Complete genome sequence of Alfalfa mosaic virus, infecting Mentha haplocalyx in China

Mentha haplocalyx (Lamiaceae) is a herbaceous perennial economic plant which is widely cultivated in China. Plants of M. haplocalyx with mosaic symptoms were collected from Zhaotong, Yunnan Province. Alfalfa mosaic virus (AMV) was detected from symptomatic leaf samples using small RNA sequencing and RT-PCR. The complete genome sequence of AMV-Mint was determined. AMV-Mint RNA1 was 3,644 nt, RNA2 was 2,594 nt and RNA3 was 2,040 nt, encoding P1 of 1,126 amino acids (aa), P2 of 794 aa, MP of 300 aa and CP of 218 aa. The genome structure of AMV-Mint was similar to those reported previously, except for an insertion of one adenine nucleotide at 2,389 nt of the RNA2, which results in reading frame shift mutation of the P2. Phylogenetic analysis based on RNA3 sequences grouped AMV-Mint into the Group I clade, with closest relationship to AMV-Lst. No recombination event was detected in the genome of AMV-Mint. This is the first report of the complete genome sequence of AMV from M. haplocalyx.