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Rapid Evolution of Avirulence Genes in Rice Blast Fungus Magnaporthe Oryzae

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Rapid Evolution of Avirulence Genes in Rice Blast Fungus Magnaporthe Oryzae

Ju Huang et al. BMC Genet.

Abstract

Background: Rice blast fungus Magnaporthe oryzae is one of the most devastating pathogens in rice. Avirulence genes in this fungus share a gene-for-gene relationship with the resistance genes in its host rice. Although numerous studies have shown that rice blast R-genes are extremely diverse and evolve rapidly in their host populations, little is known about the evolutionary patterns of the Avr-genes in the pathogens.

Results: Here, six well-characterized Avr-genes and seven randomly selected non-Avr control genes were used to investigate the genetic variations in 62 rice blast strains from different parts of China. Frequent presence/absence polymorphisms, high levels of nucleotide variation (~10-fold higher than non-Avr genes), high non-synonymous to synonymous substitution ratios, and frequent shared non-synonymous substitution were observed in the Avr-genes of these diversified blast strains. In addition, most Avr-genes are closely associated with diverse repeated sequences, which may partially explain the frequent presence/absence polymorphisms in Avr-genes.

Conclusion: The frequent deletion and gain of Avr-genes and rapid non-synonymous variations might be the primary mechanisms underlying rapid adaptive evolution of pathogens toward virulence to their host plants, and these features can be used as the indicators for identifying additional Avr-genes. The high number of nucleotide polymorphisms among Avr-gene alleles could also be used to distinguish genetic groups among different strains.

Figures

Figure 1
Figure 1
The phylogenic trees of Avr-genes. In this Figure, each tree represents the phylogenetic relationship of one AVR gene. The colored shape indicates the origin of the strain, and the number of strains is labeled behind the shape if there are more than one member at the the same position. In the tree of PWL2, there are only two kinds of alleles. One of them is the wild type, which is intoxical, while the other is inefficient and toxical.
Figure 2
Figure 2
The genomic composition of the flanking sequences. The copy numbers of the flanking sequences of different loci are shown in this Figure. Each line displays the 10 kb flanking sequence of a gene (for ACE1 the flanking length is 30 kb as this gene is too long). The green region shows the position of the target gene. the red region indicates that this part of sequence has more than 5 copies in the whole genome while grey region only has one copy. Blue region has copy numbers ranging from 2 to 5.

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