Comparative Pathogenomics Reveals Horizontally Acquired Novel Virulence Genes in Fungi Infecting Cereal Hosts

Abstract

Comparative analyses of pathogen genomes provide new insights into how pathogens have evolved common and divergent virulence strategies to invade related plant species. Fusarium crown and root rots are important diseases of wheat and barley world-wide. In Australia, these diseases are primarily caused by the fungal pathogen Fusarium pseudograminearum. Comparative genomic analyses showed that the F. pseudograminearum genome encodes proteins that are present in other fungal pathogens of cereals but absent in non-cereal pathogens. In some cases, these cereal pathogen specific genes were also found in bacteria associated with plants. Phylogenetic analysis of selected F. pseudograminearum genes supported the hypothesis of horizontal gene transfer into diverse cereal pathogens. Two horizontally acquired genes with no previously known role in fungal pathogenesis were studied functionally via gene knockout methods and shown to significantly affect virulence of F. pseudograminearum on the cereal hosts wheat and barley. Our results indicate using comparative genomics to identify genes specific to pathogens of related hosts reveals novel virulence genes and illustrates the importance of horizontal gene transfer in the evolution of plant infecting fungal pathogens.

Using dynamic diversity to achieve durable disease resistance in agricultural ecosystems

“…In addition, co-infection by different pathogen species increases the likelihood of horizontal transfer of genes among pathogens infecting the same host, as reported recently for several wheat pathogens (e.g. Friesen et al 2006;Gardiner et al 2012;McDonald et al 2013).…”

Rapid emergence of pathogens in agro-ecosystems: global threats to agricultural sustainability and food security

“…The higher host and pathogen density found in agro-ecosystems also increases the likelihood of co-infection by different pathogen species, which also selects for higher virulence as a result of competition among pathogen species for the same host resources [12]. Co-infection by different pathogen species also increases the likelihood of horizontal gene transfer, as already described for several crop pathogens [13][14][15] that acquired genes affecting virulence, in some cases from other pathogens infecting the same host [13]. Finally, the global trade in agricultural products accelerated the movement of crop pathogens around the world and led to the rapid global spread of novel, highly damaging pathogens (e.g.…”

Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen

“…Various mechanisms have been described that facilitate rapid development of novel effector genes in pathogenic microbes, including diversity at genomic locations enriched for transposons, mutation, and recombination in subtelomeric regions (McDonagh et al 2008;Chuma et al 2011), coregulated gene clusters (Pallmer and Keller 2010;Schirawski et al 2010), small dispensable chromosomes (Coleman et al 2009;Ma et al 2010;Stukenbrock et al 2010;Goodwin et al 2011;Raffaele and Kamoun 2012), gene sparse regions (Raffaele et al 2010), ATrich isochore-like regions (van der Wouw et al 2010; Rouxel et al 2011), genome hybridization , and horizontal gene transfer (Friesen et al 2006;de Jonge et al 2012;Gardiner et al 2012). However, most of these mechanisms have been described in species that can reproduce sexually, and of which the genomes were shaped by repeat-driven expansion (Raffaele and Kamoun 2012).…”