Comparative Microbiome Study of Mummified Peach Fruits by Metagenomics and Metatranscriptomics
Abstract
:1. Introduction
2. Results
2.1. Identification of Organisms in the Mummified Peach Fruits by DNA Shotgun Sequencing and RNA-Sequencing
2.2. Taxonomic Classification Using KRAKEN 2 Program
2.3. Classification of Identified Organisms on the Three Mummified Peach Fruits According to Domain
2.4. Classification of Identified Fungi According to Fungal Taxonomy
2.5. Major Fungal Species in Each Library
2.6. Comparison of Identified Fungal Species among Different Libraries and Samples
2.7. Classification of Identified Bacteria According to Bacterial Taxonomy
2.8. Identification of Viruses from Six Libraries
2.9. Identification of Plant Viruses, Viroids and a Novel Mycovirus
3. Discussion
4. Materials and Methods
4.1. Sample Collection
4.2. Extraction of Nucleic Acids from the Mummified Peach Fruits
4.3. Library Preparation and Next-Generation Sequencing
4.4. Bioinformatic Analyses
4.5. De Novo Transcriptome Assembly and Virus Identification
4.6. RT-PCR and Sanger-Sequencing
4.7. Construction of Phylogenetic Tree for the Novel Virus
4.8. Confirmation of the Host for the Novel Mycovirus
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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R1 | R4 | R7 | ||||||
---|---|---|---|---|---|---|---|---|
Virus | Accession No. | Size | Coverage | Reads | Coverage | Reads | Coverage | Reads |
Apple chlorotic leaf spot virus | NC_001409.1 | 7555 | 0 | 0 | 0.3273 | 36 | 0 | 0 |
Hop stunt viroid | NC_001351.1 | 302 | 0.5364 | 2 | 19.3444 | 68 | 0 | 0 |
Peach latent mosaic viroid | NC_003636.1 | 337 | 7.5905 | 30 | 8.095 | 35 | 1.9822 | 8 |
Asian prunus virus 2 | NC_028868.1 | 9362 | 0.0092 | 1 | 0.9509 | 110 | 0 | 0 |
Asian prunus virus 3 | NC_028975.1 | 9654 | 0 | 0 | 0.1859 | 28 | 0 | 0 |
Monilinia umbra-like virus | MT681745 | 4147 | 29.8676 | 1272 | 117.3161 | 4904 | 0.2358 | 10 |
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Jo, Y.; Back, C.-G.; Choi, H.; Cho, W.K. Comparative Microbiome Study of Mummified Peach Fruits by Metagenomics and Metatranscriptomics. Plants 2020, 9, 1052. https://doi.org/10.3390/plants9081052
Jo Y, Back C-G, Choi H, Cho WK. Comparative Microbiome Study of Mummified Peach Fruits by Metagenomics and Metatranscriptomics. Plants. 2020; 9(8):1052. https://doi.org/10.3390/plants9081052
Chicago/Turabian StyleJo, Yeonhwa, Chang-Gi Back, Hoseong Choi, and Won Kyong Cho. 2020. "Comparative Microbiome Study of Mummified Peach Fruits by Metagenomics and Metatranscriptomics" Plants 9, no. 8: 1052. https://doi.org/10.3390/plants9081052