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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Molecular Plant Pathology Laboratory » Research » Publications at this Location » Publication #356909
Title: First report of alphapartitiviruses infecting alfalfa (Medicago sativa) in the United States

Author
item Nemchinov, Lev
item LEE, MAYA - Towson University
item Shao, Jonathan

Submitted to: Genome Announcements
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/7/2018
Publication Date: 11/29/2018
Citation: Nemchinov, L.G., Lee, M., Shao, J.Y. 2018. First report of alphapartitiviruses infecting alfalfa (Medicago sativa) in the United States. Genome Announcements. https://doi.org/mra.asm.org/content/7/21/e01266-18.

Interpretive Summary: We report a first evidence that alfalfa varieties in the United States could be widely infected with cryptic viruses. The partitiviruses are associated with persistent infections of fungal, protozoan and plant hosts. Their relationship with plant hosts is not well understood. While examining transcriptomic data derived from two US alfalfa check cultivars, we found that all alfalfa plants were infected with partitivirus recently reported from Korea. Since partitiviruses are vertically transmitted via seeds, the seeds of these standard check cultivars that are commonly used in research and breeding, were most probably infected with the virus. The biological significance or any negative effects of the virus on alfalfa are currently unknown and require further investigation. Results of this study will be of interest to the researchers in academia and government organizations working in the fields of plant virology, epidemiology and alfalfa improvement.

Technical Abstract: The partitiviruses are associated with persistent infections of fungal, protozoan and plant hosts. Plant partitiviruses are transmitted by ovule and by pollen to the seed embryo and may be associated with mutualistic effects. Two novel species of the family Partitiviridae, Medicago sativa alphapartitivirus 1 (MsAPV1) and Medicago sativa deltapartitivirus 1 (MsDPV1), belonging to the genera Alphapartitivirus and Deltapartitivirus, respectively, were recently reported from Korea. They were computationally deduced from alfalfa transcriptomic data published and uploaded online by a group of authors from China. In this work, while examining transcriptomic data derived from two US alfalfa cultivars, Maverick and ZG 9830, we found that most of the plants used in the experiment contained reads that shared high percent identity with MsAPV1 (GenBank IDs:MF443256.1 and 443257.1). Complete viral genomes were obtained from both varieties by assembly of reads generated by Illumina RNA-seq and by 5’/3’ RACE amplification of cDNA ends (cv. Maverick). The assembled viral genomes were typical for the genus Alphapartitivirus and contained two monocistronic segments: dsRNA1, encoding RNA-dependent RNA polymerase (RdRP) and dsRNA2, encoding viral coat protein (CP). Both isolates (from cv. Maverick and cv. ZG9830) were nearly identical to MsAPV1. At the nucleotide level, the dsRNA1 of Maverick and ZG9830 isolates was 98.5% and 99.9% identical to the RdRP of MsAPV1, respectively. dsRNA2 (CP) was 99.9% (Maverick) and 99.6% (ZG9830) identical to the CP segment of MsAPV1. The average percentage of the nucleotide sequences of Maverick and ZG9830 isolates aligned to the respective segments of MsAPV1 (query coverage) was 97.25% (BLAST). At the amino acid level, the RdRP of both isolates, was 100% identical to the RdRP of MsAPV1 and the CP segment was 99.6% and 99.8% identical (Maverick and ZG9830, respectively) to the CP of MsAPV1. Comparison of the two US isolates showed 98% nucleotide identity for the RdRP and 99.6% for the CP region. At the amino acid level, their RdRPs and CPs were 99.8% and 99.6% identical, respectively. Based on these findings, the US isolates of the virus represent closely related variants of MsAPV1, which may not be a coincidence, because the original transcriptomic study reported from China also employed cv. Maverick, that was introduced to China from the United States. This is the first evidence that alfalfa cultivars in the US could be widely infected with seed-transmitted cryptic virus of the genus Alphapartitivirus. The biological significance or any negative effects of the virus on alfalfa are currently unknown and require further investigation. The complete genomic sequences of the virus isolates have been deposited in GenBank.