A Novel Divergent Geminivirus Identified in Asymptomatic New World Cactaceae Plants
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection and Processing
2.2. High Throughput Sequencing and Genome Assembly
2.3. Infectivity Assays
2.4. Phylogenetic and Pairwise Identity Analyses
2.5. Capsid Protein Cluster Analysis
2.6. Recombination Analysis
2.7. Virus Purification and Transmission Electron Microscopy
3. Results and Discussion
3.1. A Novel Cactus-Infecting Geminivirus
3.2. Testing the Infectivity of the Novel Cactus-Infecting Geminiviruses
3.3. Evolutionary Dynamics of the Novel Divergent Geminivirus Group
3.4. Identification of Sub/Super- Genomic Molecules
4. Concluding Remarks
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Virus | Isolate | Accession Number | Genotype | Host species | Sampling Year | Region of Collection | Associated Insect Samples | Sub/Super-Genomic |
---|---|---|---|---|---|---|---|---|
OpV1 | 2013_1 | MN099960 | 4 | Lophocereus schottii | 2015 | Arizona, USA | ||
OpV1 | 2013_2 | MN099981 | 4 | 2015 | Arizona, USA | |||
OpV1 | 2013_3 | MN099982 | 4 | 2015 | Arizona, USA | |||
OpV1 | 2014_1 | MN099983 | 4 | Opuntia stenopetala | 2015 | Arizona, USA | ||
OpV1 | 2014_2 | MN099984 | 4 | 2015 | Arizona, USA | |||
OpV1 | 2014_3 | MN099985 | 4 | 2015 | Arizona, USA | |||
OpV1 | 2014_4 | MN099986 | 4 | 2015 | Arizona, USA | |||
OpV1 | 2014_5 | MN099987 | 4 | 2015 | Arizona, USA | |||
OpV1 | ASU_PP2 | MN099961 | 5 | Cylindropuntia fulgida | 2018 | Arizona, USA | ||
OpV1 | ASUH_12 | MN099962 | 4 | Opuntia tapona | 2002 | Baja California, Mexico | ||
OpV1 | ASUH_16 | MN099963 | 4 | Opuntia engelmannii | 2010 | Arizona, USA | ||
OpV1 | ASUH_20 | MN099964 | 4 | Opuntia santa-rita | 2002 | Sonora, Mexico | ||
OpV1 | Cacti_2_1 | MN099988 | 6 | Opuntia santa-rita | 2017 | Arizona, USA | SI_7 | |
OpV1 | Cacti_2_2 | MN099989 | 6 | 2017 | Arizona, USA | |||
OpV1 | DBG10_5 | MN099990 | 11 | Opuntia cespitosa | 2017 | Arizona, USA | OpV1 sg-1 | |
OpV1 | DBG10_9 | MN099991 | 12 | 2017 | Arizona, USA | OpV1 sg-3 | ||
OpV1 | DBG10_149 | MN099992 | 11 | 2017 | Arizona, USA | |||
OpV1 | DBG10_1972 | MN099993 | 11 | 2017 | Arizona, USA | |||
OpV1 | DBG10_2558 | MN099994 | 12 | 2017 | Arizona, USA | |||
OpV1 | DBG10_2562 | MN099995 | 11 | 2017 | Arizona, USA | |||
OpV1 | DBG13_5 | MN099996 | 11 | Opuntia basilaris | 2017 | Arizona, USA | OpV1 sg-2 | |
OpV1 | DBG13_9 | MN099997 | 11 | 2017 | Arizona, USA | OpV1 sg-4 | ||
OpV1 | DBG13_1987 | MN099998 | 1 | 2017 | Arizona, USA | |||
OpV1 | DBG_14_1 | MN100000 | 4 | Opuntia echios var. echios | 2017 | Arizona, USA | SI_1 | |
OpV1 | DBG_14_2 | MN100001 | 4 | 2017 | Arizona, USA | |||
OpV1 | DBG_14_3 | MN100002 | 7 | 2017 | Arizona, USA | |||
OpV1 | DBG_14_4 | MN100003 | 4 | 2017 | Arizona, USA | |||
OpV1 | DBG_46 | MN100013 | 4 | 2018 | Arizona, USA | |||
OpV1 | DBG_47 | MN100014 | 4 | 2018 | Arizona, USA | |||
OpV1 | DBG_48 | MN100015 | 4 | 2018 | Arizona, USA | |||
OpV1 | DBG_26 | MN100004 | 11 | Opuntia rufida | 2018 | Arizona, USA | OpV1 sg-6 | |
OpV1 | DBG_31_1 | MN100005 | 1 | Opuntia mackensenii | 2018 | Arizona, USA | ||
OpV1 | DBG_31_2 | MN100006 | 1 | 2018 | Arizona, USA | |||
OpV1 | DBG34 | MN099999 | 2 | Opuntia robusta | 2018 | Arizona, USA | SI_33 | OpV1 sg-8 |
OpV1 | DBG_34 | MN100007 | 7 | 2018 | Arizona, USA | |||
OpV1 | DBG_36 | MN100008 | 2 | Opuntia englemannii x.O. rufida | 2018 | Arizona, USA | SI_35 | |
OpV1 | DBG_38 | MN100009 | 11 | Opuntia martiniana | 2018 | Arizona, USA | ||
OpV1 | DBG_41 | MN100010 | 12 | Opuntia rooneyi | 2018 | Arizona, USA | OpV1 sg-5 | |
OpV1 | DBG_42_1 | MN100011 | 4 | Opuntia englemannii | 2018 | Arizona, USA | OpV1 sg-12 | |
OpV1 | DBG_42_2 | MN100012 | 11 | 2018 | Arizona, USA | |||
OpV1 | DBG_42_3 | MN099971 | 10 | 2018 | Arizona, USA | |||
OpV1 | DBG_56 | MN099972 | 4 | Opuntia basilaris | 2018 | Arizona, USA | ||
OpV1 | DBG_57 | MN099973 | 7 | 2018 | Arizona, USA | |||
OpV1 | DBG_57_2 | MN099974 | 7 | 2018 | Arizona, USA | |||
OpV1 | DBG_58 | MN099975 | 4 | 2018 | Arizona, USA | |||
OpV1 | DBG_72 | MN099976 | 3 | Opuntia rufida | 2018 | Arizona, USA | ||
OpV1 | DBG74 | MN099965 | 4 | Opuntia robusta | 2018 | Arizona, USA | ||
OpV1 | DBG75 | MN099966 | 4 | Opuntia basilaris | 2018 | Arizona, USA | ||
OpV1 | DBG80 | MN099967 | 4 | Cylindropuntia echinocarpa | 2018 | Arizona, USA | ||
OpV1 | DBG86 | MN099968 | 4 | Cylindropuntia spinosior | 2018 | Arizona, USA | ||
OpV1 | DBG_86 | MN099977 | 4 | 2018 | Arizona, USA | |||
OpV1 | DBG88 | MN099969 | 4 | Opuntia cf polyacantha | 2018 | Arizona, USA | ||
OpV1 | DBG90 | MN099970 | 4 | Opuntia phaeacantha | 2019 | Arizona, USA | ||
OpV1 | LCM_85 | MN100016 | 2 | Opuntia aureispina | 2015 | Texas, USA | ||
OpV1 | LCM_91_1 | MN100017 | 14 | Cylindropuntia arbuscula | 2015 | Arizona, USA | OpV1 sg-7 | |
OpV1 | LCM_91_2 | MN100018 | 15 | 2015 | Arizona, USA | |||
OpV1 | S18_1 | MN099978 | 13 | Opuntia engelmannii | 2018 | Arizona, USA | ||
OpV1 | S18_8 | MN099979 | 4 | Opuntia santa-rita | 2018 | Arizona, USA | ||
OpV1 | S18_89 | MN099980 | 8 | Opuntia engelmannii | 2018 | Arizona, USA | ||
OpV1 | TM_cacti_2_1 | MN100037 | 9 | Opuntia engelmannii. | 2018 | Arizona, USA | ||
OpV1 | TM_cacti_2_2 | MN100038 | 9 | 2018 | Arizona, USA | |||
OpV1 | SI_0_1 | MN100019 | 6 | Dactylopius sp. | 2017 | Arizona, USA | ||
OpV1 | SI_0_2 | MN100020 | 6 | 2017 | Arizona, USA | |||
OpV1 | SI_0_3 | MN100021 | 6 | 2017 | Arizona, USA | |||
OpV1 | SI_0_4 | MN100022 | 6 | 2017 | Arizona, USA | |||
OpV1 | SI_1_1 | MN100023 | 4 | Dactylopius sp. | 2017 | Arizona, USA | DBG14 | |
OpV1 | SI_1_2 | MN100024 | 4 | 2017 | Arizona, USA | |||
OpV1 | SI_1_3 | MN100025 | 4 | 2017 | Arizona, USA | |||
OpV1 | SI_1_4 | MN100026 | 4 | 2017 | Arizona, USA | |||
OpV1 | SI_7_1 | MN100027 | 6 | Dactylopius sp. | 2017 | Arizona, USA | Cacti 2 | |
OpV1 | SI_7_2 | MN100028 | 6 | 2017 | Arizona, USA | |||
OpV1 | SI_7_3 | MN100029 | 6 | 2017 | Arizona, USA | |||
OpV1 | SI_9_1 | MN100030 | 6 | Dactylopius sp. | 2017 | Arizona, USA | ||
OpV1 | SI_9_2 | MN100031 | 6 | 2017 | Arizona, USA | |||
OpV1 | SI_23 | MN100032 | 11 | Dactylopius sp. | 2018 | Arizona, USA | ||
OpV1 | SI_28 | MN100033 | 1 | Dactylopius sp. | 2018 | Arizona, USA | ||
OpV1 | SI_33 | MN100034 | 2 | Dactylopius sp. | 2018 | Arizona, USA | DBG34 | OpV1 sg-9 |
OpV1 | SI_35 | MN100035 | 11 | Dactylopius sp. | 2018 | Arizona, USA | DBG36 | |
OpV1 | SI_39 | MN100036 | 12 | Dactylopius sp. | 2018 | Arizona, USA | ||
DBG_28 | Opuntia spinosibacca | 2018 | Arizona, USA | OpV1 sg-14 | ||||
DBG_69 | Opuntia rufida | 2018 | Arizona, USA | OpV1 sg-13 | ||||
S18_9 | Opuntia santa-rita | 2018 | Arizona, USA | OpV1 sg-10 | ||||
OpV1 sg-11 |
Recombination Event | Region | Recombinant Sequence(s) | Minor Parental Sequence(s) | Major Parental Sequence(s) | Detection Methods | p-Value |
---|---|---|---|---|---|---|
1 | 2156–4 | Genotype 12 | Genotype 2 | Genotype 11 | RGBMCST | 1.41 × 10−69 |
2 | 1915–2 | Genotype 1 | Genotype 4 | Genotype 7 | RGBMCST | 4.11 × 10−56 |
3 | 2338–2878 | Genotype 14 | Genotype 2 | Genotype 15 | RBMCS | 1.74 × 10−34 |
Genotype 7 | ||||||
4 | 2066–42 | Genotype 2 | Genotype 4 | Genotype 9 | RGBMCS | 9.95 × 10−39 |
Genotype 7 | ||||||
5 | 2088–2961 | Genotype 11 | Genotype 8 | Genotype 10 | RGBMCS | 6.08 × 10−29 |
Genotype 12 (tr) | Genotype 5 | |||||
6 | 2304–2819 | Genotype 10 | Genotype 6 | Genotype 11 | RGBMCST | 1.08 × 10−24 |
7 | 2301–2844 | Genotype 15 | Genotype 7 | Genotype 11 | RGBMCS | 4.94 × 10−17 |
Genotype 14 (tr) | Genotype 4 | |||||
8 | 2333–2939 | Genotype 13 | Genotype 4 | Genotype 11 | RGBMCS | 7.33 × 10−29 |
Genotype 7 | ||||||
9 | 1088–1957 | Genotype 3 | Genotype 7 | Genotype 4 | RGBMCST | 1.17 × 10−24 |
10 | 1582–1765 | Genotype 3 | Genotype 13 | Genotype 2 | RBCS | 2.05 × 10−13 |
Genotype 1 | Genotype 4 | |||||
Genotype 7 | ||||||
11 | 2860–2946 | Genotype 10 | Genotype 6 | Genotype 11 | RGMCST | 2.04 × 10−10 |
12 | 2928–1156 | Genotype 6 | Genotype 4 | Genotype 9 | RBMCS | 6.50 × 10−26 |
Genotype 3 | Genotype 11 | |||||
Genotype 13 | ||||||
Genotype 12 | ||||||
13 | 514–1166 | Genotype 5 | Genotype 4 | Genotype 11 | RGBMCS | 6.12 × 10−18 |
Genotype 3 | ||||||
14 | 31 *–512 | Genotype 10 | Genotype 3 | Genotype 14 | RBMC | 4.05 × 10−9 |
Genotype 12 (tr) | Genotype 7 | Genotype 9 | ||||
Genotype 11 (tr) | ||||||
15 | 1494 *–1866 | Genotype 5 | Genotype 6 | Genotype 11 | RGBMCST | 2.93 × 10−10 |
Genotype 10 | ||||||
Genotype 12 | ||||||
16 | 2332–2719 | Genotype 4 | Unknown | Genotype 6 | RGBMCST | 1.88 × 10−32 |
Genotype 13 | ||||||
Genotype 2 | ||||||
Genotype 12 | ||||||
Genotye1 | ||||||
17 | 30 *–489 | Genotype 13 | Genotype 3 | Genotype 14 | GBMCST | 9.73 × 10−9 |
Genotype 15 | ||||||
18 | 2846 *–216 | Genotype 9 | Genotype 15 | Genotype 7 | RMC | 1.71 × 10−8 |
Genotype 14 | ||||||
19 | 1791–1855 | Genotype 10 | Genotype 2 | Genotype 12 | GBT | 9.66 × 10−6 |
Genotype 13 (tr) | Genotype 11 | |||||
20 | 27–373 | Genotype 3 | Genotype 7 | Genotype 4 | RBMCT | 5.80 × 10−6 |
Genotype 1 | ||||||
21 | 2445 *–2543 | Genotype 15 | Genotype 11 | Unknown | RGBC | 1.77 × 10−05 |
Genotype 7 | Genotype 8 | |||||
22 | 1881–26 * | Genotype 12 | Genotype 4 | Genotype 14 | GBMCST | 8.71 × 10−5 |
Genotype 11 (tr) | Genotype 15 | |||||
23 | 1132–1462 | Genotype 15 | Unknown | Genotype 12 | MCT | 5.90 × 10−3 |
Genotype 14 | Genotype 11 |
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Fontenele, R.S.; Salywon, A.M.; Majure, L.C.; Cobb, I.N.; Bhaskara, A.; Avalos-Calleros, J.A.; Argüello-Astorga, G.R.; Schmidlin, K.; Khalifeh, A.; Smith, K.; et al. A Novel Divergent Geminivirus Identified in Asymptomatic New World Cactaceae Plants. Viruses 2020, 12, 398. https://doi.org/10.3390/v12040398
Fontenele RS, Salywon AM, Majure LC, Cobb IN, Bhaskara A, Avalos-Calleros JA, Argüello-Astorga GR, Schmidlin K, Khalifeh A, Smith K, et al. A Novel Divergent Geminivirus Identified in Asymptomatic New World Cactaceae Plants. Viruses. 2020; 12(4):398. https://doi.org/10.3390/v12040398
Chicago/Turabian StyleFontenele, Rafaela S., Andrew M. Salywon, Lucas C. Majure, Ilaria N. Cobb, Amulya Bhaskara, Jesús A. Avalos-Calleros, Gerardo R. Argüello-Astorga, Kara Schmidlin, Anthony Khalifeh, Kendal Smith, and et al. 2020. "A Novel Divergent Geminivirus Identified in Asymptomatic New World Cactaceae Plants" Viruses 12, no. 4: 398. https://doi.org/10.3390/v12040398