Molecular Characterization of a New Virus Species Identified in Yam (Dioscorea spp.) by High-Throughput Sequencing
Abstract
:1. Introduction
2. Results
2.1. High Throughput Sequencing (HTS) Analysis
2.2. Genome Organization
2.3. Phylogenetic Analysis
2.4. Prevalence and Diversity of the New Virus
3. Discussion
4. Materials and Methods
4.1. Plant Material
4.2. RNA Extraction and High Throughput Sequencing (HTS)
4.3. Reverse Transcription Polymerase Chain Reaction (RT-PCR)
4.4. Phylogenetic and Sequence Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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ORFs 1 | Gene 2 | Length (nt/aa) | % Identity (nt/aa) YVY-Dan vs. YVY-Mak | |
---|---|---|---|---|
YVY-Dan | YVY-Mak | |||
1 | Replicase | 5451/1816 | 5454/1817 | 83/93 |
2 | TGB1 | 702/233 | 702/233 | 84/91 |
3 | TGB2 | 348/115 | 348/115 | 86/92 |
4 | TGB3 | 198/65 | 198/65 | 86/89 |
5 | CP | 711/236 | 711/236 | 85/94 |
Virus | YMV + | YMV − | Total |
---|---|---|---|
YVY + | 23 (42%) | 8 (15%) | 31 |
YVY − | 8 (15%) | 16 (29%) | 24 |
Total | 31 | 24 | 55 |
Name | Sequence (5′–3′) | Product Size (bp) | Location |
---|---|---|---|
YVY-RdRp1-PF | GTAATTGAAAATCACAGTGAGC | 790 | RdRp |
YVY-RdRp1-PR | CTTCAAGTGCATAATTGTCTAT | ||
YVY-CP-F | TTGATTAGTTAAGTATTTAGC | 788 | CP-3′UTR |
YVY-CP-R | CCAGTTTTTCCTGCTGGCAAAC |
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Silva, G.; Bömer, M.; Rathnayake, A.I.; Sewe, S.O.; Visendi, P.; Oyekanmi, J.O.; Quain, M.D.; Akomeah, B.; Kumar, P.L.; Seal, S.E. Molecular Characterization of a New Virus Species Identified in Yam (Dioscorea spp.) by High-Throughput Sequencing. Plants 2019, 8, 167. https://doi.org/10.3390/plants8060167
Silva G, Bömer M, Rathnayake AI, Sewe SO, Visendi P, Oyekanmi JO, Quain MD, Akomeah B, Kumar PL, Seal SE. Molecular Characterization of a New Virus Species Identified in Yam (Dioscorea spp.) by High-Throughput Sequencing. Plants. 2019; 8(6):167. https://doi.org/10.3390/plants8060167
Chicago/Turabian StyleSilva, Gonçalo, Moritz Bömer, Ajith I. Rathnayake, Steven O. Sewe, Paul Visendi, Joshua O. Oyekanmi, Marian D. Quain, Belinda Akomeah, P. Lava Kumar, and Susan E. Seal. 2019. "Molecular Characterization of a New Virus Species Identified in Yam (Dioscorea spp.) by High-Throughput Sequencing" Plants 8, no. 6: 167. https://doi.org/10.3390/plants8060167
APA StyleSilva, G., Bömer, M., Rathnayake, A. I., Sewe, S. O., Visendi, P., Oyekanmi, J. O., Quain, M. D., Akomeah, B., Kumar, P. L., & Seal, S. E. (2019). Molecular Characterization of a New Virus Species Identified in Yam (Dioscorea spp.) by High-Throughput Sequencing. Plants, 8(6), 167. https://doi.org/10.3390/plants8060167