title: Putative recombination signature and significance of insertion/deletion events in the RNA-dependent RNA polymerase coding region of sugarcane yellow leaf virus.
abstract: The 5898 nucleotide single-strand RNA genome of Sugarcane yellow leaf virus (SCYLV) contains one long open reading frame, which is translated into a 120.6 kDa polyprotein. The sequences of SCYLV isolates from the two SCYLV-susceptible cultivars from Hawaii had a deletion of 48-51 nt in ORF1. SCYLV from 12 sugarcane hybrid cultivars from different origins were tested by RT-PCR using a specific set of primers, to investigate the genome segment for this deletion. Only three cultivars were found not to have the deletion (H87-4319, JA-605 and CP52-43), while SCYLV from nine cultivars (H73-6110, H87-4094, H78-7750, GT54-9, G84-47, H78-4153, H65-7052, C1051-73, Ph-8013) along with aphid (Melanaphis sacchari), which fed on SCYLV-infected H73-6110, contained a deletion of about 50 nt. The deleted sequence was located in the overlap frameshift of ORF1 and ORF2. Thus, ORFs 1 and 2 of SCYLV are translated via ribosomal frameshift and yield the 120.6 kDa viral replicase. ORF1 plays most likely a role in the replication and is a source of large variability among the virus population. To identify possible recombination events located in the RdRp domain of the Hawaiian isolates, two programs were used: RDP v.4.3 and RECCO. It is noteworthy that according both methods Haw73-6110 was found as a potential recombinant. On the other hand, opposed to the RDP package, RECCO revealed that Haw87-4094 isolate was also a recombinant whereas Haw87-4319 was not.
authors.affiliation: Biochemistry Department, Faculty of Agriculture, Zagazig University, 44519 Zagazig, Egypt. aelsayed@zu.edu.eg
authors.forename: Abdelaleim Ismail
authors.initials: AI
authors.lastname: ElSayed
authors.forename: Moncef
authors.initials: M
authors.lastname: Boulila
authors.forename: Ewald
authors.initials: E
authors.lastname: Komor
authors.forename: Yun J
authors.initials: YJ
authors.lastname: Zhu
mesh_terms: D000818:Animals; D001042:Aphids / Q000821:virology; D001483:Base Sequence; D054643:INDEL Mutation / Q000235:genetics*; D052679:Luteoviridae / Q000235:genetics*; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics*; D011995:Recombination, Genetic / Q000235:genetics*; D031786:Saccharum / Q000235:genetics / Q000821:virology
chemical_list: D012324:RNA-Dependent RNA Polymerase