Identification of Loci Associated with Enhanced Virulence in Spodoptera litura Nucleopolyhedrovirus Isolates Using Deep Sequencing

Mark P. Zwart*, Ghulam Ali, Elisabeth A. van Strien, Elio G.W.M. Schijlen, Manli Wang, Wopke van der Werf, Just M. Vlak

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

Spodoptera litura is an emerging pest insect in cotton and arable crops in Central Asia. To explore the possibility of using baculoviruses as biological control agents instead of chemical pesticides, in a previous study we characterized a number of S. litura nucleopolyhedrovirus (SpltNPV) isolates from Pakistan. We found significant differences in speed of kill, an important property of a biological control agent. Here we set out to understand the genetic basis of these differences in speed of kill, by comparing the genome of the fast-killing SpltNPV-Pak-TAX1 isolate with that of the slow-killing SpltNPV-Pak-BNG isolate. These two isolates and the SpltNPV-G2 reference strain from China were deep sequenced with Illumina. As expected, the two Pakistani isolates were closely related with >99% sequence identity, whereas the Chinese isolate was more distantly related. We identified two loci that may be associated with the fast action of the SpltNPV-Pak-TAX1 isolate. First, an analysis of rates of synonymous and non-synonymous mutations identified neutral to positive selection on open reading frame (ORF) 122, encoding a viral fibroblast growth factor (vFGF) that is known to affect virulence in other baculoviruses. Second, the homologous repeat region hr17, a putative enhancer of transcription and origin of replication, is absent in SpltNPV-Pak-TAX1 suggesting it may also affect virulence. Additionally, we found there is little genetic variation within both Pakistani isolates, and we identified four genes under positive selection in both isolates that may have played a role in adaptation of SpltNPV to conditions in Central Asia. Our results contribute to the understanding of the enhanced activity of SpltNPV-Pak-TAX1, and may help to select better SpltNPV isolates for the control of S. litura in Pakistan and elsewhere.

Original languageEnglish
Article number872
JournalViruses
Volume11
Issue number9
DOIs
Publication statusPublished - 17 Sep 2019

Fingerprint

Biological Control Agents
Central Asia
Nucleopolyhedrovirus
High-Throughput Nucleotide Sequencing
Spodoptera
Baculoviridae
Pakistan
Virulence
Replication Origin
Fibroblast Growth Factors
Pesticides
Open Reading Frames
Insects
China
Genome
Mutation
Genes

Keywords

  • deep sequencing
  • genomics
  • Illumina
  • SpltNPV
  • Spodoptera litura nucleopolyhedrovirus
  • virulence

Cite this

@article{15eb1f672af64743a3882b349f8b4991,
title = "Identification of Loci Associated with Enhanced Virulence in Spodoptera litura Nucleopolyhedrovirus Isolates Using Deep Sequencing",
abstract = "Spodoptera litura is an emerging pest insect in cotton and arable crops in Central Asia. To explore the possibility of using baculoviruses as biological control agents instead of chemical pesticides, in a previous study we characterized a number of S. litura nucleopolyhedrovirus (SpltNPV) isolates from Pakistan. We found significant differences in speed of kill, an important property of a biological control agent. Here we set out to understand the genetic basis of these differences in speed of kill, by comparing the genome of the fast-killing SpltNPV-Pak-TAX1 isolate with that of the slow-killing SpltNPV-Pak-BNG isolate. These two isolates and the SpltNPV-G2 reference strain from China were deep sequenced with Illumina. As expected, the two Pakistani isolates were closely related with >99{\%} sequence identity, whereas the Chinese isolate was more distantly related. We identified two loci that may be associated with the fast action of the SpltNPV-Pak-TAX1 isolate. First, an analysis of rates of synonymous and non-synonymous mutations identified neutral to positive selection on open reading frame (ORF) 122, encoding a viral fibroblast growth factor (vFGF) that is known to affect virulence in other baculoviruses. Second, the homologous repeat region hr17, a putative enhancer of transcription and origin of replication, is absent in SpltNPV-Pak-TAX1 suggesting it may also affect virulence. Additionally, we found there is little genetic variation within both Pakistani isolates, and we identified four genes under positive selection in both isolates that may have played a role in adaptation of SpltNPV to conditions in Central Asia. Our results contribute to the understanding of the enhanced activity of SpltNPV-Pak-TAX1, and may help to select better SpltNPV isolates for the control of S. litura in Pakistan and elsewhere.",
keywords = "deep sequencing, genomics, Illumina, SpltNPV, Spodoptera litura nucleopolyhedrovirus, virulence",
author = "Zwart, {Mark P.} and Ghulam Ali and {van Strien}, {Elisabeth A.} and Schijlen, {Elio G.W.M.} and Manli Wang and {van der Werf}, Wopke and Vlak, {Just M.}",
year = "2019",
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language = "English",
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journal = "Viruses",
issn = "1999-4915",
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Identification of Loci Associated with Enhanced Virulence in Spodoptera litura Nucleopolyhedrovirus Isolates Using Deep Sequencing. / Zwart, Mark P.; Ali, Ghulam; van Strien, Elisabeth A.; Schijlen, Elio G.W.M.; Wang, Manli; van der Werf, Wopke ; Vlak, Just M.

In: Viruses, Vol. 11, No. 9, 872, 17.09.2019.

Research output: Contribution to journalArticleAcademicpeer-review

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T1 - Identification of Loci Associated with Enhanced Virulence in Spodoptera litura Nucleopolyhedrovirus Isolates Using Deep Sequencing

AU - Zwart, Mark P.

AU - Ali, Ghulam

AU - van Strien, Elisabeth A.

AU - Schijlen, Elio G.W.M.

AU - Wang, Manli

AU - van der Werf, Wopke

AU - Vlak, Just M.

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AB - Spodoptera litura is an emerging pest insect in cotton and arable crops in Central Asia. To explore the possibility of using baculoviruses as biological control agents instead of chemical pesticides, in a previous study we characterized a number of S. litura nucleopolyhedrovirus (SpltNPV) isolates from Pakistan. We found significant differences in speed of kill, an important property of a biological control agent. Here we set out to understand the genetic basis of these differences in speed of kill, by comparing the genome of the fast-killing SpltNPV-Pak-TAX1 isolate with that of the slow-killing SpltNPV-Pak-BNG isolate. These two isolates and the SpltNPV-G2 reference strain from China were deep sequenced with Illumina. As expected, the two Pakistani isolates were closely related with >99% sequence identity, whereas the Chinese isolate was more distantly related. We identified two loci that may be associated with the fast action of the SpltNPV-Pak-TAX1 isolate. First, an analysis of rates of synonymous and non-synonymous mutations identified neutral to positive selection on open reading frame (ORF) 122, encoding a viral fibroblast growth factor (vFGF) that is known to affect virulence in other baculoviruses. Second, the homologous repeat region hr17, a putative enhancer of transcription and origin of replication, is absent in SpltNPV-Pak-TAX1 suggesting it may also affect virulence. Additionally, we found there is little genetic variation within both Pakistani isolates, and we identified four genes under positive selection in both isolates that may have played a role in adaptation of SpltNPV to conditions in Central Asia. Our results contribute to the understanding of the enhanced activity of SpltNPV-Pak-TAX1, and may help to select better SpltNPV isolates for the control of S. litura in Pakistan and elsewhere.

KW - deep sequencing

KW - genomics

KW - Illumina

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KW - Spodoptera litura nucleopolyhedrovirus

KW - virulence

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DO - 10.3390/v11090872

M3 - Article

VL - 11

JO - Viruses

JF - Viruses

SN - 1999-4915

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