Sugarcane Yellow Leaf Virus: An Emerging Virus That Has Evolved by Recombination between Luteoviral and Poleroviral Ancestors

Abstract

We have derived the genomic nucleotide sequence of an emerging virus, the Sugarcane yellow leaf virus (ScYLV), and shown that it produces one to two subgenomic RNAs. The family Luteoviridae currently includes the Luteovirus, Polerovirus, and Enamovirus genera. With the new ScYLV nucleotide sequence and existing Luteoviridae sequence information, we have utilized new phylogenetic and evolutionary methodologies to identify homologous regions of Luteoviridae genomes, which have statistically significant altered nucleotide substitution ratios and have produced a reconstructed phylogeny of the Luteoviridae. The data indicate that Pea enation mosaic virus-1 (PEMV-1), Soybean dwarf virus (SbDV), and ScYLV exhibit spatial phylogenetic variation (SPV) consistent with recombination events that have occurred between poleroviral and luteoviral ancestors, after the divergence of these two progenitor groups. The reconstructed phylogeny confirms a contention that a continuum in the derived sequence evolution of the Luteoviridae has been established by intrafamilial as well as extrafamilial RNA recombination and expands the database of recombinant Luteoviridae genomes that are currently needed to resolve better defined means for generic discrimination in the Luteoviridae (D'Arcy, C. J. and Mayo, M. 1997. Arch. Virol. 142, 1285-1287). The analyses of the nucleotide substitution ratios from a nucleotide alignment of Luteoviridae genomes substantiates the hypothesis that hot spots for RNA recombination in this virus family are associated with the known sites for the transcription of subgenomic RNAs (Miller et al. 1995. Crit. Rev. Plant Sci. 14, 179-211), and provides new information that might be utilized to better design more effective means to generate transgene-mediated host resistance.

An attempt to identify recombinants between two sobemoviruses in doubly infected oat plants

“…As no recombinants were detected between the two sobemoviruses, it is not clear whether the reason is the extent and/or the content of identical blocks or not. It was surprising that no recombination events in the putative subgenomic promoter area were identified, as the evolution of Pro-VPg-RdRp/CP region in the "supergroup" of luteo-sobemo-tombusviruses is modular (aus dem Siepen et al, 2005;Gibbs and Cooper, 1995;Martin et al, 1990;Mayo and Jolly, 1991;Mayo and Ziegler-Graff, 1996;Miller and Rasochova, 1997;Moonan and Mirkov, 2002;Moonan et al, 2000). Thus, although the evolutionary analysis supports the idea of frequent recombinations within this supergroup, this study was unable to confirm that RNA recombinations take place during the replication of sobemoviruses.…”

No recombination detected in artificial potyvirus mixed infections and between potyvirus derived transgenes and heterologous challenging potyviruses

“…This was shown for recombination between the cucumoviruses CMV and tomato aspermy virus (TAV) (Fernandez-Cuartero et al, 1994). Also, viable Sugarcane yellow leaf virus arose from a recombination event in a luteovirus/polerovirus combination (Moonan et al, 2000). In the absence of specific selection pressure, we cannot rule out that in the investigated potyvirus combinations tested recombination occurred below the detection limit or in genomic regions that were excluded from the screening.…”

Detection of Sugarcane Yellow Leaf Luteovirus of India

“…cDNA was constructed from SCYLV genomic RNA following the method of RT -PCR . The RNA was polyadenylated with yeast polyA polymerase and oligo (dt) 30 primer was used for the RT-PCR as described by Moonan et al,(2000). For the coat protein amplification reverse primer = 5'-CGGATCGTTACCATCCG-3'and forward primer 5'GCTATGGGCAGATGCCC-3' was used (designed based on sequence already in the gene bank).…”

“…Research Centre, Gorakhpur, Uttar Pradesh, India. The virion was purified by enzymedigested method as described by Vega et al, (1997) and SCYLV genomic RNA was performed from the purified virions by phenol extraction as described by Moonan et al, (2000). cDNA was constructed from SCYLV genomic RNA following the method of RT -PCR .…”

“…Based on the sequence data presented here SCYLVIndia belongs to the same cluster in the Luteovirus genus as other SCYLV isolates. It can therefore be compared to a sequence comparison conducted by Moonan et al (2000).Due to its importance for diagnostic purposes (serological methods), the resulting Comparative sequence analysis showed that SCYLV India shared 100% sequence identity with SCYLV Texas, Florida and CP 92-1654 of Australia at nucleotide (97-100%) as well as amino acid (92-100%) levels (Table 1). Since the coat protein gene sequence similarity of SCYLV-India with Texas and CP isolates was above the threshold level of 90%, it is proposed that SCYLV-India should be regarded as a strain of SCYLV belonging to luteovirus, henceforth designated as SCYLV-India.…”