Related Experiment Videos
Deciphering Single Nucleotide Polymorphisms and Evolutionary Trends in Isolates of the Cydia pomonella granulovirus
Jörg T Wennmann1, Pit Radtke2, Karolin E Eberle3,4
1Institute for Biological Control, Federal Research Centre for Cultivated Plants, Julius Kühn Institute, Heinrichstraße 243, 64287 Darmstadt, Germany. joerg.wennmann@julius-kuehn.de.
Abstract:
Six complete genome sequences of Cydia pomonella granulovirus (CpGV) isolates from Mexico (CpGV-M and CpGV-M1), England (CpGV-E2), Iran (CpGV-I07 and CpGV-I12), and Canada (CpGV-S) were aligned and analyzed for genetic diversity and evolutionary processes. The selected CpGV isolates represented recently identified phylogenetic lineages of CpGV, namely, the genome groups A to E. The genomes ranged from 120,816 bp to 124,269 bp. Several common differences between CpGV-M, -E2, -I07, -I12 and -S to CpGV-M1, the first sequenced and published CpGV isolate, were highlighted. Phylogenetic analysis based on the aligned genome sequences grouped CpGV-M and CpGV-I12 as the most derived lineages, followed by CpGV-E2, CpGV-S and CpGV-I07, which represent the most basal lineages. All of the genomes shared a high degree of co-linearity, with a common setup of 137 (CpGV-I07) to 142 (CpGV-M and -I12) open reading frames with no translocations. An overall trend of increasing genome size and a decrease in GC content was observed, from the most basal lineage (CpGV-I07) to the most derived (CpGV-I12). A total number of 788 positions of single nucleotide polymorphisms (SNPs) were determined and used to create a genome-wide SNP map of CpGV. Of the total amount of SNPs, 534 positions were specific for exactly one of either isolate CpGV-M, -E2, -I07, -I12 or -S, which allowed the SNP-based detection and identification of all known CpGV isolates.
Insights
This study sequenced six Cydia pomonella granulovirus (CpGV) genomes, revealing genetic diversity and evolutionary relationships. Single nucleotide polymorphisms (SNPs) were mapped, enabling precise identification of CpGV isolates.
Area of Science:
- Virology
- Genomics
- Evolutionary Biology
Background:
- Cydia pomonella granulovirus (CpGV) is a significant pest control agent.
- Understanding CpGV genetic diversity is crucial for effective pest management strategies.
- Previous sequencing efforts have identified distinct phylogenetic lineages of CpGV.
Purpose of the Study:
- To analyze the genetic diversity and evolutionary processes of six CpGV isolates from different geographic regions.
- To compare complete genome sequences and identify variations among CpGV isolates.
- To develop a genome-wide SNP map for CpGV isolate identification.
Main Methods:
- Whole-genome sequencing of six CpGV isolates.
- Alignment and comparative analysis of genome sequences.
- Phylogenetic analysis to determine evolutionary relationships.
- Identification and mapping of single nucleotide polymorphisms (SNPs).
Main Results:
- Genome sizes ranged from 120,816 bp to 124,269 bp with high co-linearity.
- Phylogenetic analysis revealed distinct basal and derived lineages.
- An increasing trend in genome size and decreasing GC content was observed from basal to derived lineages.
- A total of 788 SNPs were identified, with 534 being isolate-specific, enabling precise identification.
Conclusions:
- The study provides a comprehensive genomic comparison of CpGV isolates, clarifying their evolutionary relationships.
- The developed SNP map is a valuable tool for the accurate detection and identification of CpGV isolates.
- Findings contribute to a deeper understanding of CpGV evolution and facilitate targeted pest control strategies.