Phylogeny and genetic recombination of <em>Grapevine fanleaf virus</em> isolates from naturally infected vineyards in Tunisia

Abstract

The genetic diversity of Grapevine fanleaf virus (GFLV) was investigated in 11 isolates recovered from naturally infected vineyards located in the Cap Bon and Tunis regions. Virions were collected by immunocapture, and a 321 bp fragment containing part of the viral coat protein gene (CP) was amplifi ed by RT-PCR. Amplicons were cloned into a pMosBlue vector and sequenced. The evolutionary historical relationships were determined by constructing a dendrogram using Maximum-parsimony (MP), Maximum-Likelihood (ML) and Neighbor-Joining (NJ), all of which gave similar results. Besides phylogeny, recombination also explains a considerable amount of genetic diversity in natural populations. Recombinational events were detected by a variety of bioinformatic programs. Different recombination breakpoints were determined with a particularly strong signal located downstream nt 272 of the amplicon (the position in the CP gene as determined by the RECCO algorithm is: 456–467). Interestingly, it was found that recombination is widespread in the CP gene even though only a short part of the CP cistron was analyzed. As a result of this analysis, it appears that recombination may explain in part the great number of GFLV isolates described worldwide. Apart from recombination, reassortment is still an open question among many others, and may represent another way to explore the genetic diversity of GFLV.