Abstract
Maize chlorotic mottle virus has been rapidly spreading around the globe over the past decade. The interactions of maize chlorotic mottle virus with Potyviridae viruses causes an aggressive synergistic viral condition - maize lethal necrosis, which can cause total yield loss. Maize production in sub-Saharan Africa, where it is the most important cereal, is threatened by the arrival of maize lethal necrosis. We obtained maize chlorotic mottle virus genome sequences from across East Africa and for the first time from Ecuador and Hawaii, and constructed a phylogeny which highlights the similarity of Chinese to African isolates, and Ecuadorian to Hawaiian isolates. We used a measure of clustering, the adjusted Rand index, to extract region-specific SNPs and coding variation that can be used for diagnostics. The population genetics analysis we performed shows that the majority of sequence diversity is partitioned between populations, with diversity extremely low within China and East Africa.
Highlights
Maize chlorotic mottle virus (MCMV) is a positive-sense single-stranded RNA virus, and the sole member of the Machlomovirus genus in the Tombusviridae family
The interaction causes a more aggressive condition known as maize lethal necrosis (MLN)
The recent spread of MLN reflects the spread of MCMV since sugarcane mosaic virus (SCMV) has been present in East Africa, China and South America for decades[17,18,19]
Summary
Between 2012 and 2016, we collected MCMV-infected maize leaves and generated 37 novel MCMV genome sequences from Kenya (n = 24), Ethiopia (n = 5), Rwanda (n = 4), USA (Hawaii, n = 1), and Ecuador (n = 3) (Supplemental Table S1). Including all GenBank isolates, nucleotide identity between genomes ranged from 100% to 96.55%. There is clear separation of isolates from different regions, indicating that there has been no recombination between MCMV genomes in geographically isolated regions (Fig. 2a). To construct an unrooted phylogenetic tree, we used a nucleotide alignment containing all novel MCMV isolates, including ambiguous bases at the 10% threshold, and genome sequences available in GenBank. We chose nucleotide alignment to enhance resolution due to the low divergence between MCMV isolates, and used Bayesian inference (MrBayes 3.2) to generate the tree (Fig. 2b). The phylogenetic tree shows clear separation between geographic regions, with the exception of Hawaii and Ecuador. Sequence type Genome CP CP CP, in 81nt winows CP, in 81nt winows 183 K ORF 1a, CP, 20k ORF CP CP Two CP genes Genome (satellite)
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