Skip to main content
ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Molecular Plant Pathology Laboratory » Research » Publications at this Location » Publication #338503

Title: Complete nucleotide sequence and genome organization of a novel allexivirus from alfalfa (Medicago sativa)

item Nemchinov, Lev
item Grinstead, Sam
item Mollov, Dimitre

Submitted to: APS Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 3/15/2017
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: A new species of the family Alphaflexiviridae provisionally named Alfalfa virus S (AVS) was diagnosed in alfalfa samples originating from Sudan. A complete nucleotide sequence of the viral genome consisting of 8,349 nucleotides excluding the 3’ poly(A) tail was determined by Illumina NGS technology and 5’ RACE system (Thermo Fisher Scientific) using total RNA extracted from infected plants. BLAST search revealed that the virus shares the greatest degree of sequence identity with members of the family Alphaflexiviridae, genus Allexivirus. The AVS genome contains six computationally predicted tentative open reading frames (ORF): viral replication protein, triple gene block protein 1 (TGB1), TGB2, putative TGB 3-like protein, unknown 38.4 kDa protein resembling serine-rich 40 kDa protein characteristic for allexiviruses, and coat protein (CP). However, it appears that AVS lacks a clear 3’ proximal ORF that is typical for allexiviruses and encodes a nucleic acid-binding protein. On the nucleotide level, the next closest species to the AVS are not yet classified Arachis pintoi virus A (54.6% identities); unassigned species within the family Alphaflexiviridae, Blackberry virus E (50.6%); and the type member of the genus Allexivirus, Shallot virus X (49.7%) (PASC tool, Bao et al., 2014). DIG-labeled RNA probes generated from cloned AVS P38.4 and CP cDNAs successfully hybridized to the total RNA extracted from infected alfalfa tissues in dot blot assays thus confirming identity of the virus. To the best of our knowledge, this is the first report on the presence of a putative allexivirus in alfalfa (Medicago sativa).