HTS-Based Diagnostics of Sugarcane Viruses: Seasonal Variation and Its Implications for Accurate Detection

Autor:	Clint McFarland, Joseph A Foster, Bishwo N. Adhikari, Martha Malapi-Wight, Leticia Hendrickson, Clarissa J. Maroon-Lango, Jing Zhou, Oscar P. Hurtado-Gonzales
Rok vydání:	2021
Předmět:	Germplasm Genome Viral Computational biology Biology sugarcane virus Microbiology Genome Article Deep sequencing Plant Viruses law.invention chemistry.chemical_compound sequencing depth law Virology Quarantine Virus classification Plant Diseases seasonal variation metagenomics quarantine High-Throughput Nucleotide Sequencing Reproducibility of Results RNA QR1-502 Saccharum Infectious Diseases chemistry Metagenomics Seasons DNA
Zdroj:	Viruses, Vol 13, Iss 1627, p 1627 (2021) Viruses Volume 13 Issue 8
ISSN:	1999-4915
DOI:	10.3390/v13081627
Popis:	Rapid global germplasm trade has increased concern about the spread of plant pathogens and pests across borders that could become established, affecting agriculture and environment systems. Viral pathogens are of particular concern due to their difficulty to control once established. A comprehensive diagnostic platform that accurately detects both known and unknown virus species, as well as unreported variants, is playing a pivotal role across plant germplasm quarantine programs. Here we propose the addition of high-throughput sequencing (HTS) from total RNA to the routine quarantine diagnostic workflow of sugarcane viruses. We evaluated the impact of sequencing depth needed for the HTS-based identification of seven regulated sugarcane RNA/DNA viruses across two different growing seasons (spring and fall). Our HTS analysis revealed that viral normalized read counts (RPKM) was up to 23-times higher in spring than in the fall season for six out of the seven viruses. Random read subsampling analyses suggested that the minimum number of reads required for reliable detection of RNA viruses was 0.5 million, with a viral genome coverage of at least 92%. Using an HTS-based total RNA metagenomics approach, we identified all targeted viruses independent of the time of the year, highlighting that higher sequencing depth is needed for the identification of DNA viruses.
Databáze:	OpenAIRE
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