Genetic Variation between Asian and Mediterranean Populations of Cucurbit Aphid-Borne Yellows Virus
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sampling
2.2. RNA Extraction, RT-PCR
2.3. Recombination Analysis
2.4. Phylogenetic Analysis
Country | Isolates/strains | Host | Accession Number | Collection Date |
---|---|---|---|---|
South Korea (30) | SW1, SW2, CY3, C-HS1, WM-YS10, NW2, GS2, CY6, NW5, GM16, HS1,GS6, HD118, HD1, GS1, SW25, SW1(14), HS2, NW18, GM7, NW1, NW2(14), SW64, CY4,melon-GJ, Cumber-AS-kr1, M-CY31, M-BY1, C-AS1, K1 | melon, melon, melon, cucumber, watermelon, melon, melon, melon, melon, melon, melon, melon, melon, melon, melon, melon, melon, melon, melon, melon, melon, melon, melon, melon, melon, cucumber, melon, melon, cucumber, melon | KR231959, KR231961, KR231942, MG257900, MG257903, KR231955, KR231948, KR231944, KR231957, KR231946, KR231952, KR231949, KR231951, KR231950, KR231947, KR231962, KR231960, KR231953, KR231958, KR231945, KR231954, KR231956, KR231963, KR231943, MW509732, MZ508305, MG257902, MG257901, MG257899, LC082306 | 2014, 2014, 2013, 2016, 2016, 2013, 2014, 2014, 2013, 2013, 2014, 2014, 2014,2014, 2014, 2014, 2014, 2014, 2014, 2013, 2014, 2014, 2014, 2013, 2020, 2021, 2016, 2016, 2016, 2014 |
Japan: Okayama (1) | CABYV-JAN | Cucumber | GQ221224 | - |
China (5) | CABYV-FJ, -, -, CABYV-CZ, CABYV-QY | Squash, cantaloupe, cucurbit, zucchini, suakwa vegetable sponge | GQ221223, EU636992, EU000535, HQ439023, MT943520 | -, -, -, -, 2017 |
USA (1) | BL-4 | Pumpkin | MK055337 | 2017 |
Spain (29) | Sq/2004/1.9, Sq/2003/7.2, MEC-12, LP63, 64.2M/M, 9.2Z/A, 9.1M/M, 9.1M/M, 8.1M/M, 8.1Me/A, 7.1M/M, 67.1Z/M, 59.1M/A, 53.1M/M, 3.2M/M, 23.1M/M, 22.1Z/M, 2.1Z/M, 2.1M/M, 2.1M/M, 19.1Z/A, 19.1M/M, 19.1M/M, 18.1Z/A, 18.1M/A, 11.1Z/M, 10.1Z/M, 1.1M/M, Sq/2005/9.2 | -, -, melon, watermelon, melon, zucchini, melon, melon, melon, melon, melon, zucchini, melon, melon, melon, melon, zucchini, zucchini, melon, melon, zucchini, melon, melon, zucchini, melon, zucchini, zucchini, melon, - | JF939814, JF939812, MW051362, MW051363, OM948857, OM948856, OM948855, OM948854, OM948853, OM948852, OM948851, OM948850, OM948849, OM948848, OM948847, OM948846, OM948845, OM948844, OM948843, OM948842, OM948841, OM948840, OM948839, OM948838, OM948837, OM948836, OM948835, OM948834, JF939813 | 2017, -, -, 2014, 2019, 2018, 2013, 2019, 2014, 2016, 2014, 2013, 2018, 2020, 2020, 2017, 2015, 2019, 2015, 2013, 2011, 2019, 2019, 2015, 2015, 2016, 2012, 2020, 2014, - |
Papua New Guinea (1) | 10PN | cucumber | MG780352 | 2016 |
Taiwan (2) | CABYV-R-TW82, CABYV-C-TW20 | Luffa aegyptiaca, Momordica charantia | JQ700306, JQ700305 | 2009, 2008 |
France (1) | EM160093 | melon | MT027103 | 2016 |
Indonesia (1) | - | cucumber | LC472499 | 2017 |
India (2) | POL-WM, POL-SQ | watermelon, squash | MN688220, MN688219 |
2.5. Population Genetic Parameters
2.6. Molecular Dating Analysis
3. Results
3.1. Field Observation
3.2. PCR Amplification
3.3. Recombination Isolates
3.4. Phylogenetic Analysis
3.5. Genetic Variation and Selection Pressure Analyses
3.6. Neutrality Test
3.7. Genetic Differentiation
3.8. Divergence Time Analysis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Population | N | h | Hd | S | η | k | π | dS | dN | ω |
---|---|---|---|---|---|---|---|---|---|---|
Complete genome | 44 | 43 | 0.999 | 1575 | 1889 | 359.165 | 0.06459 | 0.14167 | 0.04046 | 0.2855 |
Phylogroups (Complete Genome) | ||||||||||
Asian | 31 | 31 | 1.000 | 802 | 843 | 142.168 | 0.02505 | 0.05880 | 0.01464 | 0.2489 |
Mediterranean | 11 | 10 | 0.982 | 470 | 488 | 162.145 | 0.02860 | 0.07279 | 0.01495 | 0.2053 |
ORF0 | 44 | 38 | 0.990 | 216 | 247 | 48.854 | 0.06814 | 0.10700 | 0.05564 | 0.5200 |
ORF1 + 2 | 44 | 43 | 0.999 | 860 | 1000 | 187.080 | 0.05920 | 0.10641 | 0.04486 | 0.4215 |
ORF4 | 50 | 26 | 0.960 | 24 | 25 | 6.167 | 0.02909 | 0.06467 | 0.01814 | 0.2805 |
ORF3 + 5 | 44 | 42 | 0.998 | 573 | 710 | 132.185 | 0.06633 | 0.19262 | 0.02610 | 0.1354 |
ORF3 (CP) | 50 | 26 | 0.960 | 24 | 25 | 6.167 | 0.02909 | 0.04990 | 0.02143 | 0.4294 |
Phylogroups (new isolates) (Coat Protein) | ||||||||||
Asian | 27 | 12 | 0.900 | 13 | 13 | 2.365 | 0.01115 | 0.03583 | 0.00621 | 0.1733 |
Mediterranean | 23 | 14 | 0.945 | 12 | 12 | 3.036 | 0.01432 | 0.05017 | 0.02311 | 0.4606 |
Population | Fu and Li’s D* | Fu and Li’s F* | Tajima’s D |
---|---|---|---|
Complete genome | −0.85487 ns | −0.92764 ns | −0.64287 ns |
Phylogroup | |||
Asian | −1.10647 ns | −1.37784 ns | −1.26911 ns |
Mediterranean | 0.31512 ns | 0.22766 ns | −0.13000 ns |
ORF3 (CP) | −1.02637 ns | −0.64835 ns | 0.34283 ns |
Phylogroup | |||
Asian | −1.49049 ns | −1.57070 ns | −1.00962 ns |
Mediterranean | −0.25873 ns | −0.29129 ns | −0.22998 ns |
ORF4 (MP) | −1.02637 ns | −0.64835 ns | 0.34283 ns |
ORF0 | −0.84544 ns | −0.86372 ns | −0.51353 ns |
ORF1 + 2 | −0.83674 ns | −0.93552 ns | −0.69127 ns |
ORF3 + 5 | −0.95533 ns | −1.03074 ns | −0.70499 ns |
Comparison | αKS* | αKST* | p Value | αZ* | p Value | Snn | p Value | βFST |
---|---|---|---|---|---|---|---|---|
Complete genome | ||||||||
Phylogroup | ||||||||
All (n = 44)/Asian (n = 31) | 5.1803 | 0.0002 | 0.422 ns | 6.9397 | 0.633 ns | 0.1733 | 1.000 ns | 0.104 |
All (n = 44)/Mediterranean (n = 11) | 5.3621 | 0.0423 | 0.000 *** | 6.1228 | 0.000 *** | 0.6242 | 0.774 ns | 0.482 |
Asian (n = 31)/Mediterranean (n = 11) | 4.7411 | 0.1243 | 0.000 *** | 5.2430 | 0.000 *** | 1.000 | 0.000 *** | 0.758 |
ORF4 (CP) | ||||||||
Phylogroup | ||||||||
All (n = 50)/Asian (n = 27) | 1.5485 | 0.0566 | 0.000 *** | 6.9248 | 0.000 *** | 0.5202 | 0.656 ns | 0.243 |
All (n = 50)/Mediterranean (n = 23) | 1.6342 | 0.0718 | 0.000 *** | 6.7496 | 0.000 *** | 0.5191 | 0.815 ns | 0.293 |
Asian (n = 27)/Mediterranean (n = 23) | 1.1987 | 0.3256 | 0.000 *** | 5.4576 | 0.000 *** | 1.000 | 0.000 *** | 0.718 |
Species | Mean Patristic Distance | Ratios of CABYV and Other Patristic Distances |
---|---|---|
CABYV | 0.20 | 1 |
MABYV | 0.20 | 1 |
SABYV | 0.32 | 1.6 |
Pumpkin polerovirus | 0.32 | 1.6 |
PABYV | 0.32 | 1.6 |
CpCSV | 0.35 | 1.75 |
FBPV-1 | 0.35 | 1.75 |
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Pouraziz, P.; Yousefi, M.; Santosa, A.I.; Koolivand, D. Genetic Variation between Asian and Mediterranean Populations of Cucurbit Aphid-Borne Yellows Virus. Viruses 2023, 15, 1714. https://doi.org/10.3390/v15081714
Pouraziz P, Yousefi M, Santosa AI, Koolivand D. Genetic Variation between Asian and Mediterranean Populations of Cucurbit Aphid-Borne Yellows Virus. Viruses. 2023; 15(8):1714. https://doi.org/10.3390/v15081714
Chicago/Turabian StylePouraziz, Parastoo, Milad Yousefi, Adyatma Irawan Santosa, and Davoud Koolivand. 2023. "Genetic Variation between Asian and Mediterranean Populations of Cucurbit Aphid-Borne Yellows Virus" Viruses 15, no. 8: 1714. https://doi.org/10.3390/v15081714
APA StylePouraziz, P., Yousefi, M., Santosa, A. I., & Koolivand, D. (2023). Genetic Variation between Asian and Mediterranean Populations of Cucurbit Aphid-Borne Yellows Virus. Viruses, 15(8), 1714. https://doi.org/10.3390/v15081714