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Background  Whiteflies are a threat to cassava ( Manihot esculenta ), an important staple food in many tropical/subtropical regions. Understanding the molecular mechanisms regulating cassava’s responses against this pest is crucial for developing control strategies. Pathogenesis-related (PR) protein families are an integral part of plant immunity. With the availability of whole genome sequences, the annotation and expression programs of the full complement of  PR  genes in an organism can now be achieved. An understanding of the responses of the entire complement of  PR  genes during biotic stress and to the defense hormones, salicylic acid (SA) and jasmonic acid (JA), is lacking. Here, we analyze the responses of cassava  PR  genes to whiteflies, SA, JA, and other biotic aggressors.    Results  The cassava genome possesses 14 of the 17 plant  PR  families, with a total of 447  PR  genes. A cassava  PR  gene nomenclature is proposed. Phylogenetic relatedness of cassava PR proteins to each other and to homologs in poplar, rice and Arabidopsis identified cassava-specific  PR  gene family expansions. The temporal programs of  PR  gene expression in response to the whitefly ( Aleurotrachelus socialis ) in four whitefly-susceptible cassava genotypes showed that 167 of the 447  PR  genes were regulated after whitefly infestation. While the timing of  PR  gene expression varied, over 37% of whitefly-regulated  PR  genes were downregulated in all four genotypes. Notably, whitefly-responsive  PR  genes were largely coordinately regulated by SA and JA. The analysis of cassava  PR  gene expression in response to five other biotic stresses revealed a strong positive correlation between whitefly and  Xanthomonas axonopodis  and  Cassava Brown Streak Virus  responses and negative correlations between whitefly and  Cassava Mosaic Virus  responses .  Finally, certain associations between  PR  genes in cassava expansions and response to biotic stresses were observed among  PR  families.    Conclusions  This study represents the first genome-wide characterization of  PR  genes in cassava.  PR  gene responses to six biotic stresses and to SA and JA are demonstrably different to other angiosperms. We propose that our approach could be applied in other species to fully understand  PR  gene regulation by pathogens, pests and the canonical defense hormones SA and JA.

bmc genomics

Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid