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ARS Home » Southeast Area » Auburn, Alabama » Soil Dynamics Research » Research » Publications at this Location » Publication #402495
Research Project: GxExM Systems Approach to Crop Disease Management

Location: Soil Dynamics Research

Title: Metatranscriptomics approach to study the virome of economically important crops

Author
item ESCALANTE, CESAR - Auburn University
item JACOBSON, ALANA - Auburn University
item Balkcom, Kipling
item CONNER, KASSIE - Auburn University

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 5/16/2023
Publication Date: 8/14/2023
Citation: Escalante, C., Jacobson, A., Balkcom, K.S., Conner, K. 2023. Metatranscriptomics approach to study the virome of economically important crops [ABSTRACT]. In Ravnikar, M., Kutnjak D., Giovani, B., Fox, A., Botermans, M., Oplaat, C., & Mollov, D. (Eds.), Book of abstracts of the ICPP Satellite Event: High-throughput sequencing in plant virology: from discovery to diagnostics (Version v2). Zenodo. https://doi.org/10.5281/zenodo.8298516.
DOI: https://doi.org/10.5281/zenodo.8298516

Interpretive Summary:

Technical Abstract: The use of high throughput sequencing (HTS) has expanded our perspective on the distribution and diversity of plant viruses. Furthermore, due to the increasing number of versatile and improved HTS technologies and the decrease in the cost per sample, implementing HTS has facilitated the diagnosis and discovery of novel viruses. This study aimed to examine the putative virome of economically important crops. Leaf samples were collected from vegetables, ornamentals, and row crops. Information on different nucleic acid extraction methods for HTS, including double-stranded RNA and total RNA, will be presented. Library preparation was performed from pooled samples before sequencing in an Illumina platform. The sequenced libraries were mapped to the host’s reference genome, and the resulting sequences were de novo assembled. Both nucleic acid extraction methods successfully yielded sequences of good quality. A metatranscriptomics analysis revealed complete genome contigs of a variety of known and unidentified putative RNA and DNA plant viruses co-infecting the same host. The information obtained in this investigation will help develop a broader perspective on other viruses present in the tested plant species to determine whether co-infections with other viruses are a factor that might influence (negatively or positively) plant physiology, product quality, and yield.