Pathogens shape diversity and species abundances in plant communities, as shown in studies where locally rare species were more sensitive to pathogen-mediated negative density dependence (NDD). Transcritome data for six species Beilschmiedia pendula, Brosimum alicastrum, Brosimum alicastrum, Eugenia nesiotica, Lacmellea panamensis, and Virola surinamensis) in this study were used to demonstrate that locally rare species in a Panamanian forest have reduced allelic diversity in pathogen resistance (R) genes, in a manner correlated with differences in NDD. Maternal seedling cohorts of less abundant tree species were more co-susceptible to microbial pathogens, had reduced defense gene induction following exposure to live soil, and provoked less self-defense in their root-associated fungi. Locally rare species showed no reduction in transcriptome-wide polymorphism or hormonally induced defenses downstream of pathogen recognition. These results indicate that disproportionate reduction in diversity of allele-rich R genes increases pathogen co-susceptibility and NDD. Locally rare species may be hindered from increasing in abundance without genetic boosts to defense via immigration of novel R gene alleles from a larger and more diverse regional population.Post-dispersal seeds were collected from the ground beneath the canopy of five fruiting trees from each of six species. These species were chosen to match as closely as possible a set of species tested previously for effects of exposure to conspecific soil (Mangan et al. 2010). One of the species in that previous study, Tetragastris panamensis, was not in fruit when seed collection took place and was replaced by Dipteryx oleifera. Seeds were surface sterilized (15 minutes 70% ETOH, 10 minutes 10% chlorine, 5 minutes ETOH and rinsed with water) then germinated in a twice autoclaved (220oC, 1 hour each) sand-field soil mix in germination trays. Seedlings were then transplanted into individual 1-L pots filled with twice autoclaved soil/sand. We grew 15 seedlings per parent, divided evenly among three soil treatments: Control; sterile soil; SA: sterile soil soaked 48 hrs prior to harvest with salicylic acid (0.3g of SA to 100ml of distilled water per pot; volume of all pots were identical and weighed approximately 1kg); Live Soil inoculation: at 60 hrs pre-harvest a small quantity (50 ml) of live soil comprising a standardized mix from multiple sites on the study plot (one from beneath a tree of each focal species) was added to each seedling pot. The 1-mo seedlings were uprooted, roots were washed free of soil, flash-frozen, and shipped under permits and IP agreements involving Smithsonian Tropical Research Institute, Panama, USDA, and Penn State University. Using the root sample from each individual seedling, high quality RNA was isolated via a CTAB protocol (adapted from (Gambino et al. 2008)), 75 RNA samples per species [except Beilschmiedia, which has N=50], mean RIN numbers 7.5 - 8.4). Pools of RNA (5 seedlings per pool) submitted for sequencing (N = 10 to 15 pools per species) were prepared using equal amounts of total RNA from each individual (800ng) within each combination of parent tree (N = 5) and seedling treatment (N = 3). For each tree species, the PSU Genomics Core Facility prepared 15 bar coded libraries (TruSeq Stranded mRNA Sample Preparation Kit) and combined equimolar quantities for one lane of 2 x 150 bp paired-end sequencing on PSU's Illumina HiSeq 2500.