Genome characterization of an Argentinean isolate of alfalfa leaf curl virus

Abstract

We investigated the molecular characteristics of an Argentinean isolate of alfalfa leaf curl virus (ALCV-Arg), a virus of the genus Capulavirus in the family Geminiviridae that was isolated from alfalfa plants showing dwarfism. The genome was found to be 2,750 nucleotides in length. In pairwise comparisons, this ALCV isolate shared 83.2% to 92.6% sequence identity with European ALCV isolates. Sequence comparisons and phylogenetic analysis showed that this isolate combines features of strains A and B of ALCV. Recombination analysis showed that ALCV-Arg is a recombinant isolate that was generated by intraspecific recombination between ALCV strains A and B. The results of this study not only show that ALCV-Arg is unique because it combines features of strains A and B but also show that ALCV naturally infects this forage crop on the American continent.

The Westward Journey of Alfalfa Leaf Curl Virus

“…In addition, this study suggested that ALCV was probably widely distributed across the Mediterranean basin [ 11 ]. Consistent with this hypothesis, ALCV was subsequently reported in 2018 from Jordan, Syria, Lebanon, and Tunisia [ 12 ] as well as from the non-Mediterranean countries Iran [ 13 ] and Argentina [ 14 ].…”

“…All samples from Namibia and South Africa tested negative for ALCV. Overall, 85 full length genome sequences were reported in this study (GenBank accession numbers: MG792020–MG792053; MH603810–MH603860), which were analyzed together with the 35 complete genome sequences recovered in previous studies [ 7 , 11 , 12 , 13 , 14 ] ( Supplementary Materials Table S1 ). The sizes of these 120 complete ALCV genome sequences ranged from 2712 nt to 2769 nt, and they all shared >80.2% genome-wide pairwise identity.…”

Viromes of Ten Alfalfa Plants in Australia Reveal Diverse Known Viruses and a Novel RNA Virus

“…An HTS study of small RNAs from alfalfa in China recently detected AMV, ADV, and ALCV [73] that had previously been identified as components of alfalfa dwarf disease in Argentina [7,8,12]. Recently, a suite of 23 viruses were identified in 655 publicly available alfalfa transcriptome datasets [74].…”

“…For example, in 2010, alfalfa dwarf disease (ADD), which affects hay yield and quality of alfalfa, was reported from Argentina [7]. HTS of ADD-diseased plants revealed the presence of several RNA viruses, AMV, BLRV, alfalfa dwarf virus (ADV; genus Cytorhabdovirus, family Rhabdoviridae) and alfalfa enamovirus 1 (genus Enamovirus, family Luteoviridae), and the DNA virus alfalfa leaf curl virus (ALCV; genus Capulavirus, family Geminiviridae) [8][9][10][11][12]. More recently, alfalfa-associated nucleorhabdovirus (genus Nucleorhabdovirus, family Rhabdoviridae), alfalfa virus F (genus Marafivirus, family Tymoviridae), alfalfa virus S (genus Allexivirus, family Alphaflexiviridae), Medicago sativa deltapartitivirus (genus Deltpartitivirus, family Partitiviridae), and alphapartitiviruses including Medicago sativa alphapatitivirus 1 and 2 (family Partitiviridae) were identified in alfalfa with HTS [13][14][15][16][17][18].…”

Redefining the medicago sativa alphapartitivirus genome sequences

“…In 2011, we observed alfalfa plants showing symptoms of shortened internodes (bushy appearance), leaf puckering and varying-sized vein enations on abaxial leaf surfaces (Bejerman et al, 2011). Deep sequencing of alfalfa plants collected in central region of Argentina showing the dwarfism symptoms, revealed the presence of four RNA viruses: alfalfa mosaic virus (AMV), alfalfa dwarf virus (ADV), alfalfa enamovirus-1 (AEV-1) and bean leaf roll virus (BLRV) (Bejerman et al, 2015; 2016; Trucco et al, 2014, 2016) and one DNA virus: alfalfa leaf curl virus (ALCV) (Bejerman et al, 2018). Furthermore, four assembled sequences (contigs) analyzed by BlastX searches shared significant identity (E-value = 0), to the capsid and replication proteins encoded by alphapartitiviruses.…”