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

Abstract

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.

Effect of the AM Fungus Sieverdingia tortuosa on Common Vetch Responses to an Anthracnose Pathogen

“…Our results showed that the AM fungus improved the resistance of plants to pathogens by regulating PR proteins, since the expression of their genes was upregulated. It was worth noting that JA and SA can induce PR protein-related gene expression in plants (Irigoyen et al, 2020). The upregulation of the genes for PR proteins in AM plants is linked with the higher concentrations of JA and SA in the plant shoots.…”

Viral inosine triphosphatase: A mysterious enzyme with typical activity, but an atypical function

“…Several studies have shown that cassava responds to (U)CBSV infection with increased expression of genes belonging to the pathogenesis‐related (PR) gene family (Amuge et al, 2017; Anjanappa et al, 2018; Irigoyen et al, 2020). PR proteins are frequently used as biomarkers for defence signalling pathways and are associated with increases in plant hormones such as salicylic acid (SA) (Ali et al, 2018).…”

Changes in gene expression in potato meristems treated with the sprout suppressor 1,4-dimethylnaphthalene are dependent on tuber age and dormancy status

“…PR5 has been shown to be induced in response to salt and drought stress [ 21 ]. The results from Gene Ontology analysis demonstrate gene networks linked to SA are increased in response to DMN and previous research has shown that SA and Jasmonic acid alter the expression of PR proteins [ 22 ]. Thus, DMN may be functioning through this SA signaling mechanism in potato tubers to induce the drought associated protein PR5.…”