Abstract
The genomes of plant pathogenic fungi and oomycetes are often exposed to strong positive selection pressure. During speciation, shifts in host range and preference can lead to major adaptive changes. Furthermore, evolution of total host resistance to most isolates can force rapid evolutionary changes in host-specific pathogens. Crop pathogens are subjected to particularly intense selective pressures from monocultures and fungicides. Detection of the footprints of positive selection in plant pathogen genomes is a worthwhile endeavor as it aids understanding of the fundamental biology of these important organisms. There are two main classes of test for detection of positively selected alleles. Tests based on the ratio of non-synonymous to synonymous substitutions per site detect the footprints of multiple fixation events between divergent lineages. Thus, they are well-suited to the study of ancient adaptation events spanning speciations. On the other hand, tests that scan genomes for local fluctuations in allelic diversity within populations are suitable for detection of recent positive selection in populations. In this review, I briefly describe some of the more widely used tests of positive selection and the theory underlying them. I then discuss various examples of their application to plant pathogen genomes, emphasizing the types of genes that are associated with signatures of positive selection. I conclude with a discussion of the practicality of such tests for identification of pathogen genes of interest and the important features of pathogen ecology that must be taken into account for accurate interpretation.
Highlights
The theory underpinning the evolution of nucleic acid sequences can be traced all the way back to On the Origin of Species by Means of Natural Selection (Darwin, 1859), which was published in 1859
The extended haplotype homozygosity (EHH) test was originally developed to scan for selective sweeps in the human genome (Sabeti et al, 2002)
A common format for the studies performed on plant pathogens is a description of population sub-structure based on allele frequencies, analysis of population demographics, and, detection of regions of the genome with significant evidence of positive selection
Summary
The theory underpinning the evolution of nucleic acid sequences can be traced all the way back to On the Origin of Species by Means of Natural Selection (Darwin, 1859), which was published in 1859. It seems many effector sequences evolve as part of a trench warfare system and have no homologs in other species, there are some examples with reliable enough homologs for application of ω based tests of positive selection These will be discussed along with other pathogen proteins exhibiting evidence of positive selection at the codon level. In Melampsora larici-populina, which is a biotrophic rust-causing fungus in the Pucciniomyctina subdivision, a large number of genes encoding paralogous predicted effectors exhibit evidence of positive selection The residues in these proteins that appear to have undergone diversifying selection are predominantly located at the C-terminus, which suggests that this is a major site for interaction with host proteins. Future studies could shift focus toward such genes as their functions are less explored in pathogens
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