Analyses of Genotypic Diversity among North, South, and Central American Isolates ofSugarcane Yellow Leaf Virus: Evidence for Colombian Origins and for Intraspecific Spatial Phylogenetic Variation

Abstract

We have analyzed the genotypic diversity of Sugarcane yellow leaf virus (SCYLV) collected from North, South, and Central America by fingerprinting assays and selective cDNA cloning and sequencing. One group of isolates from Colombia, designated the C-population, has been identified as residing at the root node between a separable superpopulation structure of SCYLV and other members of the family Luteoviridae, indicating that the progenitor viruses of the North, South, and Central American isolates of the SCYLV superpopulation most likely arose from a C-population structure. From a model of intrafamilial evolution (F. Moonan et al., Virology 269:156-171, 2000), a prediction could be made that within the SCYLV species, the capacity of genomic sequence divergence would range from lowest in the capsid protein open reading frame 3 (ORF 3) to highest in a region spanning across the carboxy-terminal end of the RNA-dependent RNA polymerase ORF. We have demonstrated the validity and applicability of this intrafamilial model for the prediction of intraspecies SCYLV diversity. Analysis of spatial phylogenetic variation (SPV) within the SCYLV isolates could not be assessed by application of a "partial likelihoods assessed through optimization" (PLATO)-derived intraspecies model alone. However, application of a PLATO-derived intrafamilial model with the intraspecies-derived model allowed distinction of three forms of SPV. Two of the SPV forms identified correspond to the extremes in a continuum of sequence evolution displayed in a SCYLV superpopulation structure, and the third form was diagnostic of a C-population structure. The application of these types of models has value in terms of predicting the types of SCYLV intraspecies diversity that may exist worldwide, and in general, may be useful in application for more informed design of transgenes for use in the elicitation of homology-dependent virus resistance mechanisms in transgenic plants.In the Americas, Sugarcane yellow leaf virus (SCYLV) is associated with a disease referred to as yellow leaf syndrome (YLS [3,5,6,47,55]), although a similar disease via phytoplasma infection may produce otherwise identical symptomology and is also currently referred to as YLS disease in certain areas of the world (6, 45). In sugarcane, losses of as high as 50% have been estimated to have occurred in field sites as the result of virus-induced YLS (55).The complete SCYLV genome has been sequenced and characterized and most closely resembles viruses of the family Luteoviridae in the genus Polerovirus (36, 48). The results of these studies indicate that SCYLV, like Polerovirus members of the family Luteoviridae, encode at least six definable open reading frames (ORFs) typically listed as ORFs 0 to 5 (4,7,31,32,35,36,43,48). ORFs 0 and 1 are thought to produce peptides via alternate translational start sites from the monopartite genomic RNA of SCYLV, and ORFs 3 and 4 are thought to produce peptides via alternate translation from a subgenomic RNA. These studies also indicate that a fusion pe...

Long-Term Evolution of theLuteoviridae: Time Scale and Mode of Virus Speciation

“…S1 and S2 in the supplemental material). Strikingly, between 66 and 100% of the recombination breakpoints detected here were located at gene boundaries, similar to results reported previously (51,52,72).…”

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.…”

Sugarcane yellow leaf virus introduction and spread in Hawaiian sugarcane industry: Retrospective epidemiological study of an unnoticed, mostly asymptomatic plant disease

“…Later, similar symptoms were reported from mainland United States (Comstock et al 1994), Brazil (Vega et al 1997), Mauritius (Moutia and Saumtally 1999) and many other sugarcane countries (Bailey et al 1996;Victoria et al 1998;Lockhart and Cronje 2000). The polerovirus Sugarcane yellow leaf virus (SCYLV) was identified as a possible causal agent (Vega et al (Smith et al 2000;Moonan et al 2000) and 3-4 clusters of strains could be grouped, whereby a Colombian strain was proposed as the original population, which diverged out of the polerovirus group (Moonan and Mirkov 2002;Abu Ahmad et al 2006). The fact that the disease was detected not earlier than in the 1990s points to a more recent worldwide distribution, even though a report in 1968 about yellow wilt in sugarcane in Eastern Africa is attributed as, possibly, a first account of yellow leaf (Ricaud 1968;Bailey et al 1996).…”