Molecular phylogenetic analysis of partitivirus CPs and plant PCLSs.
A phylogenetic tree was generated based on an alignment (see Figure S2) of the entire region of partitivirus CP-related sequences. Analyzed sequences were from 7 fungal partitiviruses (shown in red), 10 plant partitiviruses (in blue), 1 F. pratensis EST-derived sequence (shown in purple), 4 accessions of Ar. thaliana, and 16 other plant species (in green) (See Tables 1 and S4 for their descriptions). The assembled sequence from the F. pratensis ESTs in the database is believed to be of plant-infecting partitivirus origin because the library contains EST entries of RdRp sequences and some had interrupted poly(A) tails typical of a partitiviral mRNA. Viruses analyzed phylogenetically are: Rosellinia necatrix partitivirus 2, RnPV2; Sclerotinia sclerotiorum partitivirus S, SsPV-S; Chondrostereum purpureum cryptic virus, CPCV; Raphanus sativus cryptic virus 1, RSCV1; white clover cryptic virus 1, WCCV1; vicia cryptic virus, VCV; carrot cryptic virus 1, CaCV1; beet cryptic virus 1, BCV1; Amasya cherry disease associated partitivirus, ACD-PV; cherry chlorotic rusty spot-associated partitivirus, CCRS-PV; Heterobasidion RNA virus 3, HetRV3; Flammulina velutipes browning virus, FvBV; beet cryptic virus 2, BCV2; Raphanus sativus cryptic virus 3, RSCV3; Fragaria chiloensis cryptic virus, FCCV; rose cryptic virus 1, RoCV; Raphanus sativus cryptic virus 2, RSCV2. Note that RSCV1 CP gene and RSCV1 dsRNA3, BCV2 dsRNA2 and 3, and RSCV2 dsRNA2 and 3 are assumed to be from two independent viruses although the same virus name was assigned to the segments in the database. Numbers at the branches show aLRT values using an SH-like calculation (only values greater than 0.5 are shown). The scale bar represents the relative genetic distance (number of substitutions per nucleotide).
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