Recent Advances on Detection and Characterization of Fruit Tree Viruses Using High-Throughput Sequencing Technologies
Abstract
:1. Introduction
2. Principles and Technologies of High-Througput Sequencing
3. High-Throughput Sequencing Methodology Applied to the Detection of Fruit Tree Viruses
3.1. Sample Preparation
3.2. Bioinformatics
4. Application of High-Throughput Sequencing Technology to Detection and Discovery of Fruit Tree Viruses
4.1. Identification of New Viruses in Fruit Tree Species with the Aid of High-Throughput Sequencing
4.2. Application of High-Throughput Sequencing to Detection and Virus Genetic Variability Studies
5. Advantages and Disadvantages of High-Throughput Sequencing Compared to Classical Diagnostic Approaches
6. Future Directions of High-Throughput Sequencing in Fruit Tree Virology
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Platform | Maximum Read Length (bp) | Sequencing Output | Maximum Number of Reads per Run | Run Time | |
---|---|---|---|---|---|
PCR based HTS | |||||
Illumina | iSeq 100 System | 2 × 150 | 1.2 Gb | 4 million | 9–17.5 h |
MiniSeq System | 2 × 150 | 7.5 Gb | 25 million | 4–24 h | |
MiSeq System | 2 × 300 | 15 Gb | 25 million | 4–55 h | |
NextSeq 550 System | 2 × 150 | 120 Gb | 400 million | 12–30 h | |
HiSeq 2500 System | 2 × 125/2 × 250 | 1000Gb/300 Gb | 4 billion/600 million | 29 h–6 days/7–60 h | |
HiSeq 3000 System | 2 × 150 | 750 Gb | 2.5 billion | <1–3.5 days | |
HiSeq 4000 System | 2 × 150 | 1500 Gb | 5 billion | <1–3.5 days | |
HiSeq X Series | 2 × 150 | 1800 Gb | 6 billion | <3 days | |
NovaSeq 6000 System | 2 × 150 | 6000 Gb | 20 billion | 16–44 h | |
Ion Torrent | PGM (314 chip) | 200/400 | 50/100 Mb | 550 thousand | 2.3/3.7 hr |
PGM (316 chip) | 200/400 | 300 Mb/1 Gb | 3 million | 3.0/4.9 hr | |
PGM (318 chip) | 200/400 | 1/2 Gb | 5.5 million | 4.4/7.3 h | |
Proton PI chip | 200 | 10 Gb | 80 million | 2–4 h | |
Ion Gene Studio S5 (510 chip) | 200/400 | 0.5/1 Gb | 3 million | 4.5/10.5 | |
Ion Gene Studio S5 (520 chip) | 200/400/600 | 1/2/1.5 Gb | 6/6/4 million | 7.5/12/12 h | |
Ion Gene Studio S5 (530 chip) | 200/400/600 | 4/8/4.5 Gb | 20/20/12 million | 10.5/21.5/21 h | |
Ion Gene Studio S5 (540 chip) | 200 | 15 Gb | 60 million | 19 h | |
Ion Gene Studio S5 Plus (550 chip) | 200 | 25 Gb | 100 million | 11.5 h | |
SMS NGS | |||||
Pacific Biosciences | Sequel System | >1000 | 1–10 Gb | 500.000 | 0.5–10 h |
PacBioRS II | >1000 (average 10.000) up to 60.000 | 1–10 Gb | 1–10 million | 0.5–6 h | |
Oxford Nanopore | MinION | 5000 to >100.000 | 10–20 Gb | - | 48 h |
GridIONx5 | 5000 to >100.000 | 50–100 Gb | - | 48 h | |
PromethION | 5000 to >100.000 | 1.2 Tb | - | 48 h |
Virus | Genus | Family | Host | Reference |
---|---|---|---|---|
Actinidia chlorotic ringspot-associated virus | Emaravirus | Fimoviridae | Actinidia | Zheng et al. [89] |
Actinidia seed-borne latent virus | Prunevirus | Betaflexiviridae | Veerakone et al. [90] | |
Apple-associated luteovirus | Luteovirus | Luteoviridae | apple | Shen et al. [84] |
Apple geminivirus | Geminivirus | Geminiviridae | Liang et al. [34] | |
Apple necrotic mosaic virus | Ilarvirus | Bromoviridae | Liang et al. [34] | |
Apple rubbery wood virus 1 | (?) | Phenuiviridae | Rott et al. [83] | |
Apple rubbery wood virus 2 | (?) | Phenuiviridae | Rott et al. [83] | |
Citrus concave gum-associated virus | Phlebovirus(?) | Phenuiviridae | Citrus | Navarro et al. [68] |
Citrus jingmen-like virus | Flavivirus | Flaviviridae | Matsumura et al. [69] | |
Citrus leprosis virus-N | Dichoravirus | Rhabdoviridae | Roy et al. [65] | |
Citrus leprosis virus-C2 | Cilevirus | Roy et al. [63] | ||
Citrus yellow vein clearing virus | Mandarivirus | Alphaflexiviridae | Loconsole et al. [61] | |
Citrus vein enation virus | Enamovirus | Luteoviridae | Vives et al. [62] | |
Citrus virga-like virus | Virgavirus | Virgaviridae | Matsumura et al. [69] | |
Citrus chlorotic dwarf-associated virus | Geminivirus | Geminiviridae | Loconsole et al. [52] | |
Cherry Rusty Mottle-associated virus | Robigovirus | Betaflexiviridae | cherry | Villamor et al. [75] |
Cherry Twisted Leaf-associated virus | Robigovirus | Betaflexiviridae | Villamor et al. [75] | |
Prunus virus F | Fabavirus | Secoviridae | Villamor et al. [49] | |
Cherry virus F | Fabavirus | Secoviridae | sweet cherry, sour cherry | Koloniuk et al. [40] |
Mulberry mosaic dwarf-associated virus | (?) | Geminiviridae | mulberry | Ma et al. [87] |
Mulberry badnavirus 1 | Badnavirus | Caulimoviridae | mulberry | Chiumenti et al. [35] |
Nectarine stem pitting-associated virus | Luteovirus | Luteoviridae | peach | Bag et al. [73] |
Nectarine virus M | Marafivirus | Tymoviridae | Villamor et al. [74] | |
Peach leaf pitting-associated virus | Fabavirus | Secoviridae | He et al. [38] | |
Peach virus D | Marafivirus | Tymoviridae | Igori et al. [77] | |
Persimmon cryptic virus | Deltapartitivirus | Partitiviridae | persimmon | Morelli et al. [86] |
Persimmon virus A | Cytorhabdovirus | Rhabdoviridae | Ito et al. [85] | |
Apricot vein clearing associated virus | Prunevirus | Betaflexiviridae | Prunus | Elbeaino et al. [44] |
Caucasus prunus virus | Prunevirus | Betaflexiviridae | Marais et al. [70] | |
Cherry-associated luteovirus | Luteovirus | Luteoviridae | Lenz et al. [48] | |
Mume virus A | Capillovirus | Betaflexiviridae | Marais et al. [71] | |
Prunus virus T | Tepovirus | Betaflexiviridae | Marais et al. [45] |
Virus | Genus | Family | Host | Aim of the research & New Findings | Reference |
---|---|---|---|---|---|
Apple stem grooving virus | Capillovirus | Betaflexiviridae | apple | Differential expression of siRNAs in symptomless infections | Visser et al. [33] |
Apple stem grooving virus | Capillovirus | Betaflexiviridae | Actinidia | First HTS-obtained ASGV genome in kiwi | Wang et al. [88] |
Asian prunus virus 1 | Foveavirus | Betaflexiviridae | Prunus | Genome reconstruction of Asian prunus viruses from 5 samples: phylogenetic and recombination implications | Marais et al. [46] |
Asian prunus virus 2 | Foveavirus | Betaflexiviridae | Marais et al. [46] | ||
Asian prunus virus 3 | Foveavirus | Betaflexiviridae | Marais et al. [46] | ||
cherry-associated luteovirus | Luteovirus | Luteoviridae | peach | Highly divergent isolate in a new host (peach) | Igori et al. [76] |
Cherry necrotic rusty mottle virus | Robigovirus | Betaflexiviridae | cherry | One CNRMV and three CGRMV isolates sequenced from a collection survey | Špak et al. [106] |
Cherry green ring mottle virus | Robigovirus | Betaflexiviridae | |||
Cherry virus A | Capillovirus | Betaflexiviridae | apricot | First complete sequence by HTS (apricot isolate); Description in apricot on propagation material | Koinuma et al. [104]; Barath et al. [41] |
Cherry virus A | Capillovirus | Betaflexiviridae | cherry | New isolate from China | Wang et al. [105] |
Cherry virus A | Capillovirus | Betaflexiviridae | Coinfection of two divergent variants in a wild cherry tree | Glasa et al. [9] | |
Cherry virus A | Capillovirus | Betaflexiviridae | HTS survey on 39 Prunus samples: 75 full genomes and phylogenetic implications | Kesanakurti et al. [50] | |
Cherry virus F | Fabavirus | Secoviridae | sweet cherry, sour cherry | Virome of 9 samples: co-infection of different viruses and co-existence of multiple fabavirus variants | Koloniuk et al. [40] |
Citrus sudden death virus | Marafivirus | Tymoviridae | Citrus | Virome analysis of CSD-affected plants: wide variability of genotypes and mixed infections with different viruses | Matsumura et al. [69] |
Citrus tristeza virus | Closterovirus | Closteroviridae | Genotyping 3 cross-protecting CTV strains in grapefruit; CTV p33 amplicons sequencing on 92 field samples: high diversity between and within samples | Zablocki & Pietersen [92]; Read & Pietersen [93] | |
Citrus tristeza virus | Closterovirus | Closteroviridae | siRNAs study: altered siRNAs pattern in CTV-infected plants, hot spot on CTV genome | Visser et al. [94] | |
Citrus tristeza virus | Closterovirus | Closteroviridae | siRNAs analysis: mixed CTV genotypes in resistance-breaking isolates | Yokomi et al. [17] | |
Citrus tristeza virus | Closterovirus | Closteroviridae | Phylogenetic analysis on 2 CTV populations on 225 samples for epidemiology and risk assessment | Licciardello et al. [96] | |
Citrus tristeza virus | Closterovirus | Closteroviridae | siRNAs sequencing of an old lemon isolate of CTV | Varveri et al. [109] | |
Citrus Yellow vein clearing virus | Mandarivirus | Alphaflexiviridae | siRNAs analysis and phylogeny of 10 isolates of CYVCV | Yu et al. [98] | |
Citrus vein enation virus | Enamovirus | Luteoviridae | Characterization of 5 Japanese genomes of Citrus vein enation virus | Nakazono-Nakaoga et al. [97] | |
Little cherry virus 1 | Velarivirus | Closteroviridae | peach | A new isolate sequenced from South Korea in alternate host (peach) | Lim et al. [102]; |
Little cherry virus 1 | Velarivirus | Closteroviridae | sweet cherry | New isolate in China | Wang et al. [103] |
Little cherry virus 1 | Velarivirus | Closteroviridae | cherry | Genetic diversity among isolates and co-infection of different variants | Katsiani et al. [110] |
Little cherry virus 1 | Velarivirus | Closteroviridae | Prunus | First description in Hungary on apricot and in Spain on sweet cherry | Baràth et al. [41]; Ruiz-Garcia et al. [36] |
Plum bark necrosis stem pitting-associated virus | Ampelovirus | Closteroviridae | Prunus | 4 full genomes sequenced from Prunus sources | Marais et al. [100] |
Plum bark necrosis stem pitting-associated virus | Ampelovirus | Closteroviridae | cherry | One complete genome from sweet cherry | Wang et al. [101] |
Prunus necrotic ringspot virus | Ilarvirus | Bromoviridae | Prunus | Ilarvirus RNA2 generic amplicons from 61 trees: new potential ilarviruses; 53 PNRSV-infected sources: genetic strains network designed; incidence and genotyping of Australian ApMV and PDV | Kinoti et al. [99]; Kinoti et al. [107]; Kinoti et al. [108] |
Prune dwarf virus & Apple mosaic virus | Ilarvirus | Bromoviridae | |||
Prunus virus F | Fabavirus | Secoviridae | sweet cherry, sour cherry | Virome of 9 samples: co-infection of different viruses and co-existence of multiple fabavirus variants | Koloniuk et al. [40] |
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Maliogka, V.I.; Minafra, A.; Saldarelli, P.; Ruiz-García, A.B.; Glasa, M.; Katis, N.; Olmos, A. Recent Advances on Detection and Characterization of Fruit Tree Viruses Using High-Throughput Sequencing Technologies. Viruses 2018, 10, 436. https://doi.org/10.3390/v10080436
Maliogka VI, Minafra A, Saldarelli P, Ruiz-García AB, Glasa M, Katis N, Olmos A. Recent Advances on Detection and Characterization of Fruit Tree Viruses Using High-Throughput Sequencing Technologies. Viruses. 2018; 10(8):436. https://doi.org/10.3390/v10080436
Chicago/Turabian StyleMaliogka, Varvara I., Angelantonio Minafra, Pasquale Saldarelli, Ana B. Ruiz-García, Miroslav Glasa, Nikolaos Katis, and Antonio Olmos. 2018. "Recent Advances on Detection and Characterization of Fruit Tree Viruses Using High-Throughput Sequencing Technologies" Viruses 10, no. 8: 436. https://doi.org/10.3390/v10080436