Identification of emerging viral genomes in transcriptomic datasets of alfalfa (Medicago sativa L.)

Authors: Jiang, Peng; Shao, Jonathan; Nemchinov, Lev

Submitted to: Virology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/22/2019
Publication Date: 12/10/2019
Citation: Jiang, P., Shao, J.Y., Nemchinov, L.G. 2019. Identification of emerging viral genomes in transcriptomic datasets of alfalfa (Medicago sativa L.). Virology Journal. 16:153. https://doi.org/10.1186/s12985-019-1257-y.
DOI: https://doi.org/10.1186/s12985-019-1257-y

Interpretive Summary: Publicly available transcriptomic datasets became a valuable tool for discovery of new pathogens, particularly viruses. In this study, several emerging viral genomes previously not found or experimentally confirmed in alfalfa were identified in the plant datasets retrieved from the National Center for Biotechnology Information. The results improve our knowledge on diversity of viruses infecting alfalfa and demonstrate utility of transcriptomic databases for discovery of new pathogens. Data reported in this study can be used by plant pathologists and extension specialists for diagnostics and identification of these viruses in alfalfa.

Technical Abstract: Alfalfa (Medicago sativa L.) is one of the most extensively cultivated forage legume in the world. It has recently become the third most valuable field crop in the United States with an estimated worth of over $9.3 billion, $1.2 billion more than wheat, according to the National Alfalfa and Forage Alliance. Alfalfa productivity is often limited by various biotic and abiotic components in the ecosystem. With the increase in production of monocropped alfalfa, infectious diseases, including viruses, became more common. Traditionally, viral infections of alfalfa are considered by producers, breeders, growers and research community as diseases of limited importance. Nonetheless, they are widespread in major alfalfa cultivation areas and their contribution to the severity of complex infections involving multi-pathogens is poorly known. Recently, many emerging viral diseases of alfalfa have been described that have a potential to cause serious yield losses. These include a rhabdovirus, diagnosed in alfalfa plants displaying multiple abnormalities; a new enamovirus from Argentina, alfalfa enamovirus-1 (AEV-1), detected in alfalfa plants showing dwarfism symptoms; an AEV isolate from Sudan, designated AEV-2; a new species of the family Alphaflexiviridae discovered in alfalfa samples exhibiting chlorosis and stunting and alfalfa leaf curl virus found in plants displaying leaf curling symptoms. Alfalfa appears to be widely infected with seed-transmitted partitiviruses and their biological significance on alfalfa is currently unknown and require further investigation. Publicly available transcriptomic datasets became a valuable tool for discovery of new pathogens, particularly viral sequences. Retrieval of complete or nearly complete viral genomes from transcriptomic data improves our knowledge on the diversity and host range of these pathogens and provides essential instruments for their diagnostics and characterization. In this study, we performed a systematic survey of alfalfa transcriptomic datasets publicly available at NCBI. The survey indicated that ~ 60% of Medicago sativa samples employed in generation of the deposited datasets contained viruses. Three emerging viruses in a coding-complete state have been identified that were never reported in M. sativa prior to this study: two strains of cnidium vein yellowing virus, lychnis mottle virus and Cactus virus X. We have also presented a first in silico and experimental identification of Medicago sativa amalgavirus 1 in US alfalfa germplasm, significant because amalgaviruses are known to be vertically transmitted through seeds. The results improve our knowledge on the diversity and host range of viruses infecting alfalfa and provide essential instruments for their diagnostics and characterization. Further research is required to confirm in silico identification of these viruses, determine their symptomatology, geographic distribution and economic importance to the alfalfa industry.