The Incidence and Genetic Diversity of Potato virus S in Serbian Seed Potato Crops

Ristić, Danijela; Vučurović, Ivan; Kuzmanović, Slobodan; Pfaf-Dolovac, Erika; Aleksić, Goran; Vučurović, Ana; Starović, Mira

doi:10.1007/s11540-018-9395-y

Cited by 4 publications

(2 citation statements)

References 23 publications

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“…Potato virus S, the full-length genome of which was also identified in this work, belongs to the RNA-containing viruses of the Betaflexviridae family. Despite having less pronounced disease symptoms in the affected plants, Potato virus S can destroy up to 20% of the crops [33]. These results confirm the presence of vast amounts of potato viruses in L. decemlineata tissues and especially in gut and head samples.…”

Section: Plant Virusessupporting

confidence: 66%

The metagenomic analysis of viral diversity in Colorado potato beetle public NGS data

Starchevskaya

Kamanova

Vyatkin

et al. 2023

Preprint

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The Colorado potato beetle (CPB) is one of the most serious insect pests with high ecological plasticity and ability to rapidly develop resistance to insecticides. The use of biological insecticides based on viruses is a promising approach to control insect pests, but the information on viruses, which infect leaf feeding beetles, is scarce. We performed the metagenomic analysis of 297 CPB genomic and transcriptomic samples from public NBCI SRA database. The reads that were not aligned to the reference genome were assembled with metaSPAdes and 13314 selected contigs were analyzed with BLAST tools. The contigs and non-aligned reads were also analyzed with Kraken2 software. 3137 virus-positive contigs were attributed to different viruses belonging to 6 types, 17 orders and 32 families, matching over 97 viral species. The annotated sequences can be divided into several groups: homologous to genetic sequences of insect viruses (Adintoviridae, Ascoviridae, Baculoviridae, Dicistroviridae, Chuviridae, Hytrosaviridae, Iflaviridae, Iridoviridae, Nimaviridae, Nudiviridae, Phasmaviridae, Picornaviridae, Polydnaviriformidae, Xinmoviridae etc.), plant viruses (Betaflexiviridae, Bromoviridae, Kitaviridae, Potyviridae), and endogenous retroviral elements (Retroviridae, Metaviridae). Also, the full-length genomes and near-full length genome sequences of several viruses were assembled. We have also found the sequences belonging to Bracoviriform viruses and for the first time experimentally validated the presence of bracoviral genetic fragments in CPB genome. Our work is the first attempt to discover the viral genetic material in CPB samples and we hope that further studies will help to identify new viruses to extend the arsenal of biopesticides against CPB. The analytical pipeline and additional materials are available at https://github.com/starchevskayamaria17/uncoVir

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Section: Plant Virusessupporting

confidence: 66%

The metagenomic analysis of viral diversity in Colorado potato beetle public NGS data

Starchevskaya

Kamanova

Vyatkin

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…Potato virus S , the full-length genome of which was also identified in this work, belongs to the RNA-containing viruses of the Betaflexviridae family. Despite having less pronounced disease symptoms in the affected plants, Potato virus S can destroy up to 20% of crops [ 40 ]. These results confirm the presence of vast amounts of potato viruses in L. decemlineata tissues and especially in gut and head samples.…”

Section: Discussionmentioning

confidence: 99%

The Metagenomic Analysis of Viral Diversity in Colorado Potato Beetle Public NGS Data

Starchevskaya

Kamanova

Vyatkin

et al. 2023

Viruses

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The Colorado potato beetle (CPB) is one of the most serious insect pests due to its high ecological plasticity and ability to rapidly develop resistance to insecticides. The use of biological insecticides based on viruses is a promising approach to control insect pests, but the information on viruses which infect leaf feeding beetles is scarce. We performed a metagenomic analysis of 297 CPB genomic and transcriptomic samples from the public National Center for Biotechnology Information Sequence Read Archive (NCBI SRA) database. The reads that were not aligned to the reference genome were assembled with metaSPAdes, and 13314 selected contigs were analyzed with BLAST tools. The contigs and non-aligned reads were also analyzed with Kraken2 software. A total of 3137 virus-positive contigs were attributed to different viruses belonging to 6 types, 17 orders, and 32 families, matching over 97 viral species. The annotated sequences can be divided into several groups: those that are homologous to genetic sequences of insect viruses (Adintoviridae, Ascoviridae, Baculoviridae, Dicistroviridae, Chuviridae, Hytrosaviridae, Iflaviridae, Iridoviridae, Nimaviridae, Nudiviridae, Phasmaviridae, Picornaviridae, Polydnaviriformidae, Xinmoviridae etc.), plant viruses (Betaflexiviridae, Bromoviridae, Kitaviridae, Potyviridae), and endogenous retroviral elements (Retroviridae, Metaviridae). Additionally, the full-length genomes and near-full length genome sequences of several viruses were assembled. We also found sequences belonging to Bracoviriform viruses and, for the first time, experimentally validated the presence of bracoviral genetic fragments in the CPB genome. Our work represents the first attempt to discover the viral genetic material in CPB samples, and we hope that further studies will help to identify new viruses to extend the arsenal of biopesticides against CPB.

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Improving Resistance to Diseases and Pests: A Dynamic Situation

Bradshaw¹

2021

Potato Breeding: Theory and Practice

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The Incidence and Genetic Diversity of Potato virus S in Serbian Seed Potato Crops

Cited by 4 publications

References 23 publications

The metagenomic analysis of viral diversity in Colorado potato beetle public NGS data

The metagenomic analysis of viral diversity in Colorado potato beetle public NGS data

The Metagenomic Analysis of Viral Diversity in Colorado Potato Beetle Public NGS Data

Improving Resistance to Diseases and Pests: A Dynamic Situation

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