Molecular Variability of the Genomes of Capilloviruses from Apple, Japanese Pear, European Pear, and Citrus Trees

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Abstract
The 3'-terminal regions of the genomes of apple stem grooving virus (ASGV), isolated from apple, Japanese pear, and European pear plants, and citrus tatter leaf virus (CTLV), isolated from citrus plants, were amplified by reverse transcription-polymerase chain reaction. The DNA products were cloned and sequenced. The results indicated that the ASGV isolates from apple, Japanese pear, and European pear comprise at least two to four "sequence variants" that differ considerably from each other in nucleotide sequence. Comparison of the amino acid (aa) sequences of the open reading frame (ORF) 1- and 2-encoded proteins among isolates or sequence variants, including isolates of ASGV and CTLV reported previously, showed that the aa sequences of the ORF2-encoded protein (320 aa) and the putative coat protein (CP) (237 aa), which was equivalent to aa positions 1869 to 2105 of the ORF1-encoded protein of ASGV (P-209), were highly conserved among isolates and sequence variants. Identities ranged from 92.8 to 100% for the ORF2-encoded protein among 15 isolates and sequence variants and from 92.4 to 100% for the CP among 21 isolates and sequence variants. On the other hand, the aa sequence identities of a variable 284-aa region (designated the V-region), equivalent to aa positions 1585 to 1868 of the ORF1-encoded protein (which also encoded the ORF2-encoded protein in another frame), were highly variable (53.2 to 99.3%) among 15 isolates and sequence variants. The percentage of conserved V-region aa in all 15 isolates was only 20.4%. Phylogenetic trees constructed from the aa sequences of the V-region, coat, and ORF2-encoded proteins showed that isolates and sequence variants were separated into several clusters, regardless of the source host plant species (apple, Japanese pear, European pear, citrus, and lily). In a tree constructed for the V-region proteins, two CTLV isolates were grouped into two clusters, each of which contained isolates and sequence variants from apple and Japanese pear. These results suggest that both CTLV from citrus and ASGV from Rosaceous plants should be considered isolates of ASGV.