Deep sequencing of virus derived small interfering RNAs and RNA from viral particles shows highly similar mutational landscape of a plant virus population
RNA viruses exist within a host as a population of mutant sequences, often referred to as quasispecies. Within a host, sequences of RNA viruses constitute several distinct but interconnected pools, such as RNA packed in viral particles, double-stranded RNA, and virus-derived small interfering RNAs....
| Main Authors: | , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
American Society for Microbiology
2015
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/65099 |
| _version_ | 1855528151047733248 |
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| author | Kutnjak, D. Rupar, M. Gutiérrez Aguirre, I. Curk, T. Kreuze, Jan F. Ravnikar, M. |
| author_browse | Curk, T. Gutiérrez Aguirre, I. Kreuze, Jan F. Kutnjak, D. Ravnikar, M. Rupar, M. |
| author_facet | Kutnjak, D. Rupar, M. Gutiérrez Aguirre, I. Curk, T. Kreuze, Jan F. Ravnikar, M. |
| author_sort | Kutnjak, D. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | RNA viruses exist within a host as a population of mutant sequences, often referred to as quasispecies. Within a host, sequences of RNA viruses constitute several distinct but interconnected pools, such as RNA packed in viral particles, double-stranded RNA, and virus-derived small interfering RNAs. We aimed to test if the same representation of within-host viral population structure could be obtained by sequencing different viral sequence pools. Using ultradeep Illumina sequencing, the diversity of two coexisting Potato virus Y sequence pools present within a plant was investigated: RNA isolated from viral particles and virus-derived small interfering RNAs (the derivatives of a plant RNA silencing mechanism). The mutational landscape of the within-host virus population was highly similar between both pools, with no notable hotspots across the viral genome. Notably, all of the single-nucleotide polymorphisms with a frequency of higher than 1.6% were found in both pools. Some unique single-nucleotide polymorphisms (SNPs) with very low frequencies were found in each of the pools, with more of them occurring in the small RNA (sRNA) pool, possibly arising through genetic drift in localized virus populations within a plant and the errors introduced during the amplification of silencing signal. Sequencing of the viral particle pool enhanced the efficiency of consensus viral genome sequence reconstruction. Nonhomologous recombinations were commonly detected in the viral particle pool, with a hot spot in the 3′ untranslated and coat protein regions of the genome. We stress that they present an important but often overlooked aspect of virus population diversity.IMPORTANCE This study is the most comprehensive whole-genome characterization of a within-plant virus population to date and the first study comparing diversity of different pools of viral sequences within a host. We show that both virus-derived small RNAs and RNA from viral particles could be used for diversity assessment of within-plant virus population, since they show a highly congruent portrayal of the virus mutational landscape within a plant. The study is an important baseline for future studies of virus population dynamics, for example, during the adaptation to a new host. The comparison of the two virus sequence enrichment techniques, sequencing of virus-derived small interfering RNAs and RNA from purified viral particles, shows the strength of the latter for the detection of recombinant viral genomes and reconstruction of complete consensus viral genome sequence. |
| format | Journal Article |
| id | CGSpace65099 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2015 |
| publishDateRange | 2015 |
| publishDateSort | 2015 |
| publisher | American Society for Microbiology |
| publisherStr | American Society for Microbiology |
| record_format | dspace |
| spelling | CGSpace650992025-11-06T14:06:11Z Deep sequencing of virus derived small interfering RNAs and RNA from viral particles shows highly similar mutational landscape of a plant virus population Kutnjak, D. Rupar, M. Gutiérrez Aguirre, I. Curk, T. Kreuze, Jan F. Ravnikar, M. potatoes rna nucleotide sequence RNA viruses exist within a host as a population of mutant sequences, often referred to as quasispecies. Within a host, sequences of RNA viruses constitute several distinct but interconnected pools, such as RNA packed in viral particles, double-stranded RNA, and virus-derived small interfering RNAs. We aimed to test if the same representation of within-host viral population structure could be obtained by sequencing different viral sequence pools. Using ultradeep Illumina sequencing, the diversity of two coexisting Potato virus Y sequence pools present within a plant was investigated: RNA isolated from viral particles and virus-derived small interfering RNAs (the derivatives of a plant RNA silencing mechanism). The mutational landscape of the within-host virus population was highly similar between both pools, with no notable hotspots across the viral genome. Notably, all of the single-nucleotide polymorphisms with a frequency of higher than 1.6% were found in both pools. Some unique single-nucleotide polymorphisms (SNPs) with very low frequencies were found in each of the pools, with more of them occurring in the small RNA (sRNA) pool, possibly arising through genetic drift in localized virus populations within a plant and the errors introduced during the amplification of silencing signal. Sequencing of the viral particle pool enhanced the efficiency of consensus viral genome sequence reconstruction. Nonhomologous recombinations were commonly detected in the viral particle pool, with a hot spot in the 3′ untranslated and coat protein regions of the genome. We stress that they present an important but often overlooked aspect of virus population diversity.IMPORTANCE This study is the most comprehensive whole-genome characterization of a within-plant virus population to date and the first study comparing diversity of different pools of viral sequences within a host. We show that both virus-derived small RNAs and RNA from viral particles could be used for diversity assessment of within-plant virus population, since they show a highly congruent portrayal of the virus mutational landscape within a plant. The study is an important baseline for future studies of virus population dynamics, for example, during the adaptation to a new host. The comparison of the two virus sequence enrichment techniques, sequencing of virus-derived small interfering RNAs and RNA from purified viral particles, shows the strength of the latter for the detection of recombinant viral genomes and reconstruction of complete consensus viral genome sequence. 2015-05 2015-04-17T18:48:25Z 2015-04-17T18:48:25Z Journal Article https://hdl.handle.net/10568/65099 en Open Access application/pdf American Society for Microbiology Kutnjak, D.; Rupar, M.; Gutierrez Aguirre, I.; Curk, T.; Kreuze, J.F.; Ravnikar, M. 2015. Deep sequencing of virus derived small interfering RNAs and RNA from viral particles shows highly similar mutational landscape of a plant virus population. Journal of Virology. (USA). 89(9):4760-4969. |
| spellingShingle | potatoes rna nucleotide sequence Kutnjak, D. Rupar, M. Gutiérrez Aguirre, I. Curk, T. Kreuze, Jan F. Ravnikar, M. Deep sequencing of virus derived small interfering RNAs and RNA from viral particles shows highly similar mutational landscape of a plant virus population |
| title | Deep sequencing of virus derived small interfering RNAs and RNA from viral particles shows highly similar mutational landscape of a plant virus population |
| title_full | Deep sequencing of virus derived small interfering RNAs and RNA from viral particles shows highly similar mutational landscape of a plant virus population |
| title_fullStr | Deep sequencing of virus derived small interfering RNAs and RNA from viral particles shows highly similar mutational landscape of a plant virus population |
| title_full_unstemmed | Deep sequencing of virus derived small interfering RNAs and RNA from viral particles shows highly similar mutational landscape of a plant virus population |
| title_short | Deep sequencing of virus derived small interfering RNAs and RNA from viral particles shows highly similar mutational landscape of a plant virus population |
| title_sort | deep sequencing of virus derived small interfering rnas and rna from viral particles shows highly similar mutational landscape of a plant virus population |
| topic | potatoes rna nucleotide sequence |
| url | https://hdl.handle.net/10568/65099 |
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