High-Throughput Sequencing Reveals Tobacco and Tomato Ringspot Viruses in Pawpaw
Pawpaw (<i>Asimina triloba</i>) trees exhibiting stunting and foliar mosaic, chlorosis, or distortions were observed in New York. In 2021, leaf samples from two symptomatic trees and a sapling, as well as two asymptomatic trees, were tested for the presence of viruses and viroids by high...
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| Format: | Article |
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MDPI AG
2022-12-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/11/24/3565 |
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| author | Jiyeong Choi Anya Clara Osatuke Griffin Erich Kristian Stevens Min Sook Hwang Maher Al Rwahnih Marc Fuchs |
| author_facet | Jiyeong Choi Anya Clara Osatuke Griffin Erich Kristian Stevens Min Sook Hwang Maher Al Rwahnih Marc Fuchs |
| author_sort | Jiyeong Choi |
| collection | DOAJ |
| description | Pawpaw (<i>Asimina triloba</i>) trees exhibiting stunting and foliar mosaic, chlorosis, or distortions were observed in New York. In 2021, leaf samples from two symptomatic trees and a sapling, as well as two asymptomatic trees, were tested for the presence of viruses and viroids by high-throughput sequencing (HTS) using total RNA after ribosomal RNA depletion. HTS sequence information revealed tobacco ringspot virus (TRSV) and tomato ringspot virus (ToRSV) in symptomatic but not in asymptomatic leaves. HTS reads and de novo-assembled contigs covering the genomes of both viruses were obtained, with a higher average read depth for RNA2 than RNA1. The occurrence of TRSV and ToRSV was confirmed in the original leaf samples used for HTS and 12 additional trees and saplings from New York and Maryland in 2022 by RT-PCR combined with Sanger sequencing, and DAS-ELISA. Single infections by TRSV in 11 of 14 trees and dual infections by TRSV and ToRSV in 3 of 14 trees were identified. The nucleotide sequence identity of partial gene fragments of TRSV and ToRSV was high among pawpaw isolates (94.9–100% and 91.8–100%, respectively) and between pawpaw isolates and isolates from other horticultural crops (93.6–100% and 71.3–99.3%, respectively). This study is the first to determine the virome of pawpaw. |
| first_indexed | 2024-03-09T15:56:12Z |
| format | Article |
| id | doaj.art-223997924f5043e5a7dc0fb0ad66d3c1 |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-09T15:56:12Z |
| publishDate | 2022-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-223997924f5043e5a7dc0fb0ad66d3c12023-11-24T17:29:28ZengMDPI AGPlants2223-77472022-12-011124356510.3390/plants11243565High-Throughput Sequencing Reveals Tobacco and Tomato Ringspot Viruses in PawpawJiyeong Choi0Anya Clara Osatuke1Griffin Erich2Kristian Stevens3Min Sook Hwang4Maher Al Rwahnih5Marc Fuchs6School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456, USACornell Cooperative Extension, Cornell University, Ithaca, NY 14853, USASchool of Integrative Plant Science, Horticulture, Cornell University, Ithaca, NY 14853, USADepartment of Plant Pathology, Foundation Plant Services, University of California, Davis, CA 95616, USADepartment of Plant Pathology, Foundation Plant Services, University of California, Davis, CA 95616, USADepartment of Plant Pathology, Foundation Plant Services, University of California, Davis, CA 95616, USASchool of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456, USAPawpaw (<i>Asimina triloba</i>) trees exhibiting stunting and foliar mosaic, chlorosis, or distortions were observed in New York. In 2021, leaf samples from two symptomatic trees and a sapling, as well as two asymptomatic trees, were tested for the presence of viruses and viroids by high-throughput sequencing (HTS) using total RNA after ribosomal RNA depletion. HTS sequence information revealed tobacco ringspot virus (TRSV) and tomato ringspot virus (ToRSV) in symptomatic but not in asymptomatic leaves. HTS reads and de novo-assembled contigs covering the genomes of both viruses were obtained, with a higher average read depth for RNA2 than RNA1. The occurrence of TRSV and ToRSV was confirmed in the original leaf samples used for HTS and 12 additional trees and saplings from New York and Maryland in 2022 by RT-PCR combined with Sanger sequencing, and DAS-ELISA. Single infections by TRSV in 11 of 14 trees and dual infections by TRSV and ToRSV in 3 of 14 trees were identified. The nucleotide sequence identity of partial gene fragments of TRSV and ToRSV was high among pawpaw isolates (94.9–100% and 91.8–100%, respectively) and between pawpaw isolates and isolates from other horticultural crops (93.6–100% and 71.3–99.3%, respectively). This study is the first to determine the virome of pawpaw.https://www.mdpi.com/2223-7747/11/24/3565pawpawnepovirustobacco ringspot virustomato ringspot virushigh-throughput sequencing |
| spellingShingle | Jiyeong Choi Anya Clara Osatuke Griffin Erich Kristian Stevens Min Sook Hwang Maher Al Rwahnih Marc Fuchs High-Throughput Sequencing Reveals Tobacco and Tomato Ringspot Viruses in Pawpaw Plants pawpaw nepovirus tobacco ringspot virus tomato ringspot virus high-throughput sequencing |
| title | High-Throughput Sequencing Reveals Tobacco and Tomato Ringspot Viruses in Pawpaw |
| title_full | High-Throughput Sequencing Reveals Tobacco and Tomato Ringspot Viruses in Pawpaw |
| title_fullStr | High-Throughput Sequencing Reveals Tobacco and Tomato Ringspot Viruses in Pawpaw |
| title_full_unstemmed | High-Throughput Sequencing Reveals Tobacco and Tomato Ringspot Viruses in Pawpaw |
| title_short | High-Throughput Sequencing Reveals Tobacco and Tomato Ringspot Viruses in Pawpaw |
| title_sort | high throughput sequencing reveals tobacco and tomato ringspot viruses in pawpaw |
| topic | pawpaw nepovirus tobacco ringspot virus tomato ringspot virus high-throughput sequencing |
| url | https://www.mdpi.com/2223-7747/11/24/3565 |
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