Characterizing the Virome of Apple Orchards Affected by Rapid Decline in the Okanagan and Similkameen Valleys of British Columbia (Canada)
Abstract
:1. Introduction
2. Results
2.1. Detection of 21 Plant Viruses and One Plant Viroid by NGS in Apple Orchards Affected by RAD
2.2. Virus Prevalence in Apple Orchards Affected by RAD
2.3. Complete Genome Sequence and Phylogenetic Analysis of Apple Ilarvirus 2
3. Discussion
4. Materials and Methods
4.1. Sample Collection and Preparation
4.2. High Throughput Sequencing and Analyses
4.3. Analysis of Virus Prevalence Using RT-PCR
4.4. Determination of the Complete Genome Sequence of AIV2
4.5. Phylogenetic Analyses
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Orchards * | Number of Samples | Scions | Number of Samples | Rootstocks | Number of Samples | RAD Symptoms | Number of Samples |
---|---|---|---|---|---|---|---|
A | 14 | Ambrosia | 78 | M9 | 104 | Yes | 80 |
B | 14 | Honey Crisp | 26 | Nic29 | 19 | No | 68 |
C | 30 | Salish | 10 | Others (17) | 25 | ||
D | 19 | Gala | 12 | ||||
E | 13 | Others (14) | 19 | ||||
F | 15 | Unknown | 3 | ||||
G | 10 | ||||||
H | 10 | ||||||
I | 20 | ||||||
J | 3 |
NGS Samples * | Orchards | Scions | Rootstocks | RAD Symptoms ** |
---|---|---|---|---|
HX1 | B | Fuji, Honey Crispy, 8S-54-28 | M9 | Yes (3) |
HX2 | A | Ambrosia, Spartan | M9 | Yes (3) |
HX3 | D, E, F | Ambrosia, Honey Crisp | M9, Nic29 | Yes (2), No (1) |
HX4 | I, J | Ambrosia, Pink Lady | M9, G11 | Yes (3) |
HX5 | C | Honey Crisp | G935N, Bud9, Bud 71-7-22 | No (2), Yes (1) |
HX6 | C | Honey Crisp | G4124, G2034, Bud9 | No (3) |
HX7 | C | G. Reinette, Mcintosh, Rein Russ | M9 | No (2), Yes (1) |
HX8 | C | Winter banana, Splendour, Bisbee RD | M9 | No (3) |
HX9 | B | 8S-06-28, 8S-56-50, 9C-06-140 | M9 | Yes (3) |
HX10 | A, E | Ambrosia | M9 | Yes (2), No (1) |
Acronym | Virus or Viroid Name | Species Name | GenBank Accession Number of Reference Isolate | Genus | Family |
---|---|---|---|---|---|
AHVd | Apple hammerhead viroid | Apple hammerhead viroid | NC_028132.1 | Pelamoviroid | Avsunviroidae |
ACLSV | Apple chlorotic leaf spot virus | Apple chlorotic leaf spot virus | NC_001409.1 | Trichovirus | Betaflexiviridae |
ASGV | Apple stem grooving virus | Apple stem grooving virus | NC_001749.2 | Capillovirus | |
CVA | Cherry virus A | Cherry virus A | NC_003689.1 | ||
ASPV | Apple stem pitting virus | Apple stem pitting virus | NC_003462.2 | Foveavirus | |
ALV1 | Apple luteovirus 1 | Apple luteovirus 1 | NC_040680.1 | Luteovirus | Tombusviridae |
TCV | Turnip crinkle virus | Turnip crinkle virus | NC_003821.3 | Betacarmovirus | |
ARWaV-1 | Apple rubbery wood virus 1 | Apple rubodvirus 1 | NC_055390.1, NC_055391.1, NC_055392.1 | Rubodvirus | Phenuiviridae |
ARWaV-2 | Apple rubbery wood virus 2 | Apple rubodvirus 2 | NC_055533.1, NC_055534.1, NC_055535.1, NC_055536.1, NC_055537.1 | ||
CCGaV | Citrus concave gum-associated virus | Citrus coguvirus | NC_035759.1, NC_035454.1 | Coguvirus | |
AIV2 | Apple ilarvirus 2 | Identified in this study, not classified | ON932434, ON932435, ON932436 | Ilarvirus | Bromoviridae |
ApMV | Apple mosaic virus | Apple mosaic virus | NC_003464.1, NC_003465.1, NC_003480.1 | ||
SNIV | Solanum nigrum ilarvirus | Not classified | MN216370.1, MN216373.1, MN216376.1 | ||
TSV | Tobacco streak virus | Tobacco streak virus | NC_003844.1, NC_003842.1, NC_003845.1 | ||
AIV1 | Apple ilarvirus 1 | Not classified | MN386957.1, MN386958.1 | ||
PNRSV | Prunus necrotic ringspot virus | Prunus necrotic ringspot virus | NC_004362.1, NC_004363.1, NC_004364.1 | ||
AlMV | Alfalfa mosaic virus | Alfalfa mosaic virus | NC_001495.1, NC_002024.2, NC_002025.1 | Alfamovirus | |
CYMV | Clover yellow mosaic virus | Clover yellow mosaic virus | NC_001753.1 | Potexvirus | Alphaflexiviridae |
WClMV | White clover mosaic virus | White clover mosaic virus | NC_003820.1 | ||
TVCV | Turnip vein clearing virus | Turnip vein-clearing virus | NC_001873.1 | Tobamovirus | Virgaviridae |
TuMV | Turnip mosaic virus | Turnip mosaic virus | NC_002509.2 | Potyvirus | Potyviridae |
SoMV | Sowbane mosaic virus | Sowbane mosaic virus | NC_011187.1 | Sobemovirus | Solemoviridae |
NGS Samples | HX1 | HX2 | HX3 | HX4 | HX5 | HX6 | HX7 | HX8 | HX9 | HX10 |
---|---|---|---|---|---|---|---|---|---|---|
Total reads | 103,066,652 | 81,797,780 | 101,947,128 | 86,362,078 | 81,880,242 | 102,784,288 | 71,349,254 | 94,601,674 | 85,908,874 | 77,797,014 |
Reads Mapped to Malus Domestica | 97,549,197 | 75,364,116 | 95,651,348 | 80,689,725 | 72,958,929 | 92,960,006 | 65,850,694 | 87,214,426 | 79,122,763 | 71,389,255 |
Reads not Mapped to M. domestica | 5,517,455 | 6,433,664 | 6,295,780 | 5,672,353 | 8,921,313 | 9,824,282 | 5,498,560 | 7,387,248 | 6,786,111 | 6,407,759 |
Reads Mapped to Plant Viruses | 40,286 | 161 | 132,732 | 52,869 | 1994 | 986 | 148,093 | 357,639 | 4838 | 76,969 |
AHVd | 8699 | 3435 | 704 | 54 | 63,949 | 180,962 | 200 | |||
ACLSV | 12,174 | 20,423 | 8 | 12,801 | 10,955 | 677 | ||||
ASGV | 9785 | 4467 | 2643 | |||||||
CVA | 187 | |||||||||
ASPV | 5 | 35,542 | 11,105 | 8 | 12 | 43,759 | 151,192 | 6532 | ||
ALV1 | 39,292 | 12,494 | 1978 | 10,409 | 7413 | |||||
ARWaV-1 | 3840 | 15,168 | 3970 | |||||||
ARWaV-2 | 41,807 | 6141 | 232 | 874 | ||||||
CCGaV | 10,782 | 9 | 12,967 | 56,775 | ||||||
AIV2 * | 114 | 156 | 1389 | 120 | 1257 | 882 | 1656 | 1521 | 848 | 1652 |
ApMV | 931 | |||||||||
SNIV | 110 | 211 | 30 | 36 | 14 | 22 | ||||
TSV | 202 | |||||||||
AIV1 | 81 | 10 | ||||||||
PNRSV | 250 | |||||||||
AlMV | 16 | 14 | 10 | 14 | ||||||
CYMV | 149 | 10 | 7 | 7 | 71 | |||||
WClMV | 116 | 8 | 18 | 6 | ||||||
TVCV | 40 | 6 | 149 | |||||||
TuMV | 12 | 46 | 6 | |||||||
TCV | 10 | |||||||||
SoMV | 22 |
Number of Viruses and/or Viroid | Number of Samples | Percentage of Samples (%) |
---|---|---|
0 | 1 | 0.7 |
1 | 26 | 17.6 |
2 | 26 | 17.6 |
3 | 24 | 16.2 |
4 | 15 | 10.1 |
5 | 29 | 19.6 |
6 | 15 | 10.1 |
7 | 9 | 6.1 |
8 | 3 | 2.0 |
Viruses Tested | RAD Symptoms (80) * | No RAD Symptoms (68) | All Samples (148) | |||
---|---|---|---|---|---|---|
No. of Positive Samples | Percentage of Positive Samples (%) | No. of Positive Samples | Percentage of Positive Samples (%) | No. of Positive Samples | Percentage of Positive Samples (%) | |
AIV2 | 46 | 57.5 | 48 | 70.6 | 94 | 63.5 |
CCGaV | 49 | 61.3 | 43 | 63.2 | 92 | 62.2 |
ASPV | 43 | 53.8 | 38 | 55.9 | 81 | 54.7 |
ACLSV | 36 | 45.0 | 38 | 55.9 | 74 | 50.0 |
ASGV | 34 | 42.5 | 28 | 41.2 | 62 | 41.9 |
AHVd | 15 | 18.8 | 19 | 27.9 | 34 | 23.0 |
ALV1 | 15 | 18.8 | 12 | 17.6 | 27 | 18.2 |
ARWaV2 | 14 | 17.5 | 9 | 13.2 | 23 | 15.5 |
TSV | 6 | 7.5 | 8 | 11.8 | 14 | 9.5 |
ARWaV1 | 8 | 10.0 | 5 | 7.4 | 13 | 8.8 |
SNIV | 7 | 8.8 | 4 | 5.9 | 11 | 7.4 |
ApMV | 5 | 6.3 | 1 | 1.5 | 6 | 4.1 |
PNRSV | 1 | 1.3 | 0 | 0.0 | 1 | 0.7 |
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Xiao, H.; Hao, W.; Storoschuk, G.; MacDonald, J.L.; Sanfaçon, H. Characterizing the Virome of Apple Orchards Affected by Rapid Decline in the Okanagan and Similkameen Valleys of British Columbia (Canada). Pathogens 2022, 11, 1231. https://doi.org/10.3390/pathogens11111231
Xiao H, Hao W, Storoschuk G, MacDonald JL, Sanfaçon H. Characterizing the Virome of Apple Orchards Affected by Rapid Decline in the Okanagan and Similkameen Valleys of British Columbia (Canada). Pathogens. 2022; 11(11):1231. https://doi.org/10.3390/pathogens11111231
Chicago/Turabian StyleXiao, Huogen, Wenjia Hao, Gavin Storoschuk, Jesse L. MacDonald, and Hélène Sanfaçon. 2022. "Characterizing the Virome of Apple Orchards Affected by Rapid Decline in the Okanagan and Similkameen Valleys of British Columbia (Canada)" Pathogens 11, no. 11: 1231. https://doi.org/10.3390/pathogens11111231
APA StyleXiao, H., Hao, W., Storoschuk, G., MacDonald, J. L., & Sanfaçon, H. (2022). Characterizing the Virome of Apple Orchards Affected by Rapid Decline in the Okanagan and Similkameen Valleys of British Columbia (Canada). Pathogens, 11(11), 1231. https://doi.org/10.3390/pathogens11111231