Bioinformatic Detection of Positive Selection Pressure in Plant Pathogens: The Neutral Theory of Molecular Sequence Evolution in Action

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.

Genome-wide DNA Variants Identify Genetic Diversity and Population Structure of Leptosphaeria maculans in Western Canada

“…Pathologists and breeders have long understood the importance of genetic variation in L. maculans with regard to the effectiveness and durability of disease resistance; the outcome of host-pathogen interaction often leads to avirulence gene mutation in the pathogen and consequently resistance breakdown in canola/rapeseed cultivars within short periods of time [9,36). Avirulence genes are members of SSP-encoding genes that play key roles in interactions with hosts [37]. Selection pressure tends to indirectly target the genes localized in rapidly-evolving transposable element-rich regions [38].…”

Outcome of the public consultation on the draft Scientific Opinion on the evaluation of existing guidelines for their adequacy for the molecular characterisation and environmental risk assessment of genetically modified plants obtained through synthetic biology

“…The GMO Panel considers that there is an essential difference in the approach to genetic engineering, namely that SynBio strategies apply modelling and analytical approaches to improve the predictability of the engineering thereby enabling the generation of more complex traits. Unkel et al (2019) horizon scanning exercise by JKI 5 highlights that plant SynBio products reaching the market in the next ten years are likely to result from existing technologies including the insertion of transgenes and genome editing. However, the advanced traits being pursued are using engineering principles to achieve them.…”

“…Please check that the information provided in the column named "Reference" in Table 1 corresponds to the one given in the section "5 References" (for instance, "Directive 2001/18/EC" in table 1 corresponds to "EU, 2001" in the section "5 References", which should not be the case). Page 10, lines 213-214: Please add the reference "Unkel et al (2019)" at the end of the expression "the results of the horizon scanning on SynBio developments in plants" (new proposal: "the results of the horizon scanning on SynBio developments in plants (Unkel et al, 2019") and in the section "5 References". This reference is absent from the document, which should be corrected.…”

“…Furthermore, manipulating the metabolic content of plants could have a profound effect on plant-pathogen interactions. Indeed, nutrients uptake is known to be under positive selection for pathogens (Aguileta et al, 2010;Derbyshire, 2020) and many pathogen mutations affecting nutrient uptake from the host plant are deleterious for pathogen development in planta, highlighting the close relation between plant metabolic content and pathogen fitness. The potential increase in susceptibility to the main pathogens should therefore be carefully assessed before commercial cultivation of the modified crop.…”

“…The phenotypes may therefore be more complicated to assess than those considered in the case studies (e.g. altered plant composition and nutritional value, improved photosynthesis, increased tolerance/resistance to abiotic and biotic stress, better nitrogen fixation, altered plantmicrobiome interactions) selected by the EFSA GMO Panel or Unkel et al (2019).…”