Genetic variation in a plant-parasitic nematode is associated with gene expression changes conserved across evolutionarily distant host plants

ABSTRACT A hallmark of the interactions between endoparasites (parasites that live within plant tissue) and their hosts, is the parasites’ ability to hijack host gene expression to support their own existence. While a number of studies have been performed to identify plant genes that are recruited in this process, there is much that remains unknown. One mechanism by which these connections can be explored is using a traditional genetics approach – identifying connections between genetic variation and phenotype variation. To that end, we leverage experiments examining tissue from three host plants, each infected with one of two genetically distinct strains of the endoparasite Meloidogyne hapla . Using gene expression profiles, we identify plant genes that differ based on the genetic background of the parasite, and show that these signals are common across plant hosts. These results indicate that the plant genes recruited by the parasite differ according to the parasite’s genetic background, and that these alternative patterns are conserved across evolutionarily distant hosts. We also leverage public data to identify conserved host expression differences when comparing M. hapla -infected roots to uninfected root tissue. Finally, we demonstrate that parasite gene expression varies based on the parasites’ genetic background, and these signals are also conserved when inhabiting different host species.