Next Generation Sequencing for Detection and Discovery of Plant Viruses and Viroids: Comparison of Two Approaches
Next generation sequencing (NGS) technologies are becoming routinely employed in different fields of virus research. Different sequencing platforms and sample preparation approaches, in the laboratories worldwide, contributed to a revolution in detection and discovery of plant viruses and viroids. I...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2017-10-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | http://journal.frontiersin.org/article/10.3389/fmicb.2017.01998/full |
| _version_ | 1819061090929082368 |
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| author | Anja Pecman Anja Pecman Denis Kutnjak Ion Gutiérrez-Aguirre Ian Adams Adrian Fox Neil Boonham Neil Boonham Maja Ravnikar |
| author_facet | Anja Pecman Anja Pecman Denis Kutnjak Ion Gutiérrez-Aguirre Ian Adams Adrian Fox Neil Boonham Neil Boonham Maja Ravnikar |
| author_sort | Anja Pecman |
| collection | DOAJ |
| description | Next generation sequencing (NGS) technologies are becoming routinely employed in different fields of virus research. Different sequencing platforms and sample preparation approaches, in the laboratories worldwide, contributed to a revolution in detection and discovery of plant viruses and viroids. In this work, we are presenting the comparison of two RNA sequence inputs (small RNAs vs. ribosomal RNA depleted total RNA) for the detection of plant viruses by Illumina sequencing. This comparison includes several viruses, which differ in genome organization and viroids from both known families. The results demonstrate the ability for detection and identification of a wide array of known plant viruses/viroids in the tested samples by both approaches. In general, yield of viral sequences was dependent on viral genome organization and the amount of viral reads in the data. A putative novel Cytorhabdovirus, discovered in this study, was only detected by analysing the data generated from ribosomal RNA depleted total RNA and not from the small RNA dataset, due to the low number of short reads in the latter. On the other hand, for the viruses/viroids under study, the results showed higher yields of viral sequences in small RNA pool for viroids and viruses with no RNA replicative intermediates (single stranded DNA viruses). |
| first_indexed | 2024-12-21T14:37:22Z |
| format | Article |
| id | doaj.art-4a4806090bb8407ea0a04ae588a37669 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-21T14:37:22Z |
| publishDate | 2017-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-4a4806090bb8407ea0a04ae588a376692022-12-21T19:00:18ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2017-10-01810.3389/fmicb.2017.01998295761Next Generation Sequencing for Detection and Discovery of Plant Viruses and Viroids: Comparison of Two ApproachesAnja Pecman0Anja Pecman1Denis Kutnjak2Ion Gutiérrez-Aguirre3Ian Adams4Adrian Fox5Neil Boonham6Neil Boonham7Maja Ravnikar8Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, SloveniaJožef Stefan International Postgraduate School, Ljubljana, SloveniaDepartment of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, SloveniaDepartment of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, SloveniaFera Science Ltd., York, United KingdomFera Science Ltd., York, United KingdomFera Science Ltd., York, United KingdomInstitute for Agri-Food Research and Innovation, Newcastle University, Newcastle upon Tyne, United KingdomDepartment of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, SloveniaNext generation sequencing (NGS) technologies are becoming routinely employed in different fields of virus research. Different sequencing platforms and sample preparation approaches, in the laboratories worldwide, contributed to a revolution in detection and discovery of plant viruses and viroids. In this work, we are presenting the comparison of two RNA sequence inputs (small RNAs vs. ribosomal RNA depleted total RNA) for the detection of plant viruses by Illumina sequencing. This comparison includes several viruses, which differ in genome organization and viroids from both known families. The results demonstrate the ability for detection and identification of a wide array of known plant viruses/viroids in the tested samples by both approaches. In general, yield of viral sequences was dependent on viral genome organization and the amount of viral reads in the data. A putative novel Cytorhabdovirus, discovered in this study, was only detected by analysing the data generated from ribosomal RNA depleted total RNA and not from the small RNA dataset, due to the low number of short reads in the latter. On the other hand, for the viruses/viroids under study, the results showed higher yields of viral sequences in small RNA pool for viroids and viruses with no RNA replicative intermediates (single stranded DNA viruses).http://journal.frontiersin.org/article/10.3389/fmicb.2017.01998/fullnext generation sequencingsmall RNAribosomal RNA depleted total RNAdetectionplant virusesplant viroids |
| spellingShingle | Anja Pecman Anja Pecman Denis Kutnjak Ion Gutiérrez-Aguirre Ian Adams Adrian Fox Neil Boonham Neil Boonham Maja Ravnikar Next Generation Sequencing for Detection and Discovery of Plant Viruses and Viroids: Comparison of Two Approaches Frontiers in Microbiology next generation sequencing small RNA ribosomal RNA depleted total RNA detection plant viruses plant viroids |
| title | Next Generation Sequencing for Detection and Discovery of Plant Viruses and Viroids: Comparison of Two Approaches |
| title_full | Next Generation Sequencing for Detection and Discovery of Plant Viruses and Viroids: Comparison of Two Approaches |
| title_fullStr | Next Generation Sequencing for Detection and Discovery of Plant Viruses and Viroids: Comparison of Two Approaches |
| title_full_unstemmed | Next Generation Sequencing for Detection and Discovery of Plant Viruses and Viroids: Comparison of Two Approaches |
| title_short | Next Generation Sequencing for Detection and Discovery of Plant Viruses and Viroids: Comparison of Two Approaches |
| title_sort | next generation sequencing for detection and discovery of plant viruses and viroids comparison of two approaches |
| topic | next generation sequencing small RNA ribosomal RNA depleted total RNA detection plant viruses plant viroids |
| url | http://journal.frontiersin.org/article/10.3389/fmicb.2017.01998/full |
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