range than thought before and this poses questions about its epidemiology. A further characterization of ADFVd-sRNAs showed similar accumulation of (+) or (-) vd-sRNAs that mapped on the viroid genome generating hotspot profiles. Moreover, similarly to other nuclear-replicating viroids, vd-sRNAs of 21, 22 and 24 nt in size prevailed in the distribution profiles. Altogether, these data support the involvement of double-stranded RNAs and different DCLs, targeting the same restricted viroid regions, in the genesis of ADFVd-sRNAs.
Collapse
|
37
|
Velasco L, Bota J, Montero R, Cretazzo E. Differences of Three Ampeloviruses' Multiplication in Plant May Explain Their Incidences in Vineyards. PLANT DISEASE 2014; 98:395-400. [PMID: 30708447 DOI: 10.1094/pdis-04-13-0433-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Grapevine leafroll ampeloviruses have been recently grouped into two major clades, one for Grapevine leafroll associated virus (GLRaV) 1 and 3 and another one grouping GLRaV-4 and its variants. In order to understand biological factors mediating differential ampelovirus incidences in vineyards, quantitative real-time polymerase chain reactions were performed to assess virus populations in three grapevine varieties in which different infection status were detected: GLRaV-3 + GLRaV-4, GLRaV-3 + GLRaV-4 strain 5, and GLRaV-4 alone. Specific primers based on the RNA-dependent RNA polymerase (RdRp) domains of GLRaV-3, GLRaV-4, and GLRaV-4 strain 5 were used. Absolute and relative quantitations of the three viruses were achieved by normalization of data to the concentration of the endogenous gene actin. In spring, the populations of GLRaV-4 and GLRaV-4 strain 5 were 1.7 × 104 to 5.0 × 105 genomic RNA copies/mg of petiole tissue whereas, for GLRaV-3, values were significantly higher, ranging from 5.6 × 105 and 1.0 × 107 copies mg-1. In autumn, GLRaV-4 and GLRaV-4 strain 5 populations increased significantly, displaying values for genome copies between 4.1 × 105 and 6.3 × 106 copies mg-1, whereas GLRaV-3 populations displayed a less pronounced boost but were still significantly higher, ranging from 4.1 × 106 to 1.6 × 107 copies mg-1. To investigate whether additional viruses may interfere in the quantifications the small RNA populations, vines were analyzed by Ion Torrent high-throughput sequencing. It allowed the identification of additional viruses and viroids, including Grapevine virus A, Hop stunt viroid, Grapevine yellow speckle viroid 1, and Australian grapevine viroid. The significance of these findings is discussed.
Collapse
Affiliation(s)
- Leonardo Velasco
- Instituto Andaluz de Investigación y Formación Agraria, Pesquera, Alimentaria y de la Producción Ecológica (IFAPA), 29140 Churriana, Málaga, Spain
| | - Josefina Bota
- Institut de Recerca i Formació Agrària i Pesquera de les Illes Balears, 07009 Palma de Mallorca, Spain
| | - Rafael Montero
- Institut de Recerca i Formació Agrària i Pesquera de les Illes Balears, 07009 Palma de Mallorca, Spain
| | | |
Collapse
|
38
|
Morante-Carriel J, Sellés-Marchart S, Martínez-Márquez A, Martínez-Esteso MJ, Luque I, Bru-Martínez R. RNA isolation from loquat and other recalcitrant woody plants with high quality and yield. Anal Biochem 2014; 452:46-53. [PMID: 24556246 DOI: 10.1016/j.ab.2014.02.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 02/06/2014] [Accepted: 02/07/2014] [Indexed: 11/17/2022]
Abstract
RNA isolation is difficult in plants that contain large amounts of polysaccharides and polyphenol compounds. To date, no commercial kit has been developed for the isolation of high-quality RNA from tissues with these characteristics, especially for fruit. The common protocols for RNA isolation are tedious and usually result in poor yields when applied to recalcitrant plant tissues. Here an efficient RNA isolation protocol based on cetyltrimethylammonium bromide (CTAB) and two successive precipitations with 10 M lithium chloride (LiCl) was developed specifically for loquat fruits, but it was proved to work efficiently in other tissues of loquat and woody plants. The RNA isolated by this improved protocol was not only of high purity and integrity (A260/A280 ratios ranged from 1.90 to 2.04 and A260/A230 ratios were>2.0) but also of high yield (up to 720 μg on average [coefficient of variation=21%] total RNA per gram fresh tissue). The protocol was tested on loquat fruit (different stages of development, postharvest, ripening, and bruising), leaf, root, flower, stem, and bud; quince fruit and root; grapevine cells in liquid culture; and rose petals. The RNA obtained with this method is amenable to enzymatic treatments and can be efficiently applied for research on gene characterization, expression, and function.
Collapse
Affiliation(s)
- Jaime Morante-Carriel
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Faculty of Science, University of Alicante, 03690 San Vicente del Raspeig, Alicante, Spain; Biotechnology and Molecular Biology Group, Quevedo State Technical University, EC-120501 Quevedo, Ecuador
| | - Susana Sellés-Marchart
- Research Technical Facility, Proteomics and Genomics Division, University of Alicante, 03690 San Vicente del Raspeig, Alicante, Spain
| | - Ascensión Martínez-Márquez
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Faculty of Science, University of Alicante, 03690 San Vicente del Raspeig, Alicante, Spain
| | - María José Martínez-Esteso
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Faculty of Science, University of Alicante, 03690 San Vicente del Raspeig, Alicante, Spain
| | - Ignacio Luque
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, 41092 Seville, Spain
| | - Roque Bru-Martínez
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Faculty of Science, University of Alicante, 03690 San Vicente del Raspeig, Alicante, Spain.
| |
Collapse
|
39
|
Barba M, Czosnek H, Hadidi A. Historical perspective, development and applications of next-generation sequencing in plant virology. Viruses 2014; 6:106-36. [PMID: 24399207 PMCID: PMC3917434 DOI: 10.3390/v6010106] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 12/17/2013] [Accepted: 12/24/2013] [Indexed: 12/27/2022] Open
Abstract
Next-generation high throughput sequencing technologies became available at the onset of the 21st century. They provide a highly efficient, rapid, and low cost DNA sequencing platform beyond the reach of the standard and traditional DNA sequencing technologies developed in the late 1970s. They are continually improved to become faster, more efficient and cheaper. They have been used in many fields of biology since 2004. In 2009, next-generation sequencing (NGS) technologies began to be applied to several areas of plant virology including virus/viroid genome sequencing, discovery and detection, ecology and epidemiology, replication and transcription. Identification and characterization of known and unknown viruses and/or viroids in infected plants are currently among the most successful applications of these technologies. It is expected that NGS will play very significant roles in many research and non-research areas of plant virology.
Collapse
Affiliation(s)
- Marina Barba
- Consiglio per la ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per la Patologia Vegetale, Via C. G. Bertero 22, Rome 00156, Italy.
| | - Henryk Czosnek
- Consiglio per la ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per la Patologia Vegetale, Via C. G. Bertero 22, Rome 00156, Italy.
| | - Ahmed Hadidi
- Consiglio per la ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per la Patologia Vegetale, Via C. G. Bertero 22, Rome 00156, Italy.
| |
Collapse
|
40
|
Rock CD. Trans-acting small interfering RNA4: key to nutraceutical synthesis in grape development? TRENDS IN PLANT SCIENCE 2013; 18:601-10. [PMID: 23993483 PMCID: PMC3818397 DOI: 10.1016/j.tplants.2013.07.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 07/12/2013] [Accepted: 07/31/2013] [Indexed: 05/19/2023]
Abstract
The facility and versatility of microRNAs (miRNAs) to evolve and change likely underlies how they have become dominant constituents of eukaryotic genomes. In this opinion article I propose that trans-acting small interfering RNA gene 4 (TAS4) evolution may be important for biosynthesis of polyphenolics, arbuscular symbiosis, and bacterial pathogen etiologies. Expression-based and phylogenetic evidence shows that TAS4 targets two novel grape (Vitis vinifera L.) MYB transcription factors (VvMYBA6, VvMYBA7) that spawn phased small interfering RNAs (siRNAs) which probably function in nutraceutical bioflavonoid biosynthesis and fruit development. Characterization of the molecular mechanisms of TAS4 control of plant development and integration into biotic and abiotic stress- and nutrient-signaling regulatory networks has applicability to molecular breeding and the development of strategies for engineering healthier foods.
Collapse
Affiliation(s)
- Christopher D Rock
- Department of Biological Sciences, Texas Tech University (TTU), Lubbock, TX 79409-3131, USA.
| |
Collapse
|
41
|
Poojari S, Alabi OJ, Fofanov VY, Naidu RA. A leafhopper-transmissible DNA virus with novel evolutionary lineage in the family geminiviridae implicated in grapevine redleaf disease by next-generation sequencing. PLoS One 2013; 8:e64194. [PMID: 23755117 PMCID: PMC3673993 DOI: 10.1371/journal.pone.0064194] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 04/10/2013] [Indexed: 01/25/2023] Open
Abstract
A graft-transmissible disease displaying red veins, red blotches and total reddening of leaves in red-berried wine grape (Vitis vinifera L.) cultivars was observed in commercial vineyards. Next-generation sequencing technology was used to identify etiological agent(s) associated with this emerging disease, designated as grapevine redleaf disease (GRD). High quality RNA extracted from leaves of grape cultivars Merlot and Cabernet Franc with and without GRD symptoms was used to prepare cDNA libraries. Assembly of highly informative sequence reads generated from Illumina sequencing of cDNA libraries, followed by bioinformatic analyses of sequence contigs resulted in specific identification of taxonomically disparate viruses and viroids in samples with and without GRD symptoms. A single-stranded DNA virus, tentatively named Grapevine redleaf-associated virus (GRLaV), and Grapevine fanleaf virus were detected only in grapevines showing GRD symptoms. In contrast, Grapevine rupestris stem pitting-associated virus, Hop stunt viroid, Grapevine yellow speckle viroid 1, Citrus exocortis viroid and Citrus exocortis Yucatan viroid were present in both symptomatic and non-symptomatic grapevines. GRLaV was transmitted by the Virginia creeper leafhopper (Erythroneura ziczac Walsh) from grapevine-to-grapevine under greenhouse conditions. Molecular and phylogenetic analyses indicated that GRLaV, almost identical to recently reported Grapevine Cabernet Franc-associated virus from New York and Grapevine red blotch-associated virus from California, represents an evolutionarily distinct lineage in the family Geminiviridae with genome characteristics distinct from other leafhopper-transmitted geminiviruses. GRD significantly reduced fruit yield and affected berry quality parameters demonstrating negative impacts of the disease. Higher quantities of carbohydrates were present in symptomatic leaves suggesting their possible role in the expression of redleaf symptoms.
Collapse
Affiliation(s)
- Sudarsana Poojari
- Department of Plant Pathology, Washington State University, Irrigated Agriculture Research and Extension Center, Prosser, Washington, United States of America
| | | | | | | |
Collapse
|
42
|
Maree HJ, Almeida RPP, Bester R, Chooi KM, Cohen D, Dolja VV, Fuchs MF, Golino DA, Jooste AEC, Martelli GP, Naidu RA, Rowhani A, Saldarelli P, Burger JT. Grapevine leafroll-associated virus 3. Front Microbiol 2013; 4:82. [PMID: 23596440 PMCID: PMC3627144 DOI: 10.3389/fmicb.2013.00082] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 03/22/2013] [Indexed: 11/17/2022] Open
Abstract
Grapevine leafroll disease (GLD) is one of the most important grapevine viral diseases affecting grapevines worldwide. The impact on vine health, crop yield, and quality is difficult to assess due to a high number of variables, but significant economic losses are consistently reported over the lifespan of a vineyard if intervention strategies are not implemented. Several viruses from the family Closteroviridae are associated with GLD. However, Grapevine leafroll-associated virus 3 (GLRaV-3), the type species for the genus Ampelovirus, is regarded as the most important causative agent. Here we provide a general overview on various aspects of GLRaV-3, with an emphasis on the latest advances in the characterization of the genome. The full genome of several isolates have recently been sequenced and annotated, revealing the existence of several genetic variants. The classification of these variants, based on their genome sequence, will be discussed and a guideline is presented to facilitate future comparative studies. The characterization of sgRNAs produced during the infection cycle of GLRaV-3 has given some insight into the replication strategy and the putative functionality of the ORFs. The latest nucleotide sequence based molecular diagnostic techniques were shown to be more sensitive than conventional serological assays and although ELISA is not as sensitive it remains valuable for high-throughput screening and complementary to molecular diagnostics. The application of next-generation sequencing is proving to be a valuable tool to study the complexity of viral infection as well as plant pathogen interaction. Next-generation sequencing data can provide information regarding disease complexes, variants of viral species, and abundance of particular viruses. This information can be used to develop more accurate diagnostic assays. Reliable virus screening in support of robust grapevine certification programs remains the cornerstone of GLD management.
Collapse
Affiliation(s)
- Hans J. Maree
- Department of Genetics, Stellenbosch UniversityStellenbosch, South Africa
- Biotechnology Platform, Agricultural Research CouncilStellenbosch, South Africa
| | - Rodrigo P. P. Almeida
- Department of Environmental Science, Policy and Management, University of CaliforniaBerkeley, CA, USA
| | - Rachelle Bester
- Department of Genetics, Stellenbosch UniversityStellenbosch, South Africa
| | - Kar Mun Chooi
- School of Biological Sciences, University of AucklandAuckland, New Zealand
| | - Daniel Cohen
- The New Zealand Institute for Plant and Food ResearchAuckland, New Zealand
| | - Valerian V. Dolja
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA
| | - Marc F. Fuchs
- Department of Plant Pathology and Plant-Microbe Biology, Cornell UniversityGeneva, NY, USA
| | - Deborah A. Golino
- Department of Plant Pathology, University of CaliforniaDavis, CA, USA
| | - Anna E. C. Jooste
- Plant Protection Research Institute, Agricultural Research CouncilPretoria, South Africa
| | - Giovanni P. Martelli
- Department of Soil, Plant and Food Sciences, University Aldo Moro of BariBari, Italy
| | - Rayapati A. Naidu
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State UniversityProsser, WA, USA
| | - Adib Rowhani
- Department of Plant Pathology, University of CaliforniaDavis, CA, USA
| | | | - Johan T. Burger
- Department of Genetics, Stellenbosch UniversityStellenbosch, South Africa
| |
Collapse
|