Extensive recombination challenges the utility of Sugarcane mosaic virus phylogeny and strain typing

Luke Braidwood,David Baulcombe,Sebastian Y Müller

doi:10.1038/s41598-019-56227-y

Luke Braidwood, David Baulcombe + Show 1 more

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https://doi.org/10.1038/s41598-019-56227-y

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Journal: Scientific Reports	Publication Date: Dec 1, 2019
Citations: 13	License type: open-access

Affiliation: University of Cambridge

Abstract

Sugarcane mosaic virus (SCMV) is distributed worldwide and infects three major crops: sugarcane, maize, and sorghum. The impact of SCMV is increased by its interaction with Maize chlorotic mottle virus which causes the synergistic maize disease maize lethal necrosis. Here, we characterised maize lethal necrosis-infected maize from multiple sites in East Africa, and found that SCMV was present in all thirty samples. This distribution pattern indicates that SCMV is a major partner virus in the East African maize lethal necrosis outbreak. Consistent with previous studies, our SCMV isolates were highly variable with several statistically supported recombination hot- and cold-spots across the SCMV genome. The recombination events generate conflicting phylogenetic signals from different fragments of the SCMV genome, so it is not appropriate to group SCMV genomes by simple similarity.

Highlights

Sugarcane mosaic virus (SCMV) is distributed worldwide and infects three major crops: sugarcane, maize, and sorghum
Despite SCMV being present in East Africa and China for decades, its impact in both regions has been enhanced by the recent arrival of Maize chlorotic mottle virus (MCMV), and MLN12–16
The 23 assembled SCMV sequences ranged from 2,191 bp to 9,632 bp, which is 23% to 100% of the longest previously reported SCMV sequence

Summary

Introduction

Sugarcane mosaic virus (SCMV) is distributed worldwide and infects three major crops: sugarcane, maize, and sorghum. SCMV can infect three major crops: sorghum, sugarcane (10–35% yield loss), and maize (20–50% yield loss), and is thought to be one of the top-ten most economically damaging plant viruses[2,3,4]. It has been reported in 84 countries across the 6 inhabited continents and this cosmopolitan distribution is likely due to worldwide trade in its host crops for hundreds of years (Fig. 1)[5]. Recombination may impede virus detection because increased genomic variation may lead to false negative results with common techniques such as PCR and antibody ELISA11,37

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