Submitted to: Genome Announcements
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/18/2017
Publication Date: 7/6/2017
Citation: Nemchinov, L.G., Grinstead, S.C., Mollov, D.S. 2017. A first report and complete genome sequence of alfalfa enamovirus from Sudan. Genome Announcements. e00531-17. doi: 10.1128/genomeA.00531-17.
Interpretive Summary: Alfalfa is the most extensively cultivated forage legume in the world and the fourth most widely grown crop in the US, planted on more than 23 million acres in all 50 states. The estimated worth of alfalfa hay is $8.1 billion annually. Alfalfa productivity has often been affected and limited by different diseases, insect pests and abiotic stress factors. Minimizing these losses is a major area of concern in alfalfa industry. Alfalfa may serve as a natural reservoir for dissemination of viruses to other agriculturally important crops. In recent years, emerging viral diseases of alfalfa with the capacity to cause serious yield losses were described. Synergetic interactions of multiple viral infections can also threaten alfalfa production. In this work, we report a first incidence and complete genome sequence of alfalfa enamovirus in a new location: Sudan, Northern Africa. To date, this recently discovered virus has only been described in Argentina where it was associated with major alfalfa dwarfism disease threatening alfalfa production in the country. Geography of new and emerging plant pathogens and their dissemination are essential for agricultural security measures. It is also important to give the community of plant pathologists the most complete information on each novel viral sequence. Results of this study will be of interest to the researchers in academia and government organizations working in the fields of plant virology and alfalfa improvement.
Technical Abstract: A full genome sequence of a viral pathogen, provisionally named alfalfa enamovirus 2 (AEV-2), was reconstructed from short reads obtained by Illumina RNA sequencing of alfalfa sample originating from Sudan. Ambiguous nucleotides in the resultant consensus assembly and identity of the predicted virus were clarified and confirmed by RT-PCR with primers derived from the Illumina-generated sequence. The AEV-2 genome consists of 5,729 nucleotides and contains five open reading frames. Based on the high nucleotide and amino acid identity, AEV-2 represents a strain of a recently discovered alfalfa enamovirus 1 that has only been described in Argentina where it caused a major alfalfa dwarfism disease. Although the exact origin of alfalfa enamovirus is unknown, it is likely that its evolution and dissemination into novel areas are linked to the host geography. The first incidence of the virus in a different location (Sudan) may suggest that the virus is widespread and can also occur in southwestern Asia and Iran, a geographic origin of alfalfa. The complete genomic sequence of AEV-2 has been deposited in GenBank under accession number KY985463.