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ORIGINAL RESEARCH article

Front. Plant Sci.
Sec. Plant Bioinformatics
Volume 15 - 2024 | doi: 10.3389/fpls.2024.1474781

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

Provisionally accepted
Aaron Harvey Aaron Harvey 1,2Noelani Van Den Berg Noelani Van Den Berg 1,2Velushka Swart Velushka Swart 1,2*
  • 1 Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
  • 2 Forestry and Agricultural Biotechnology Institute,Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa

The final, formatted version of the article will be published soon.

    The avocado industry faces a significant threat from the hemibiotrophic oomycete pathogen Phytophthora cinnamomi. A variably expressed defence gene during an avocado infection trial was a Wall-associated kinase (WAK). 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 P. cinnamomi-avocado defence interaction, this gene family was assessed using in silico methods. In this study, previously generated RNA-sequencing data were used to associate genes with the defence response, followed by promoterand 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 Persea americana (Pa)WAKs and 62 PaWAKLs across the West-Indian (pure accession reference), Dusa ® , Leola TM and R0.12 avocado rootstock genomes. These genes showed distribution across the West-Indian genome's chromosomes, with MCScanX analyses predicting tandem duplications. PaWAK/WAKL expression profiles were compared, implicating five PaWAK/WAKLs 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.

    Keywords: Persea americana, Wall-associated kinase, wall-associated kinase-like, Promoter Analysis, expression analysis, Protein modelling, Protein-ligand binding

    Received: 02 Aug 2024; Accepted: 24 Dec 2024.

    Copyright: © 2024 Harvey, Van Den Berg and Swart. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Velushka Swart, Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, 0028, South Africa

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.