Sequence comparison of the 3'-terminal parts of the RNA of four German isolates of sugarcane mosaic potyvirus (SCMV)

Abstract

The 3'-termini of the genome of four German isolates of sugarcane mosaic potyvirus (SCMV) were cloned and sequenced. The sequence data covered the 3' non-coding region (3'NCR), coat protein and part of the nuclear inclusion b (NIb) genes of the isolates. Comparisons of the sequences revealed that the investigated isolates are very closely related. An alignment of the predicted coat protein amino acid sequences of the German isolates with sequence data for other members of the SCMV subgroup, in particular the two SCMV strains, SCMV-SC and SCMV-MDB, showed a limited degree of homology indicating that the German isolates may represent a distinct virus. However, this is mainly due to the previously reported unexpected sequence diversity in the surface exposed N-terminal region of coat protein of SCMV isolates. Comparisons of the amino acid sequences of the core region of the coat proteins and the nucleotide sequences of the 3' NCR clearly show that the German isolates are strains of SCMV.