Identification of Loci Associated with Enhanced Virulence in Spodoptera litura Nucleopolyhedrovirus Isolates Using Deep Sequencing
Abstract
:1. Introduction
2. Materials and Methods
2.1. SpltNPV Isolates, Insect Rearing, Virus Amplification, and DNA Extraction
2.2. Library Preparation and Deep Sequencing
2.3. Analysis of Deep Sequencing Data
2.4. Identification of Mutations
2.5. dN/dS and dI/dS Analyses
3. Results
3.1. Generation of SpltNPV-G2b Reference Genome
3.2. Overview of Sequencing Results for SpltNPV-Pak-BNG and SpltNPV-Pak-TAX1
3.3. Occurrence of Large Indels in both Virus Isolates and the Deletion of hr17 in SpltNPV-Pak-TAX1
3.4. High Similarity between the Two Pakistani Virus Isolates
3.5. dN/dS Analysis: Differences with the SpltNPV-G2b and Identification of Loci Associated with Virulence of the SpltNPV-Pak-Isolates
3.6. Limited Within-Isolate Polymorphism
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Isolate | Start Deletion a | End Deletion a | Size | Locus and Notes |
---|---|---|---|---|
SpltNPV-Pak-BNG | 122,661 | 123,153 | 493 | ORF125 (broB), partial deletion |
123,487 | 125,222 | 1736 | ORF126 deleted | |
SpltNPV-Pak-TAX1 | 123,487 | 125,222 | 1736 | ORF126 deleted |
137,718 | 138,035 | 319 | hr17 deleted, 33 bp insert |
Mutations | Obs. Mutations b | dN/dS or dI/dS | |||||
---|---|---|---|---|---|---|---|
Analysis | Contrasted | Approach a | NS/I | S | TTR c = 1 | TTR c = 3 | TTR c = 5 |
dN/dS | Shared | Resequencing | 183 | 428 | 0.114 | 0.150 | 0.168 |
Unique | Resequencing | 125 | 247 | 0.135 | 0.178 | 0.199 | |
De novo | 111 | 247 | 0.120 | 0.158 | 0.176 | ||
dI/dS | Shared | Resequencing | 125 | 428 | 0.490 | 0.606 | 0.655 |
Unique | Resequencing | 110 | 247 | 0.748 | 0.924 | 1.000 | |
De novo | 87 | 247 | 0.591 | 0.731 | 0.791 |
Mutations c | dN/dS | |||||||
---|---|---|---|---|---|---|---|---|
Mutations | ORF a | AA b | NS | S | TTR d = 1 | TTRd d = 3 | TTR d = 5 | Function |
Shared | 22 | 114 | 5 | 0 | 0.947 | 1.027 | 1.065 | Unknown, contains ChtBD2 chitin-binding domain |
65 | 313 | 4 | 1 | 1.150 | 1.505 | 1.672 | Putative RNA cap (nucleoside-2’-O)-methyltransferase, AcMNPV orthologue: ac69) e | |
113 | 401 | 4 | 1 | 1.064 | 1.413 | 1.578 | Unknown, gene found in many baculoviruses (AcMNPV orthologue: ac18), not essential f. | |
117 | 105 | 3 | 1 | 0.910 | 1.112 | 1.206 | Unknown | |
Unique | 25 | 59 | 1 | 0 | 0.872 | 1.040 | 1.117 | Unknown, only found in SpltNPV |
41 | 54 | 1 | 0 | 0.816 | 1.069 | 1.188 | Unknown, only found in SpltNPV and SpliNPV | |
122 | 246 | 3 | 1 | 0.824 | 1.036 | 1.134 | Viral fibroblast growth factor (vFGF), determinant of speed of kill g | |
139 | 60 | 1 | 0 | 0.608 | 0.918 | 1.069 | Unknown |
Isolate a | Mutation | Count/Coverage | Frequency | Forward/Reverse | ORF | AA Change |
---|---|---|---|---|---|---|
BNG | c35,000a | 155/3881 | 0.0399 | 44.19% | ORF36 | none |
c35,202t | 1623/3455 | 0.4698 | 49.97% | ORF36 | none | |
g41180a | 60/2910 | 0.0206 | 47.76% | ORF42 | none | |
c111904t | 407/3822 | 0.1065 | 49.34% | ORF116 | S45F | |
TAX1 | c98204a | 416/2995 | 0.1389 | 43.56% | none | none |
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Zwart, M.P.; Ali, G.; van Strien, E.A.; Schijlen, E.G.W.M.; Wang, M.; van der Werf, W.; Vlak, J.M. Identification of Loci Associated with Enhanced Virulence in Spodoptera litura Nucleopolyhedrovirus Isolates Using Deep Sequencing. Viruses 2019, 11, 872. https://doi.org/10.3390/v11090872
Zwart MP, Ali G, van Strien EA, Schijlen EGWM, Wang M, van der Werf W, Vlak JM. Identification of Loci Associated with Enhanced Virulence in Spodoptera litura Nucleopolyhedrovirus Isolates Using Deep Sequencing. Viruses. 2019; 11(9):872. https://doi.org/10.3390/v11090872
Chicago/Turabian StyleZwart, Mark P., Ghulam Ali, Elisabeth A. van Strien, Elio G. W. M. Schijlen, Manli Wang, Wopke van der Werf, and Just M. Vlak. 2019. "Identification of Loci Associated with Enhanced Virulence in Spodoptera litura Nucleopolyhedrovirus Isolates Using Deep Sequencing" Viruses 11, no. 9: 872. https://doi.org/10.3390/v11090872