Molecular characterization of the Garlic virus B genome and evidence of allexivirus recombination

CELLI M G; PEROTTO M C; LUCIANI C. E.; POZZI E. A.; CONCI V. C

EUROPEAN JOURNAL OF PLANT PATHOLOGY

SPRINGER

Año: 2019

0929-1873

ABSTRACTMolecular characterization isimportant for differentiating allexiviruses species, since detection byserological methods may be uncertain. Eight different species have beenreported as infecting garlic: Garlicvirus A, B, C, D, E, X (GarV-A, B, C, D, E, X), Shallot virus X (ShVX) and Garlicmite-borne filamentous virus (GarMbFV), and the complete genome is knownfor six of these. This work reports for the first time the complete sequence ofGarV-B and makes a phylogenetic and recombination analysis between thedifferent allexivirus species. Total RNA was obtained of a GarV-B positive garlicplant by ISEM-D using anti-GarV-B antiserum and this was sent for masssequencing. Deep sequencing revealed the first complete GarV-B genome,consisting of 8,327 nucleotides (nt). The genome contained six open readingframes (ORFs) with the typical genome organization which encodes putativeproteins of 168 kDa (ORF1), 27 kDa (ORF2), 12 kDa (ORF3), 39 kDa (ORF4), 27 kDa(ORF5) and 14 kDa (ORF6). The comparison of the gene coding for the coatprotein of the virus showed a greater identity of nt with other isolates ofGarV-B (88.4% to 99.7%) and of GarV-X (75.4% to 78.3%) published in GenBank.The GarV-B replicase gene has not been previously reported in GenBank, so thesequence was compared with GarV-A, -C, -D, -E, -X and ShVX. The highest ntidentity values were detected with isolates of GarV-X (73.5% to 74.1%) andGarV-C (71.9% to 72.8%). These results suggest that GarV-X and GarV-B may bedifferent strains of the same virus. A genetic recombination analysis was alsoperformed between the complete sequences of allexiviruses published andobtained in this work and it was detected that the species GarV-D and GarV-Emay have arisen from the recombination of the N-terminal portion of GarV-B withthe C-terminal portion of GarV-A.