In silico characterisation of the avocado WAK/WAKL gene family with a focus on genes involved in defence against Phytophthora cinnamomi

The avocado industry faces a significant threat from the hemibiotrophic oomycete pathogen <i>Phytophthora cinnamomi</i>. A variably expressed defence gene during an avocado infection trial was a <i>Wall-associated kinase</i> (<i>WAK</i>). WAK and WAK-Like (WAKL) proteins are known to bind to fragmented pectin (oligogalacturonides) produced during pathogen penetration, thereby activating downstream defence-related pathways. To better understand the <i>P. cinnamomi</i>-avocado defence interaction, this gene family was assessed using <i>in silico</i> methods. In this study, previously generated RNA-sequencing data were used to associate genes with the defence response, followed by promoter- and phylogenetic analysis of these genes/proteins. The predicted proteins from these genes were modelled with AlphaFold2, and structural similarity across different rootstocks, as well as their binding affinity for oligogalacturonides, were assessed. The analysis identified 14 <i>Persea americana</i> (<i>Pa)WAK</i>s and 62 <i>PaWAKL</i>s across the West-Indian (pure accession reference), Dusa^®, Leola™ and R0.12 avocado rootstock genomes. These genes showed distribution across the West-Indian genome's chromosomes, with MCScanX analyses predicting tandem duplications. <i>PaWAK/WAKL</i> expression profiles were compared, implicating five <i>PaWAK/WAKL</i>s in defence. Phylogenetic and promoter analyses were conducted to predict associated defence-related pathways, focusing on stress and phytohormone-responsive pathways. Structural differences and varying oligogalacturonide binding affinities of PaWAK/WAKLs were predicted across rootstocks. These defence-related genes could be incorporated into a molecular screening tool to improve the development of resistant avocado rootstocks.