Analysis of Wheat Virome in Korea Using Illumina and Oxford Nanopore Sequencing Platforms
Abstract
:1. Introduction
2. Results
2.1. Virus Identification by ONT Sequencing
2.2. Virus Identification by Illumina Sequencing
2.3. Genome Assembly
2.4. Phylogenetic Analyses of Identified Viruses
2.5. Validation of the Identified Virus by RT-PCR
3. Discussion
4. Materials and Methods
4.1. Sample Preparation and RNA Extraction
4.2. Library Preparation for ONT Platform and Virus Identification
4.3. Library Preparation for Illumina Platform and Virus Identification
4.4. Genome Mapping of Viral Sequences
4.5. Phylogenetic Analysis
4.6. Confirmation of the Identified Viruses by RT-PCR
4.7. Data Availability
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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HTS Platform | Library ID | Raw Reads | Trimmed Reads | SRA Accession Number | ||||||
Total Reads | Mini Read Length | Max Read Length | Mean Read Length | Total Reads | Mini Read Length | Max Read Length | Mean Read Length | |||
ONT | JN-ONT | 772,355 | 91 | 8222 | 412.8 | 761,277 | 1 | 8222 | 296.3 | SRR22371364 |
JB-ONT | 490,030 | 55 | 12,301 | 340.1 | 485,491 | 1 | 12,301 | 272 | SRR22371365 | |
GN-ONT | 1,177,844 | 82 | 78,921 | 325.1 | 1,160,201 | 1 | 78,921 | 221.8 | SRR22371366 | |
HTS platform | Library ID | Total reads based (bp) | Total reads | Q30 (%) | Virus data | Virus annotated contigs | SRA Accession Number | |||
Sum reads | Sum bases (bp) | |||||||||
Illumina | JN-Ill | 5,478,870,712 | 36,283,912 | 95.52 | 19,138 | 2,550,819 | 21 | SRR16774430 | ||
JB-Ill | 5,931,982,150 | 39,284,650 | 95.2 | 220,452 | 32,179,884 | 38 | SRR16774429 | |||
GN-Ill | 5,327,334,360 | 35,280,360 | 95.04 | 120,742 | 17,615,293 | 46 | SRR16774428 |
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Lee, H.-J.; Kim, S.-M.; Jeong, R.-D. Analysis of Wheat Virome in Korea Using Illumina and Oxford Nanopore Sequencing Platforms. Plants 2023, 12, 2374. https://doi.org/10.3390/plants12122374
Lee H-J, Kim S-M, Jeong R-D. Analysis of Wheat Virome in Korea Using Illumina and Oxford Nanopore Sequencing Platforms. Plants. 2023; 12(12):2374. https://doi.org/10.3390/plants12122374
Chicago/Turabian StyleLee, Hyo-Jeong, Sang-Min Kim, and Rae-Dong Jeong. 2023. "Analysis of Wheat Virome in Korea Using Illumina and Oxford Nanopore Sequencing Platforms" Plants 12, no. 12: 2374. https://doi.org/10.3390/plants12122374