New Viral Sequences Identified in the Flavescence Dorée Phytoplasma Vector Scaphoideus titanus
Abstract
:1. Introduction
2. Materials and Methods
2.1. Insect Collection
2.2. DNA Extraction, RNA Extraction, Library Preparation and Sequencing
2.3. Bioinformatic Analysis
2.4. Phylogenetic Trees
2.5. PCR and RT-PCR
3. Results
3.1. Single-Stranded Positive-Sense RNA Viruses
3.2. Single-Stranded Negative-Sense RNA Virus
3.3. Double-Stranded RNA Viruses
3.4. Virus Prevalence
3.5. Endogenous Viral Elements
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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RNA-seq LibrariesID | Country | State/Region | Sampling Sites | Latitude (Decimal Degrees) | Longitude (Decimal Degrees) | Sampling Date (yyyy/mm/dd) | Number of Sampled Individuals | Positive to Scaphoideus titanus Iflavirus 1 | Positive to Scaphoideus titanustoti-Like Virus 1 | |
---|---|---|---|---|---|---|---|---|---|---|
St_HU | Hungary | Pest | Monor | 47.354861 | 19.472177 | 2018-07-12 | 20 | 0 | 0 | |
St_HU | Hungary | Pest | Gomba | 47.349622 | 19.505863 | 2018-07-12 | 18 | 0 | 0 | |
St_FR | France | Burgundy | Corgoloin | 47.095667 | 4.908233 | 2018-07-06 | 20 | 0 | 8 | |
St_FR | France | Dordogne | Saint-Nexans | 44.472132 | 0.345279 | 2018-07-10 | 18 | 1 | 1 | |
St_IT1 | Italy | Piedmont | Asti | 44.921854 | 8.195758 | 2018-07-31 | 4 | 0 | 0 | |
St_IT1 | Italy | Piedmont | Montà | 44.807434 | 7.965787 | 2018-07-31 | 12 | 1 | 0 | |
St_IT1 | Italy | Piedmont | Portacomaro | 44.962898 | 8.26072 | 2018-08-03 | 16 | 0 | 0 | |
St_IT1 | Italy | Piedmont | Cisterna | 44.82591 | 8.008371 | 2018-08-03 | 4 | 0 | 0 | |
St_IT1 | Italy | Lombardy | Ome | 45.6302972 | 10.129867 | 2018-07-11 | 4 | 0 | 0 | |
St_IT1 | Italy | Veneto | Verona | 45.4227833 | 11.025431 | 2018-08-08 | 8 | 0 | 0 | |
St_IT2 | Italy | Friuli-Venezia Giulia | Togliano | 46.1129556 | 13.411311 | 2018-07-30 | 22 | 0 | 2 | |
St_IT2 | Italy | Friuli-Venezia Giulia | Savorgnano al Torre | 46.161786 | 13.286864 | 2018-07-31 | 24 | 0 | 1 | |
St_IT2 | Italy | Abruzzo | Vacri | 42.290333 | 14.223861 | 2018-07-16 | 12 | 0 | 2 | |
St_CH | Switzerland | Canton Vaud | Gland | 46.42616 | 6.28217 | 2018-08-09 | 16 | 0 | 4 | |
St_CH | Switzerland | Canton Valais | Pramagnon | 46.24987 | 7.45371 | 2018-08-09 | 16 | 0 | 0 | |
214 | 2 | 18 | Total | |||||||
St_USA | USA | Illinois | Muncie | 40.0893 | -87.8323 | 2018-06-11 | 3 | |||
Insects for DNA extraction1 | Country | State/Region | Sampling Sites | Latitude (Decimal Degrees) | Longitude (Decimal Degrees) | Sampling Date (yyyy/mm/dd) | Number of Sampled Individuals | |||
Italy | Piedmont | Montà | 44.807434 | 7.965787 | 2018-07-31 | 2 | ||||
Italy | Piedmont | Dogliani | 44.5362837 | 7.9312913 | 2018-08-20 | 2 |
Library ID | Accession Numbers | Sequence Length (bp) | Best Blastx Hit Description | % Identity | % Query Coverage | RPKM | Tentative Name | Genome |
---|---|---|---|---|---|---|---|---|
St_IT1 | MN982380 | 10729 | YP_009129265.1 polyprotein [Graminella nigrifrons virus 1] | 51 | 83 | 0.01 | Scaphoideus titanus iflavirus 1 | +ssRNA (monopartite) |
St_IT2 | MN982382 | 7847 | YP_003800001.1 RNA-directed RNA polymerase partial [Spissistilus festinus virus 1] | 42 | 37 | 0.002 | Scaphoideus titanus toti-like virus 1 | dsRNA (monopartite) |
St_CH | MN982383 | 7839 | YP_003800001.1 RNA-directed RNA polymerase partial [Spissistilus festinus virus 1] | 42 | 37 | 0.032 | Scaphoideus titanus toti-like virus 1 | dsRNA (monopartite) |
St_FR | MN982379 | 10693 | YP_009129265.1 polyprotein [Graminella nigrifrons virus 1] | 51 | 83 | 0.004 | Scaphoideus titanus iflavirus 1 | +ssRNA (monopartite) |
St_FR | MN982381 | 7871 | YP_003800001.1 RNA-directed RNA polymerase partial [Spissistilus festinus virus 1] | 42 | 37 | 0.023 | Scaphoideus titanus toti-like virus 1 | dsRNA (monopartite) |
St_USA | MN982384 | 4361 | API65464.1 glycoprotein precursor [Sanxia Water Strider Virus 2] | 25 | 12 | 1.016 | Scaphoideus titanus bunya-like virus 1 | −ssRNA (tripartite): segment M |
St_USA | MN982385 | 1458 | APG79297.1 putative nucleoprotein [Hubei diptera virus 7] | 27 | 43 | 0.9 | Scaphoideus titanus bunya-like virus 1 | −ssRNA (tripartite): segment S |
St_USA | MN982386 | 7740 | APT68154.1 RNA-dependent RNA polymerase [Ganda bee virus] | 33 | 74 | 0.359 | Scaphoideus titanus bunya-like virus 1 | −ssRNA (tripartite): segment L |
St_USA | MN982387 | 10519 | YP_009129265.1 polyprotein [Graminella nigrifrons virus 1] | 51 | 85 | 0.045 | Scaphoideus titanus iflavirus 2 | +ssRNA (monopartite) |
St_USA | MN982388 | 1455 | AWA82259.1 hypothetical protein, partial [Naganuma virus] | 38 | 91 | 0.145 | Scaphoideus titanus sobemo-like virus 1 | +ssRNA (bipartite) |
St_USA | MN982389 | 3213 | YP_009329970.1 hypothetical protein [Hubei sobemo-like virus 26] | 60 | 99 | 0.103 | Scaphoideus titanus sobemo-like virus 1 | +ssRNA (bipartite) |
St_USA | MN982390 | 1550 | AWA82259.1 hypothetical protein partial [Naganuma virus] | 36 | 77 | 0.231 | Scaphoideus titanus sobemo-like virus 2 | +ssRNA (bipartite) |
St_USA | MN982391 | 3100 | YP_009330073.1 hypothetical protein 2 [Hubei sobemo-like virus 24] | 46 | 97 | 0.172 | Scaphoideus titanus sobemo-like virus 2 | +ssRNA (bipartite) |
St_USA | MN982393 | 1303 | YP_009329884.1 hypothetical protein [Wuhan large pig roundworm virus 1] | 35 | 61 | 0.227 | Scaphoideus titanus-associated partiti-like virus 1 | dsRNA (bipartite) |
St_USA | MN982392 | 1558 | AVV63192.1 RNA-directed RNA polymerase [Wuhan large pig roundworm virus] | 44 | 87 | 0.272 | Scaphoideus titanus-associated partiti-like virus 1 | dsRNA (bipartite) |
St_USA | MN982394 | 5239 | YP_009337778.1 RdRp [Hubei permutotetra-like virus 9] | 39 | 39 | 0.764 | Scaphoideus titanus permutotetra-like virus 1 | +ssRNA (monopartite) |
St_USA | MN982397 | 1240 | ADN64742.1 non-structural protein [Homalodisca vitripennis reo-like virus] | 79 | 58 | 2.378 | Scaphoideus titanus reo-like virus 1 | dsRNA (multipartite): segment 10 |
St_USA | MN982398 | 1867 | ADN64768.1 minor core protein [Homalodisca vitripennis reo-like virus] | 83 | 42 | 1.146 | Scaphoideus titanus reo-like virus 1 | dsRNA (multipartite): segment 7 |
St_USA | MN982399 | 2937 | ADN64783.1 minor core protein [Homalodisca vitripennis reo-like virus] | 52 | 49 | 2.661 | Scaphoideus titanus reo-like virus 1 | dsRNA (multipartite): segment 5 |
St_USA | MN982395 | 4957 | ADN64816.1 RNA-directed RNA polymerase [Homalodisca vitripennis reo-like virus] | 87 | 61 | 5.053 | Scaphoideus titanus reo-like virus 1 | dsRNA (multipartite): segment 1 |
St_USA | MN982400 | 3560 | YP_002790885.1 RNA-binding protein [Homalodisca vitripennis reo-like virus] | 96 | 49 | 5.444 | Scaphoideus titanus reo-like virus 1 | dsRNA (multipartite): segment 2 |
St_USA | MN982401 | 1416 | Q85451.1 RecName: Full=Outer capsid protein P8 | 62 | 88 | 1.679 | Scaphoideus titanus reo-like virus 1 | dsRNA (multipartite): segment 8 |
St_USA | MN982402 | 3179 | ADN64799.1 major core protein [Homalodisca vitripennis reo-like virus] | 95 | 55 | 1.901 | Scaphoideus titanus reo-like virus 1 | dsRNA (multipartite): segment 3 |
St_USA | MN982403 | 2648 | YP_002790887.1 zinc-finger protein [Homalodisca vitripennis reo-like virus] | 73 | 30 | 3.571 | Scaphoideus titanus reo-like virus 1 | dsRNA (multipartite): segment 4 |
St_USA | MN982404 | 1778 | YP_002790889.1 non-structural protein [Homalodisca vitripennis reo-like virus] | 78 | 33 | 1.196 | Scaphoideus titanus reo-like virus 1 | dsRNA (multipartite): segment 6 |
St_USA | MN982396 | 1179 | YP_002790892.1 non-structural protein [Homalodisca vitripennis reo-like virus] | 68 | 47 | 1.802 | Scaphoideus titanus reo-like virus 1 | dsRNA (multipartite): segment 9 |
St_USA | MN982405 | 798 | YP_002790894.1 non-structural protein [Homalodisca vitripennis reo-like virus] | 48 | 45 | 4.192 | Scaphoideus titanus reo-like virus 1 | dsRNA (multipartite): segment 11 |
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Ottati, S.; Chiapello, M.; Galetto, L.; Bosco, D.; Marzachì, C.; Abbà, S. New Viral Sequences Identified in the Flavescence Dorée Phytoplasma Vector Scaphoideus titanus. Viruses 2020, 12, 287. https://doi.org/10.3390/v12030287
Ottati S, Chiapello M, Galetto L, Bosco D, Marzachì C, Abbà S. New Viral Sequences Identified in the Flavescence Dorée Phytoplasma Vector Scaphoideus titanus. Viruses. 2020; 12(3):287. https://doi.org/10.3390/v12030287
Chicago/Turabian StyleOttati, Sara, Marco Chiapello, Luciana Galetto, Domenico Bosco, Cristina Marzachì, and Simona Abbà. 2020. "New Viral Sequences Identified in the Flavescence Dorée Phytoplasma Vector Scaphoideus titanus" Viruses 12, no. 3: 287. https://doi.org/10.3390/v12030287