Studying strands polarity of different viroids and their combinations in infected hop plants
Hop plant (Humulus lupulus L.) is an important industrial crop, grown for harvesting hop cones however, it is a host to four different viroids as well. The nature of viroid infections is not entirely clarified. In our work, we focused on analyzing viroid accumulation and their strands polarity throu...
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| Language: | English |
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University of Ljubljana Press (Založba Univerze v Ljubljani)
2020-03-01
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| Series: | Acta Agriculturae Slovenica |
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| Online Access: | https://journals.uni-lj.si/aas/article/view/12896 |
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| author | Andrej SEČNIK Sebastjan RADIŠEK Nataša ŠTAJNER Jernej JAKŠE |
| author_facet | Andrej SEČNIK Sebastjan RADIŠEK Nataša ŠTAJNER Jernej JAKŠE |
| author_sort | Andrej SEČNIK |
| collection | DOAJ |
| description | Hop plant (Humulus lupulus L.) is an important industrial crop, grown for harvesting hop cones however, it is a host to four different viroids as well. The nature of viroid infections is not entirely clarified. In our work, we focused on analyzing viroid accumulation and their strands polarity through RNA sequencing and reverse transcription polymerase chain reaction in real time. RNA-seq data indicate that viroids amplify until saturation further demonstrating plant's biological capacity. Negative fold changes in accumulation of individual viroids between hop samples with single and multiple infections are suggesting an antagonistic relationship amongst viroids, where citrus bark cracking viroid seems to be the least and hop stunt viroid the most sensitive to the other two. RNA-seq data also show that on average (−) viroid strand is dominating over (+), especially for the citrus bark cracking viroid. Reverse transcription polymerase chain reaction in real time results from strand polarity analysis seem to be less consistent between different combinations of infection but are showing level of conformity with RNA-seq in the case of citrus bark cracking viroid. |
| format | Article |
| id | doaj-art-1a7633d8bbfe486291f0133c637f2f02 |
| institution | OA Journals |
| issn | 1854-1941 |
| language | English |
| publishDate | 2020-03-01 |
| publisher | University of Ljubljana Press (Založba Univerze v Ljubljani) |
| record_format | Article |
| series | Acta Agriculturae Slovenica |
| spelling | doaj-art-1a7633d8bbfe486291f0133c637f2f022025-08-20T02:05:13ZengUniversity of Ljubljana Press (Založba Univerze v Ljubljani)Acta Agriculturae Slovenica1854-19412020-03-01115119320110.14720/aas.2020.115.1.131919288Studying strands polarity of different viroids and their combinations in infected hop plantsAndrej SEČNIK0Sebastjan RADIŠEK1Nataša ŠTAJNER2Jernej JAKŠE3University of Ljubljana, Biotechnical Faculty, Dept. of Agronomy, Jamnikarjeva 101, SI-1000 Ljubljana SloveniaSlovenian Institute of Hop Research and Brewing, SloveniaUniversity of Ljubljana, Biotechnical Faculty, Dept. of Agronomy, Jamnikarjeva 101, SI-1000 Ljubljana SloveniaUniversity of Ljubljana, Biotechnical Faculty, Dept. of Agronomy, Jamnikarjeva 101, SI-1000 Ljubljana SloveniaHop plant (Humulus lupulus L.) is an important industrial crop, grown for harvesting hop cones however, it is a host to four different viroids as well. The nature of viroid infections is not entirely clarified. In our work, we focused on analyzing viroid accumulation and their strands polarity through RNA sequencing and reverse transcription polymerase chain reaction in real time. RNA-seq data indicate that viroids amplify until saturation further demonstrating plant's biological capacity. Negative fold changes in accumulation of individual viroids between hop samples with single and multiple infections are suggesting an antagonistic relationship amongst viroids, where citrus bark cracking viroid seems to be the least and hop stunt viroid the most sensitive to the other two. RNA-seq data also show that on average (−) viroid strand is dominating over (+), especially for the citrus bark cracking viroid. Reverse transcription polymerase chain reaction in real time results from strand polarity analysis seem to be less consistent between different combinations of infection but are showing level of conformity with RNA-seq in the case of citrus bark cracking viroid.https://journals.uni-lj.si/aas/article/view/12896hop plantviroidsrt-qpcrngsrna sequencing |
| spellingShingle | Andrej SEČNIK Sebastjan RADIŠEK Nataša ŠTAJNER Jernej JAKŠE Studying strands polarity of different viroids and their combinations in infected hop plants Acta Agriculturae Slovenica hop plant viroids rt-qpcr ngs rna sequencing |
| title | Studying strands polarity of different viroids and their combinations in infected hop plants |
| title_full | Studying strands polarity of different viroids and their combinations in infected hop plants |
| title_fullStr | Studying strands polarity of different viroids and their combinations in infected hop plants |
| title_full_unstemmed | Studying strands polarity of different viroids and their combinations in infected hop plants |
| title_short | Studying strands polarity of different viroids and their combinations in infected hop plants |
| title_sort | studying strands polarity of different viroids and their combinations in infected hop plants |
| topic | hop plant viroids rt-qpcr ngs rna sequencing |
| url | https://journals.uni-lj.si/aas/article/view/12896 |
| work_keys_str_mv | AT andrejsecnik studyingstrandspolarityofdifferentviroidsandtheircombinationsininfectedhopplants AT sebastjanradisek studyingstrandspolarityofdifferentviroidsandtheircombinationsininfectedhopplants AT natasastajner studyingstrandspolarityofdifferentviroidsandtheircombinationsininfectedhopplants AT jernejjakse studyingstrandspolarityofdifferentviroidsandtheircombinationsininfectedhopplants |