Complete nucleotide sequence and taxonomy of Sugarcane streak mosaic virus, member of a novel genus in the family Potyviridae

Abstract

The complete genomic sequence of a Pakistani isolate of Sugarcane streak mosaic virus (SCSMV-PAK) is determined to be 9782 nucleotides in length, excluding the 3' poly(A) tail, and it comprises a large open reading frame encoding a polyprotein of 3130 amino acid residues. The deduced polyprotein is likely to be cleaved at nine putative protease sites by three viral proteases to ten mature proteins. Conserved motifs of orthologous proteins of other potyviruses are identified in corresponding positions of SCSMV-PAK. The genomic organization is virtually identical to the genera Ipomovirus, Potyvirus, Rymovirus, and Tritimovirus in the family Potyviridae. Sequence analyses indicate that the SCSMV-PAK genomic sequence is different from those of Sugarcane mosaic virus and Sorghum mosaic virus, two viruses with very similar symptoms and host range to SCSMV-PAK. SCSMV-PAK shares 52.7% identity with Triticum mosaic virus (TriMV) and 26.4-31.5% identities with species of the existing genera and unassigned viruses in the Potyviridae at the polyprotein sequence level. Phylogenetic analyses of the polyprotein and deduced mature protein amino acid sequences reveal that SCSMV, together with TriMV, forms a distinct group in the family at the genus level. Therefore, SCSMV should represent a new genus, Susmovirus, in the Potyviridae.

Characterization and Genetic Variation of Sugarcane Streak Mosaic Virus, a Poacevirus Infecting Sugarcane in Thailand

“…The result revealed that the conserved motif, GGAAAAAAA was found at the nucleotide position 3085-3093 which is similar to that of SCSMV-PAK reported by Xu et al (2010). The deduced 139 aa of PIPO of THA-NP3 was obtained from 420 bp in the +1 frame at the nucleotide position 3091-3510 as reported by Chandran and Gajjeraman (2015).…”

“…All selected isolates yielded the expected 1094 bp RT-PCR product, from which an isolate from Kamphaeng Saen District, Nakhon Pathom Province, designated as THA-NP3 ( Figure 1a) was subjected to full length genome sequencing. Nine putative cleavage sites of the polyprotein were identified in comparison to the putative sites of SCSMV-PAK polyprotein (Xu et al, 2010) and some others (Figure 3). All cleavage sites of THA-NP3 proteins as well as the positions of the amino acids were similar to those of the SCSMV isolates, PAK, ID, JP1, JP2 and TPT but not IND671.…”

“…The polyprotein is processed by the viral protease yielding ten different proteins, namely P1, HC-Pro, P3, 6K1, CI, 6K2, NIa-VPg, NIa-Pro, NIb and CP. The first published complete genome sequence of SCSMV which was isolated from sugarcane in Pakistan, SCSMV-PAK: GQ388116, contained 9782 nucleotides (nts), excluding 3′ Poly (A) tail (Xu, Zhou, Xie, Mock, & Li, 2010). Sequence comparison and a phylogenetic tree of the complete genome revealed that SCSMV was a distinct group from those of other genus in the family Potyviridae, and has been recently named Poacevirus (Xu et al, 2010;ICTV: www.ictvonline.org).…”

“…The first published complete genome sequence of SCSMV which was isolated from sugarcane in Pakistan, SCSMV-PAK: GQ388116, contained 9782 nucleotides (nts), excluding 3′ Poly (A) tail (Xu, Zhou, Xie, Mock, & Li, 2010). Sequence comparison and a phylogenetic tree of the complete genome revealed that SCSMV was a distinct group from those of other genus in the family Potyviridae, and has been recently named Poacevirus (Xu et al, 2010;ICTV: www.ictvonline.org). More isolates of SCSMV and their complete genome sequences were reported from China (Li et al, 2011) and India (Parameswari, Bagyalakshmi, Viswanathan, & Chinnaraja, 2013).…”

Genetic variability and potential recombination events in the HC-Pro gene of sugarcane streak mosaic virus

“…SCSMV has flexuous filamentous particles (890 9 15 nm) containing a single-stranded positive-sense RNA genome of approximately 10 kb. The SCSMV genome has a single open reading frame that is translated in to a large polypeptide and subsequently cleaved into functional proteins [7,8].…”