Complete genomic sequence of turnip mosaic virus infecting passionfruit in Fujian province of China

Contigs with sequence identities to turnip mosaic virus (TuMV) were detected by deep sequencing of the small RNAs extracted from a passion fruit (Passiflora edulis) plant showing virus-like symptoms in Fujian Province, China. The complete genome of the TuMV, designated TuMV-FJ here, was determined based on the sequences of these contigs and Sanger sequencing of RT-PCR and 5′/3’ RACE amplicons. The TuMV-FJ genome consists of 9,833 nucleotides excluding the poly(A) tail. It contains an open reading frame encoding a polypeptide with 3164 amino acid residues. The polypeptide was predicted to be cleaved into ten functional proteins by viral proteases. Phylogenetic analysis indicated that TuMV-FJ is a member of a world-B phylogenetic group of TuMV. TuMV-FJ shared more than 94% nucleotide and amino acid sequence identities with its closest relative, namely BJ-B01, a TuMV isolate from Brassica oleracea. A RT-LAMP assay was developed to facilitate the molecular detection of TuMV-FJ. As far as we know, this is the first report of the complete genome sequence of TuMV infecting P. edulis. In addition, the RT-LAMP assay provides a rapid, robust and highly sensitive approach for the detection of TuMV in passion fruit.