Effects of tissue type and season on the detection of regulated sugarcane viruses by high throughput sequencing
Abstract High throughput sequencing (HTS) can supplement and may replace diagnostic tests for plant pathogens. However, the methodology and processing of HTS data must first be optimized and standardized to ensure the sensitivity and repeatability of the results. Importation of sugarcane into the Un...
Saved in:
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
CABI
2023-09-01
|
| Series: | CABI Agriculture and Bioscience |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s43170-023-00175-1 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832544917524578304 |
|---|---|
| author | Stephen Bolus Kate Wathen-Dunn Samuel C. Grinstead Xiaojun Hu Martha Malapi Dimitre Mollov |
| author_facet | Stephen Bolus Kate Wathen-Dunn Samuel C. Grinstead Xiaojun Hu Martha Malapi Dimitre Mollov |
| author_sort | Stephen Bolus |
| collection | DOAJ |
| description | Abstract High throughput sequencing (HTS) can supplement and may replace diagnostic tests for plant pathogens. However, the methodology and processing of HTS data must first be optimized and standardized to ensure the sensitivity and repeatability of the results. Importation of sugarcane into the United States is highly regulated, and sugarcane plants are subjected to strict quarantine measures and diagnostic testing, especially for the presence of certain viruses of regulatory concern. Here, we tested whether HTS could reliably detect four RNA and three DNA sugarcane viruses over three seasons (fall, winter, and spring) and in three tissue types (root, stem, and leaves). Using HTS on ribosomal depleted total RNA samples, we reliably detected RNA viruses in all tissue types and across all seasons, but we failed to confidently detect DNA viruses in some samples. We recommend that future optimization be employed to ensure the robust and reliable detection of all regulated sugarcane viruses by HTS. |
| format | Article |
| id | doaj-art-cad2190fb0eb40dc9a9bd3266d04d620 |
| institution | Kabale University |
| issn | 2662-4044 |
| language | English |
| publishDate | 2023-09-01 |
| publisher | CABI |
| record_format | Article |
| series | CABI Agriculture and Bioscience |
| spelling | doaj-art-cad2190fb0eb40dc9a9bd3266d04d6202025-02-03T08:47:22ZengCABICABI Agriculture and Bioscience2662-40442023-09-01411510.1186/s43170-023-00175-1Effects of tissue type and season on the detection of regulated sugarcane viruses by high throughput sequencingStephen Bolus0Kate Wathen-Dunn1Samuel C. Grinstead2Xiaojun Hu3Martha Malapi4Dimitre Mollov5USDA-ARS, National Germplasm Resources LaboratorySugar Research Australia LimitedUSDA-ARS, National Germplasm Resources LaboratoryUSDA-APHIS Plant Germplasm Quarantine ProgramUSDA-APHIS-BRS, Biotechnology Risk Analysis ProgramsUSDA-ARS, Horticultural Crops Disease and Pest Management Research UnitAbstract High throughput sequencing (HTS) can supplement and may replace diagnostic tests for plant pathogens. However, the methodology and processing of HTS data must first be optimized and standardized to ensure the sensitivity and repeatability of the results. Importation of sugarcane into the United States is highly regulated, and sugarcane plants are subjected to strict quarantine measures and diagnostic testing, especially for the presence of certain viruses of regulatory concern. Here, we tested whether HTS could reliably detect four RNA and three DNA sugarcane viruses over three seasons (fall, winter, and spring) and in three tissue types (root, stem, and leaves). Using HTS on ribosomal depleted total RNA samples, we reliably detected RNA viruses in all tissue types and across all seasons, but we failed to confidently detect DNA viruses in some samples. We recommend that future optimization be employed to ensure the robust and reliable detection of all regulated sugarcane viruses by HTS.https://doi.org/10.1186/s43170-023-00175-1SugarcaneVirusHigh throughput sequencingRNA-SeqSeasonTissue |
| spellingShingle | Stephen Bolus Kate Wathen-Dunn Samuel C. Grinstead Xiaojun Hu Martha Malapi Dimitre Mollov Effects of tissue type and season on the detection of regulated sugarcane viruses by high throughput sequencing CABI Agriculture and Bioscience Sugarcane Virus High throughput sequencing RNA-Seq Season Tissue |
| title | Effects of tissue type and season on the detection of regulated sugarcane viruses by high throughput sequencing |
| title_full | Effects of tissue type and season on the detection of regulated sugarcane viruses by high throughput sequencing |
| title_fullStr | Effects of tissue type and season on the detection of regulated sugarcane viruses by high throughput sequencing |
| title_full_unstemmed | Effects of tissue type and season on the detection of regulated sugarcane viruses by high throughput sequencing |
| title_short | Effects of tissue type and season on the detection of regulated sugarcane viruses by high throughput sequencing |
| title_sort | effects of tissue type and season on the detection of regulated sugarcane viruses by high throughput sequencing |
| topic | Sugarcane Virus High throughput sequencing RNA-Seq Season Tissue |
| url | https://doi.org/10.1186/s43170-023-00175-1 |
| work_keys_str_mv | AT stephenbolus effectsoftissuetypeandseasononthedetectionofregulatedsugarcanevirusesbyhighthroughputsequencing AT katewathendunn effectsoftissuetypeandseasononthedetectionofregulatedsugarcanevirusesbyhighthroughputsequencing AT samuelcgrinstead effectsoftissuetypeandseasononthedetectionofregulatedsugarcanevirusesbyhighthroughputsequencing AT xiaojunhu effectsoftissuetypeandseasononthedetectionofregulatedsugarcanevirusesbyhighthroughputsequencing AT marthamalapi effectsoftissuetypeandseasononthedetectionofregulatedsugarcanevirusesbyhighthroughputsequencing AT dimitremollov effectsoftissuetypeandseasononthedetectionofregulatedsugarcanevirusesbyhighthroughputsequencing |