Location: Soil Dynamics Research
Title: Metatranscriptomics approach to study the virome of economically important cropsAuthor
ESCALANTE, CESAR - Auburn University | |
JACOBSON, ALANA - Auburn University | |
Balkcom, Kipling | |
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. |