Deciphering Single Nucleotide Polymorphisms and Evolutionary Trends in Isolates of the Cydia pomonella granulovirus
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 rece...
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| Format: | Article |
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MDPI AG
2017-08-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/9/8/227 |
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| author | Jörg T. Wennmann Pit Radtke Karolin E. Eberle Gianpiero Gueli Alletti Johannes A. Jehle |
| author_facet | Jörg T. Wennmann Pit Radtke Karolin E. Eberle Gianpiero Gueli Alletti Johannes A. Jehle |
| author_sort | Jörg T. Wennmann |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-22T03:53:28Z |
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| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-12-22T03:53:28Z |
| publishDate | 2017-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-b7c4b831e42d4e919f9cbaf210ecc8fe2022-12-21T18:39:56ZengMDPI AGViruses1999-49152017-08-019822710.3390/v9080227v9080227Deciphering Single Nucleotide Polymorphisms and Evolutionary Trends in Isolates of the Cydia pomonella granulovirusJörg T. Wennmann0Pit Radtke1Karolin E. Eberle2Gianpiero Gueli Alletti3Johannes A. Jehle4Institute for Biological Control, Federal Research Centre for Cultivated Plants, Julius Kühn Institute, Heinrichstraße 243, 64287 Darmstadt, GermanyDepartment of Phytopathology, Agricultural Service Center Palatinate (DLR Rheinpfalz), 67435 Neustadt an der Weinstrasse, GermanyInstitute for Biological Control, Federal Research Centre for Cultivated Plants, Julius Kühn Institute, Heinrichstraße 243, 64287 Darmstadt, GermanyInstitute for Biological Control, Federal Research Centre for Cultivated Plants, Julius Kühn Institute, Heinrichstraße 243, 64287 Darmstadt, GermanyInstitute for Biological Control, Federal Research Centre for Cultivated Plants, Julius Kühn Institute, Heinrichstraße 243, 64287 Darmstadt, GermanySix 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.https://www.mdpi.com/1999-4915/9/8/227Cydia pomonella granuloviruscodling mothsingle nucleotide polymorphismmutationresistance |
| spellingShingle | Jörg T. Wennmann Pit Radtke Karolin E. Eberle Gianpiero Gueli Alletti Johannes A. Jehle Deciphering Single Nucleotide Polymorphisms and Evolutionary Trends in Isolates of the Cydia pomonella granulovirus Viruses Cydia pomonella granulovirus codling moth single nucleotide polymorphism mutation resistance |
| title | Deciphering Single Nucleotide Polymorphisms and Evolutionary Trends in Isolates of the Cydia pomonella granulovirus |
| title_full | Deciphering Single Nucleotide Polymorphisms and Evolutionary Trends in Isolates of the Cydia pomonella granulovirus |
| title_fullStr | Deciphering Single Nucleotide Polymorphisms and Evolutionary Trends in Isolates of the Cydia pomonella granulovirus |
| title_full_unstemmed | Deciphering Single Nucleotide Polymorphisms and Evolutionary Trends in Isolates of the Cydia pomonella granulovirus |
| title_short | Deciphering Single Nucleotide Polymorphisms and Evolutionary Trends in Isolates of the Cydia pomonella granulovirus |
| title_sort | deciphering single nucleotide polymorphisms and evolutionary trends in isolates of the cydia pomonella granulovirus |
| topic | Cydia pomonella granulovirus codling moth single nucleotide polymorphism mutation resistance |
| url | https://www.mdpi.com/1999-4915/9/8/227 |
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