Molecular Signature of a Novel Alternanthera Yellow Vein Virus Variant Infecting the Ageratum conyzoides Weed in Oman
Abstract
:1. Introduction
2. Material and Methods
2.1. Specimen Collection and DNA Extraction
2.2. Amplification, Cloning, and Sequencing
2.3. Bioinformatic Analysis
2.4. Population Study
3. Results
3.1. Alternanthera Yellow Vein Oman Virus Is Associated with Ageratum conyzoides
3.2. Tomato Leaf Curl Betasatellite Associated with the Disease
3.3. Recombination Analysis
3.4. Population Study
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Alternanthera Yellow Vein Virus Position of Genes (Coordinates)/No. of Amino Acids (Predicted Coding Capacity in kDa) | Tomato Leaf Curl Betasatellite | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Isolate | Acc. No. | Size (nt) | CP | V2 | Rep | TrAP | REn | C4 | Satellite | Acc. No. | Size (nt) | Position of BC1 Gene (Coordinates)/No. of Amino Acids (Predicted Coding Capacity in kDa) |
Wed39-4 | ON186760 | 2745 | 314–1084 256 | 154–501 115 | 1533–2618 362 | 1226–1630 134 | 1081–1485 134 | 2171–2467 98 | Wed39-7 | ON186763 | 1360 | 189–545 118 (13) |
Wed39-5 | ON186761 | 2747 | 314–1084 256 | 154–501 115 | 1533–2618 362 | 1226–1630 134 | 1081–1485 134 | 2171–2467 98 | Wed39-8 | ON186764 | 1360 | 189–545 118 (13) |
Wed39-6 | ON186762 | 2747 | 314–1084 256 | 154–501 115 | 1533–2618 361 | 1226–1630 134 | 1081–1485 134 | 2171–2467 98 | Wed39-9 | ON186765 | 1360 | 189–545 118 (13) |
Virus Name * | Isolate | Host Species | Family | Region/Country | GenBank Accession No. | Percent Nucleotide Sequence Identity |
---|---|---|---|---|---|---|
LUYVV | YN6153 | Ludwigia linifolia | Onagraceae | China | MN210345 | 74% |
TbLCYnV | Y161 | tomato | Solanaceae | China | AJ566744 | 73.1% |
TbLCYnV | Y143 | tobacco | Solanaceae | China | AJ512762 | 73.2% |
TbLCYnV | Y3 | tobacco | Solanaceae | China | AF240674 | 73% |
TbLCYnV | Y283 | Ageratum conyzoides | Asteraceae | China | AJ971267 | 73.2% |
TbLCYnVCN | YN3095 | Ageratum conyzoides | Asteraceae | China | MN218668_ | 73.2% |
TYLCShV | YN3383 | cowpea | Fabaceae | China | MT089918 | 73.1% |
TYLCVNV | Vt-6 | tomato | Solanaceae | Vietnam | DQ641697 | 73.2% |
AYVV | AFSP7d | Sauropus androgynus | Phyllanthaceae | Thailand | JN809824 | 73.3% |
ToLCPatV | ToLCPatV | tomato | Solanaceae | India | KM383746 | 73.3% |
PeLCV | Pk2 | Raphanus sativus | Brassicaceae | Pakistan | LT600729 | 72.5% |
PeLCV | Mad-4 | soybean | Fabaceae | Pakistan | MN910265 | 72.2% |
PeLCV | DP2 | papaya | Caricaceae | India | KX353622 | 75.5% |
AlYVV | Jabalpur_A | Alternanthera sessilis | Amaranthaceae | India | LC316182 | 92.8% |
AlYVV | Kangra | Synedrella sp. | Asteraceae | India | MG686552 | 92.6% |
AlYVV | Rumex | Rumex nepalensis | Polygonaceae | India | LN795903 | 92.5% |
AlYVV | Jabalpur_B | Alternanthera sessilis | Amaranthaceae | India | LC316183 | 92.5% |
AlYVV | Mn5 | Eclipta prostrata | Asteraceae | Pakistan | KX906696 | 92.4% |
AlYVV | Mn1 | Eclipta prostrata | Asteraceae | Pakistan | KX906695 | 91.6% |
AlYVV | YN598 | Eclipta prostrata | Asteraceae | China | FJ015062 | 91.1% |
AlYVV | G8 | Eclipta prostrata | Asteraceae | China | DQ375456 | 91.6% |
AlYVV | F31 | Eclipta prostrata | Asteraceae | China | EU286798 | 91.1% |
Virus | No of Seq | H | Hd | InDel Sites | S | Eta | Kt | π |
---|---|---|---|---|---|---|---|---|
AlYVOMV | 34 | 33 | 0.998 | 681 | 1309 | 2285 | 460 | 0.17 |
ToLCB | 35 | 33 | 0.996 | 283 | 900 | 1200 | 138 | 0.12 |
Virus Name | Isolate Name | Host Species | Family | Country or Region | Reference |
---|---|---|---|---|---|
Alternanthera yellow vein virus | AlYVV | Alternanthera sessilis | Amaranthaceae | India | [22] |
Alternanthera yellow vein virus | AlYVV | Picrorhiza kurroa | Plantaginaceae | India | [24] |
Alternanthera yellow vein virus | AlYVV | Eclipta prostrata | Asteraceae | Pakistan | [25] |
Alternanthera yellow vein virus | AlYVV | Eclipta prostrata | Asteraceae | Pakistan | [26] |
Alternanthera yellow vein virus | AlYVV | Eclipta prostrata | Asteraceae | Pakistan | [27] |
Alternanthera yellow vein virus | AlYVV | Eclipta prostrata | Asteraceae | China | [28] |
Alternanthera yellow vein virus | AlYVV | Sonchus arvensis | Asteraceae | Pakistan | [29] |
Alternanthera yellow vein virus | AlYVV | Eclipta prostrata | Asteraceae | China | [30] |
Alternanthera yellow vein virus | AlYVV | Eclipta prostrate (L.) | Compositae | China | [31] |
Ludwigia yellow vein virus | LUYVV | Ludwigia hyssopifolia | Onagraceae | China | [32] |
Alternanthera yellow vein virus | AlYVV | Alternanthera philoxeroides | Amaranthaceae | China | [33] |
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Shafiq, M.; Ondrasek, G.; Al-Sadi, A.M.; Shahid, M.S. Molecular Signature of a Novel Alternanthera Yellow Vein Virus Variant Infecting the Ageratum conyzoides Weed in Oman. Viruses 2023, 15, 2381. https://doi.org/10.3390/v15122381
Shafiq M, Ondrasek G, Al-Sadi AM, Shahid MS. Molecular Signature of a Novel Alternanthera Yellow Vein Virus Variant Infecting the Ageratum conyzoides Weed in Oman. Viruses. 2023; 15(12):2381. https://doi.org/10.3390/v15122381
Chicago/Turabian StyleShafiq, Muhammad, Gabrijel Ondrasek, Abdullah Mohammed Al-Sadi, and Muhammad Shafiq Shahid. 2023. "Molecular Signature of a Novel Alternanthera Yellow Vein Virus Variant Infecting the Ageratum conyzoides Weed in Oman" Viruses 15, no. 12: 2381. https://doi.org/10.3390/v15122381
APA StyleShafiq, M., Ondrasek, G., Al-Sadi, A. M., & Shahid, M. S. (2023). Molecular Signature of a Novel Alternanthera Yellow Vein Virus Variant Infecting the Ageratum conyzoides Weed in Oman. Viruses, 15(12), 2381. https://doi.org/10.3390/v15122381