Sequence analysis of nuclear inclusion b gene of Papaya ringspot virus isolates from Luzon, Philippines
2016
Belen, G.B. | Sta. Cruz, F.C. | Diaz, M.G.Q.
The sequences of the nuclear inclusion b (Nlb) gene of Papaya ringspot virus (PRSV) isolates from six provinces in Luzon, Philippines, were analyzed to determine the size and cleavage sites of the gene, and the sequence similarity of the virus isolates and their phylogenetic relationship. Nucleotide and deduced amino acid sequences of the Nlb gene were compared among the PRSV isolates from Albay, Bulacan, Cavite, Marinduque, Isabela and Laguna; and with those published PRSV sequences from the National Center for Biotechnology Information (NCBI) GenBank. Amino acid residues of the Nlb gene of PRSV isolates from Albay, Bulacan, Cavite and Marinduque were cleaved at specific sites following the V(Q-S) rule at the NIa/Nlb junction, and a new V(E-L) motif was observed at NIb/CP junction, giving a predicted size of 1551 nucleotides with coding capacity of 517 amino acid residues. Correspondingly, the PRSV Isabela and PRSV Laguna had 1526 and 1527 bases, which represent the partial size of Nlb gene of these isolates. The known consensus sequences YCDADGS, GNNSGQPSTVVDNT(S)LMV, and NGDDL-X34-K which are implicated for the putative RNA polymerase function of potyviruses were conserved in the Nlb gene sequences of all PRSV isolates. Nucleotide sequence identities of the full-length Nlb gene of PRSV isolates from Albay, Bulacan, Cavite and Marinduque ranging 95.5-96.6% were very close to isolates from Vietnam (94-95%) but relatively differed with those of PRSV from China, Taiwan, Mexico, India and Thailand (82-89%). Likewise, the full-length Nlb gene of Philippine PRSV isolates had amino acid sequence identities of 97.3-98.5%. Phylogenetic analysis of PRSV utilizing the Nlb gene showed that all six PRSV Philippine isolates were clearly separated from isolates in South and Southeast Asia except those from Vietnam.
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