Molecular evidence for a new potyvirus species in yam (Dioscorea spp.) on the island of Guadeloupe

Prevalence of yam potyviruses in the French Caribbean islands of Guadeloupe was evaluated in 142 samples collected from yams showing symptoms of mosaic and mottling and belonging to D. rotundata (52 samples), D. alata (52 samples) and D. trifida (38 samples). Samples were screened by enzyme-linked immunosorbent assay (ELISA) with universal potyvirus monoclonal antibodies (AGDIA) and by immunocapture reverse-transcriptase polymerase chain reaction (IC-RT-PCR) for the specific detection of Yam mosaic virus (YMV) (Bousalem et al., 2000a) and Yam mild mosaic virus (YMMV) (Bousalem et al., 2003).

15% of the samples were positive in the broad-spectrum ELISA used but negative in both the specific IC-RT-PCR tests used, suggesting one or more other potyviruses might be present in the ELISA-positive samples. The highest proportion was in D. rotundata (15/52; 29 %), followed by D. trifida (5/38; 13%), and D. alata (2/52; 4%). In an attempt to characterize those potential yam potyviruses, total RNA was extracted from one D. trifida sample (TGwadE2) and universal potyvirus degenerate primers (Colinet et al., 1994) were used to amplify the core and C-terminal region of the coat protein (CP) and the 3'untranslated region (3'UTR) which are commonly used as markers of genetic relatedness of potyviruses.

Sequence information generated (GenBank AY821494) from the cloned fragment was compared with sequences of other potyviruses by a BLAST search and by pairwise sequence comparison carried out on 209 potyviruses sequences aligned by the Clustal algorithm from the MegAlign software of DNASTAR package. The partial amino acid (aa) sequence available for the CP (152 aa) had the highest similarity with Zucchini yellow mosaic virus (66 % identity) whereas the 3'UTR (126 nucleotides) had the highest similarity with Potato virus Y (35 % identity). Sequence comparisons of the CP (aa) and 3'UTR with YMMV isolates (Bousalem et al., 2003), YMV isolates (Bousalem et al., 2000b) and Japanese yam mosaic virus isolate (JYMV, AB016500) showed the highest similarity at the amino acid level (62,5 % identity) with the JYMV CP and highest similarity of the 3'UTR with the YMMV (32 % identity).

According to molecular taxonomy, TGawdE2 isolate should be regarded as a distinct member of the genus Potyvirus (family Potyviridae) and was tentatively named Dioscorea mosaic virus.