Detection and classification of allexiviruses from garlic in China

Abstract

Degenerate primers for RT-PCR were designed and used to amplify genome fragments ( c. 750 nt in the coat protein-ORF6 region) of allexiviruses from a total of 28 garlic samples from 24 provinces in China. Many samples contained more than one distinct sequence. A total of 60 different sequences were obtained. Phylogenetic analysis and two-way comparisons were used to assess the status of the sequences and to re-examine the criteria for distinguishing species within the genus. Most of the sequences could be allocated to either Garlic virus D or Garlic virus X on the basis of sequence similarity but some appeared to be intermediate between existing species. There were no sequences of Garlic virus C or Shallot virus X. A comparison with the related genera Carlavirus, Foveavirus and Potexvirus suggests that the published allexivirus species demarcation criteria may have been drawn too tightly and should be re-examined.

Elimination of shallot bulb viruses through heat treatment

“…The PCR was done in a 20 ml volume solution containing: 12 µL Kapa2G Fast Ready Mix PCR Kit (Thermo Scientific), 4 µL nuclease-free water, 1 µL Poty1 reverse primer 10 µM, 1 µL pCV3t/ AlcarF/U341 forward primer 10 µM, and 1 µL cDNA template. Primer set: Poty1(IDT)/ pGV3t (Sigma) (5'-GGA TTC CGG GTT TTT TTT TTT TTT TTT V-3' (Gibbs and MacKenzie, 1997) and 5'-TGG NCN TGC TAC CAC AAN GG-3' (Chen et al, 2004)); Poty1(IDT)/AlcarF (Sigma) (5'-GGA TTC CGG GTT TTT TTT TTT TTT TTT V-3' (Gibbs and MacKenzie, 1997) and 5'-TGC TGC YTT TGA TAC YTT CGA T-3') (Gambley, 2012)); Poty1 (IDT)/U341 (Sigma) (5'-GGA TTC CGG GTT TTT TTT TTT TTT TTT V-3' (Gibbs and MacKenzie, 1997) and 5'-CCG GAA TTC ATG RTI TGG TGY ATI GAI AAY GG-3' (Langeveld et al, 1991) o C for 6 min. PCR products were separated on electrophoresis 1.5% agarose gels in TBE (Tris-Borate-EDTA) buffer 1x and then stained with ethidium bromide and visualized in a UV transilluminator.…”

The unfolded protein response and programmed cell death are induced by expression of Garlic virus X p11 in Nicotiana benthamiana

“…Garlic virus X (GarVX), a member of the genus Allexivirus (family Alphaflexiviridae) shares a similar genomic organization with carlaviruses, potexviruses and foveaviruses, and is widely detected in Allium species worldwide (Adams et al, 2004;Chen et al, 2004;Nam et al, 2015;Song et al, 1998;Wylie et al, 2011Wylie et al, , 2014. Potexviruses, carlaviruses and foveaviruses have three genes, forming the triple gene block (TGB), that are involved in virus movement.…”

Basil (Ocimum basilicum), a new host of Pepino mosaic virus

“…RNA was extracted from diseased shallot samples and the ShMbLV type isolate and tested by RT-PCR using primers that amplify a ca . 750 bp fragment between the coat protein (CP) and ORF6 region of allexiviruses (Chen et al ., 2004). For both samples, amplicons of the expected size were obtained and sequenced directly.…”