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 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 (oligogala...
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Frontiers Media S.A.
2025-01-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2024.1474781/full |
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| author | Aaron Harvey Aaron Harvey Noëlani van den Berg Noëlani van den Berg Velushka Swart Velushka Swart |
| author_facet | Aaron Harvey Aaron Harvey Noëlani van den Berg Noëlani van den Berg Velushka Swart Velushka Swart |
| author_sort | Aaron Harvey |
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| description | 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 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 Persea americana (Pa)WAKs and 62 PaWAKLs 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. 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. |
| format | Article |
| id | doaj-art-48c38dec9bdc4af18fc81cdfe19793e0 |
| institution | Kabale University |
| issn | 1664-462X |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj-art-48c38dec9bdc4af18fc81cdfe19793e02025-01-29T06:46:17ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2025-01-011510.3389/fpls.2024.14747811474781In silico characterisation of the avocado WAK/WAKL gene family with a focus on genes involved in defence against Phytophthora cinnamomiAaron Harvey0Aaron Harvey1Noëlani van den Berg2Noëlani van den Berg3Velushka Swart4Velushka Swart5Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South AfricaHans Merensky Chair in Avocado Research, Forestry & Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South AfricaDepartment of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South AfricaHans Merensky Chair in Avocado Research, Forestry & Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South AfricaDepartment of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South AfricaHans Merensky Chair in Avocado Research, Forestry & Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South AfricaThe 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 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 Persea americana (Pa)WAKs and 62 PaWAKLs 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. 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.https://www.frontiersin.org/articles/10.3389/fpls.2024.1474781/fullPersea americanawall-associated kinasewall-associated kinase-likepromoter analysisexpression analysisprotein modelling |
| spellingShingle | Aaron Harvey Aaron Harvey Noëlani van den Berg Noëlani van den Berg Velushka Swart Velushka Swart In silico characterisation of the avocado WAK/WAKL gene family with a focus on genes involved in defence against Phytophthora cinnamomi Frontiers in Plant Science Persea americana wall-associated kinase wall-associated kinase-like promoter analysis expression analysis protein modelling |
| title | In silico characterisation of the avocado WAK/WAKL gene family with a focus on genes involved in defence against Phytophthora cinnamomi |
| title_full | In silico characterisation of the avocado WAK/WAKL gene family with a focus on genes involved in defence against Phytophthora cinnamomi |
| title_fullStr | In silico characterisation of the avocado WAK/WAKL gene family with a focus on genes involved in defence against Phytophthora cinnamomi |
| title_full_unstemmed | In silico characterisation of the avocado WAK/WAKL gene family with a focus on genes involved in defence against Phytophthora cinnamomi |
| title_short | In silico characterisation of the avocado WAK/WAKL gene family with a focus on genes involved in defence against Phytophthora cinnamomi |
| title_sort | in silico characterisation of the avocado wak wakl gene family with a focus on genes involved in defence against phytophthora cinnamomi |
| topic | Persea americana wall-associated kinase wall-associated kinase-like promoter analysis expression analysis protein modelling |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2024.1474781/full |
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