Impact of network properties on evolution of the plant immune network

Abstract

This study investigates how network evolution is affected by the underlying properties of the network. The plant immune signaling network is known to be robust against network perturbations. We hypothesize that genes of this robust immune network tend to be under neutral selection because deleterious mutations in such genes do not strongly affect the immune phenotype. I examined whether remnants of the hypothesized tendency of evolution can be detected in the currently existing natural population of the model plant Arabidopsis thaliana. The genome sequences of 30 A. thaliana accessions with diverse geographical and environmental origins were obtained from the 1001 Genomes Project (1001genomes.org) for analysis. Using the TAIR8 annotation of the A. thaliana reference accession genome Col-0 a dataset of ~27,000 protein-coding genes for all accessions was generated. With such population genomic data it is feasible to study whether a group of genes are under selection different from another group, such as the entire genome. Component genes of the plant immune signaling network were identified in a relatively unbiased manner by mining AraNet, a functional gene network model of A. thaliana (functionalnet.org). Population genetic summary statistics of the core network component genes and of all the genes in the genome were compared. The Tajima’s D value distribution for all the genes in the genome had a single mode in a negative Tajima’s D value, which is suggestive of purifying selection. The Tajima’s D value distribution for the core network component genes showed that this set of network component genes was significantly enriched with genes that have Tajima’s D values near zero. This suggests that immune network genes are enriched with genes with reduced levels of purifying selection compared with the genome average, which supports our hypothesis.