Nucleotide Sequence Analysis of the Coat Protein Genes of Two Isolates of Sweet potato feathery mottle virus from Central Taiwan

Abstract

Two potyvirus-like isolates, CY1 and CY2, were collected from sweet potato displaying leaf symptoms of mosaic or vein mottling at Chia-Yi area. Taiwan, by single-lesion isolation on Chenpodium quinoa plants. Using the degenerate primers for potyviruses, a 1.2 kb and a 1.3 kb DNA fragments were amplified from CY1-and CY2-infected tissues of C. quinoa, respectively, by reverse-transcription polymerase chain reaction (RT-PCR). After clotting and sequencing, the two cDNA fragments were found to be of 1205 and 1351 bp. and corresponding to a part of the 3' end of nuclear inclusion (NIb) region and the 5' end of the coat protein (CP) region of potyviruses. For amplification of the region corresponding to the 3' end of CP region, the 3' untranslated region (3'-UTR), and the poly A tail, RT-PCR was conducted with the oligo (dT) primer and the specific Primers designed from the known sequence. The assembled cDNA sequences of 1249 and 1383 bp, respectively, from CY1 and CY2 were elucidated to reflect the 3'-terminal region of nuclear inclusion b (NIb) protein gene [85 nt (28 aa) / 213 nt (71 aa)], the complete CP gene [939 nts (313 aa) /945 nts (315 aa)], and 3'-uTR (both 225 nt) and a poly (A) tail. Sequence analysis indicated that the two viruses were isolates of Sweet potato feathery mottle virus (SPFMV). The two isolates showed 80.6% nucleotide identity and 86.3% amino acid identity in their CP genes. A putative proteolytic cleavage site Q/S was predicted between NIb protein and CP. A DAG triplet for aphid transmissibility of potyviruses was found at the 9-11 residues from the N-terminus of both CP genes. Phylogenetic analysis of CP sequences revealed that SPFMV-CY1 belonged to the group C and is as closely related to the isolates 115/1S, 5, Arua 10a, O and TZ4. The sequence relationships between the two isolates and potyviruses revealed that SPFMV-CY1, SPFMV-CY2 were closely to the sweet potato infecting potyviruses, SPVY, SPVG and SPLV, reflecting a more recent evolutionary relationship.