Molecular Characterization of Carla‐ and Potyviruses from Narcissus in China

Abstract

Conserved carlavirus and potyvirus primers were used in reverse transcriptase‐polymerase chain reaction (RT‐PCR) to amplify virus fragments from Chinese narcissus (Narcissus tazetta var. chinensis) in China and the fragments were subsequently sequenced and compared in phylogenetic analyses. Samples from Fujiang province and Shanghai contained either one or two potyviruses and a carlavirus. One potyvirus (PY1) showed a distant relationship to Iris severe mosaic virus, Onion yellow dwarf virus and Shallot yellow stripe virus, while the other (only in the Fujiang sample, PY2) was most closely related to Turnip mosaic virus (TuMV). Similar experiments using glasshouse grown Narcissus originating from the UK contained Ornithogalum mosaic virus and another potyvirus (PY3) in the TuMV/PY2 cluster. Comparisons with previously determined sequence fragments indicated that PY2 was probably Narcissus yellow stripe virus and PY3 Narcissus late season yellow virus. Carlavirus fragments from both Chinese sites seemed to be of the same virus, which was most closely related in phylogenetic analyses to Potato virus M, Aconitum latent virus and Hop latent virus. It is most probably a new member of the genus Carlavirus and has been tentatively named Narcissus common latent virus.

Molecular characterization of coat protein gene of Garlic common latent virus isolates from India: an evidence for distinct phylogeny and recombination

“…Conversely, the central and the C-terminal regions (from 49 to 319 aa) are highly conserved in all isolates (data not shown). The presence of conserved domains such as Flexi_CP_N and Flexi_CP had been previously reported in CP of carlaviruses and potexviruses [7]. In the present study, the presence of 13 different conserved domains and of 3 motifs within the CP were predicted using SMART [8] and MEME [9] programs, respectively (Suppl.…”

“…CP gene sequences could also group viruses of genus Carlavirus in two distinct phylogenetic subgroups. A similar sub grouping of Carlavirus species could also be shown when other genomic regions, i.e., nucleic acid binding protein and replicase genes, are used [7,18,19].…”

The genetic structure of populations of Turnip mosaic virus in Kyushu and central Honshu, Japan

“…The concats were used for evolutionary analyses. The corresponding regions of two sequences of Japanese yam mosaic virus (JYMV) Nakamae 1999, 2000), one of Scallion mosaic virus (ScMV) and one of Narcissus yellow stripe virus (NYSV) (Chen et al 2003) were used to align the TuMV concats as reported earlier (Tomimura et al 2004;Tomitaka and Ohshima 2006). We thus aligned all 62 P1 sequences with those of two JYMV isolates as the outgroup, the R12+Pro sequences with those of JYMV and ScMV, and the CP sequences with that of NYSV using Clustal X (Jeanmougin et al 1998).…”

“…The calculated trees were displayed by TREEVIEW (Page 1996). One ScMV and two JYMV sequences were used as the outgroup to construct a phylogenetic tree of the concats, because only the CP sequence of one NYSV isolate was available (Chen et al 2003). The JYMV and ScMV sequences corresponding to individual gene regions within the concats were aligned using their encoded amino acids as described, then reassembled to form sequences 2,979 nt long.…”

Turnip Mosaic Potyvirus Probably First Spread to Eurasian Brassica Crops from Wild Orchids about 1000 Years Ago

“…One of these is the ‘TuMV group’, which comprises TuMV and at least five other species, all from monocotyledonous plants. These include Japanese yam mosaic virus (JYMV) [10], [11], Narcissus yellow stripe virus (NYSV) [12], and Scallion mosaic virus (ScMV) [13], all known from full genomic sequences. Sequence analyses of the coat protein have shown that the TuMV group also contains Indian narcissus potyvirus and Narcissus late season yellows potyvirus.…”