Viromes of Hungarian Peach Trees Identified by High-Throughput Sequencing of Small RNAs
Abstract
:1. Introduction
2. Results
2.1. Small RNA HTS Revealed the Presence of Both Regulated and Non-Regulated Viruses
2.2. PPV Is Present in the Isolator
2.3. Luteoviruses: NSPaV and PaLV Are Present Both in the Isolator and in the Open Field
2.4. Frequent Presence of PLMVd in the Tested Trees Was Shown by sRNA HTS and RT-LAMP, but Not with Biological Assays on GF305
2.5. Infection with Luteoviruses and PLMVd Are Frequent in the Isolator, but Cannot Be Ascribed as the Only Cause of the Trees’ Decline
2.6. Phylogenetic Analysis of the Viral Strains
3. Discussion
4. Materials and Methods
4.1. Plant Material and Sample Preparation
4.2. Pipeline for the Data Evaluation of the HTS Results (Bioinformatics)
4.3. Confirmation of the Obtained Results by RT-PCR, Northern Blot and Sanger Sequencing
4.4. RT—LAMP Assay for PLMVd Detection
4.5. Biological Assay
4.6. Phylogenetical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Library code | Cultivar | Isolator House/Open Field Stock Nursery | Number of Tested Cultivars | Number of Tested Trees |
---|---|---|---|---|
1_Sc_ih | Springcrest | isolator house | 1 | 4 |
2_Sc_sn | Springcrest | stock nursery/open field | 1 | 2 |
3_Ch_ih | Cresthaven | isolator house | 1 | 4 |
4_Ch_sn | Cresthaven | stock nursery/open field | 1 | 2 |
5_Peach_ih | 1_Flavortop | isolator house | 10 | 10 |
2_Nektár H | ||||
3_Venus | ||||
4_Incrocio Pieri | ||||
5_Cresthaven | ||||
6_Redhaven | ||||
7_Champion | ||||
8_Suncrest | ||||
9_Aranycsillag | ||||
10_Apolka |
Library Code | Bioinformatics Analysis | Viruses | Viroid | |||
---|---|---|---|---|---|---|
PPV | NSPaV | PaLV | ChaLV | PLMVd | ||
1_Sc_ih | n of virus specific contigs | 94 | 2 | 17 | 0 | 0 |
n of non-redundant reads | 3867 | 1353 | 2368 | 677 | 17 | |
RPM | 4908 | 462 | 1296 | 197 | 3 | |
% coverage | 68.3 | 89.7 | 93.9 | 48.3 | 51.6 | |
2_Sc_sn | n of virus specific contigs | 1 | 0 | 13 | 1 | 0 |
n of non-redundant reads | 637 | 166 | 2547 | 714 | 6 | |
RPM | 122 | 46 | 1759 | 312 | 1 | |
% coverage | 52.0 | 32.4 | 94.3 | 51.2 | 291 | |
3_Ch_ih | n of virus specific contigs | 0 | 0 | 0 | 0 | 14 |
n of non-redundant reads | 102 | 56 | 1012 | 244 | 2817 | |
RPM | 34 | 9 | 307 | 47 | 43,915 | |
% coverage | 14.2 | 13.5 | 76.9 | 29.4 | 99.1 | |
4_Ch_sn | n of virus specific contigs | 0 | 0 | 0 | 0 | 20 |
n of non-redundant reads | 143 | 1291 | 95 | 66 | 3586 | |
RPM | 33 | 350 | 16 | 14 | 63,289 | |
% coverage | 17.1 | 81.5 | 16.5 | 12.1 | 100 | |
5_peach_ih | n of virus specific contigs | 0 | 16 | 41 | 1 | 89 |
n of non-redundant reads | 509 | 1627 | 3076 | 848 | 5462 | |
RPM | 79 | 239 | 670 | 125 | 38,197 | |
% coverage | 43.9 | 93.6 | 98.5 | 61.1 | 100 |
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Barath, D.; Jaksa-Czotter, N.; Varga, T.; Varallyay, E. Viromes of Hungarian Peach Trees Identified by High-Throughput Sequencing of Small RNAs. Plants 2022, 11, 1591. https://doi.org/10.3390/plants11121591
Barath D, Jaksa-Czotter N, Varga T, Varallyay E. Viromes of Hungarian Peach Trees Identified by High-Throughput Sequencing of Small RNAs. Plants. 2022; 11(12):1591. https://doi.org/10.3390/plants11121591
Chicago/Turabian StyleBarath, Daniel, Nikoletta Jaksa-Czotter, Tunde Varga, and Eva Varallyay. 2022. "Viromes of Hungarian Peach Trees Identified by High-Throughput Sequencing of Small RNAs" Plants 11, no. 12: 1591. https://doi.org/10.3390/plants11121591