Phylogenomic analysis reveals exceptions to the co-evolution of ZAR1 and ZRK immune gene families in plants
Abstract Background HOPZ-ACTIVATED RESISTANCE 1 (ZAR1) is a nucleotide-binding leucine-rich repeat (NLR) protein functioning as a recognition hub to initiate effector-triggered immunity against bacterial pathogens. To initiate defense, ZAR1 associates with different HOPZ-ETI-DEFICIENT 1 (ZED1)-Relat...
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2025-01-01
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| Online Access: | https://doi.org/10.1186/s12870-025-06099-4 |
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| author | Li Yang Shengyi Liu M. Eric Schranz Klaas Bouwmeester |
| author_facet | Li Yang Shengyi Liu M. Eric Schranz Klaas Bouwmeester |
| author_sort | Li Yang |
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| description | Abstract Background HOPZ-ACTIVATED RESISTANCE 1 (ZAR1) is a nucleotide-binding leucine-rich repeat (NLR) protein functioning as a recognition hub to initiate effector-triggered immunity against bacterial pathogens. To initiate defense, ZAR1 associates with different HOPZ-ETI-DEFICIENT 1 (ZED1)-Related Kinases (ZRKs) to form resistosomes to indirectly perceive effector-induced perturbations. Few studies have focused on the phylogenomic characteristics of ZAR1 and ZRK immune gene families and their evolutionary relationships. To trace the origin and divergence of ZAR1 and ZRK immune gene families across the plant kingdom, we performed phylogenomic analyses using an extended set of plant genomes. Results Genome-wide identification of ZAR1 and ZRK immune gene families by blast similarity searches combined with phylogenetic analysis showed that these two gene families have experienced frequent gene losses in massive lineages. Gene distribution patterns across the plant kingdom revealed that ZAR1 and ZRK emerged after the divergence of most angiosperms from Amborella and before the split of magnoliids, monocots, and eudicots. Co-occurrence of ZAR1-A and ZRKs was found in various plant species belonging to different angiosperm orders, but both genes were found to be absent in chlorophyta, bryophytes, lycophytes, ferns, and gymnosperms. We also detected a large number of concerted gene losses in angiosperms, especially within the orders Fabales, Cucurbitales, Asterales, and Apiales. All analysed monocot genomes thus far examined, except for the aroid Colocasia esculenta, were previously reported to lack both ZAR1-A and ZRKs. Here we now report other exceptions on the concerted ZAR1-A–ZRKs presence-absence pattern within several early diverging monocot lineages, including the genome of Acorus tatarinowii—a species representing the first branching monocot lineage. We also revealed strong variation in ZAR1-A–ZRKs co-occurrence within the asterid order Ericales, suggesting patterns of de-coevolution in angiosperms. Our research further shows that both gene families experienced significant diversification through various duplication events. Additionally, their evolutionary paths have been shaped by frequent gene losses and lineage-specific transposition. Conclusion This study provides novel findings on the evolution of ZAR1 and ZRK immune gene families across a wide range of plant species, suggesting that more potential exceptions can be expected when expanding the list of sequenced genomes from distinct orders. Our results provide new hypotheses about the origin and diversification of these critical immune genes for future functional studies. |
| format | Article |
| id | doaj-art-519c923b01c84b478a6ba423d1f8ade8 |
| institution | Kabale University |
| issn | 1471-2229 |
| language | English |
| publishDate | 2025-01-01 |
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| spelling | doaj-art-519c923b01c84b478a6ba423d1f8ade82025-01-26T12:23:27ZengBMCBMC Plant Biology1471-22292025-01-0125111710.1186/s12870-025-06099-4Phylogenomic analysis reveals exceptions to the co-evolution of ZAR1 and ZRK immune gene families in plantsLi Yang0Shengyi Liu1M. Eric Schranz2Klaas Bouwmeester3Biosystematics Group, Wageningen University and ResearchKey Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural SciencesBiosystematics Group, Wageningen University and ResearchBiosystematics Group, Wageningen University and ResearchAbstract Background HOPZ-ACTIVATED RESISTANCE 1 (ZAR1) is a nucleotide-binding leucine-rich repeat (NLR) protein functioning as a recognition hub to initiate effector-triggered immunity against bacterial pathogens. To initiate defense, ZAR1 associates with different HOPZ-ETI-DEFICIENT 1 (ZED1)-Related Kinases (ZRKs) to form resistosomes to indirectly perceive effector-induced perturbations. Few studies have focused on the phylogenomic characteristics of ZAR1 and ZRK immune gene families and their evolutionary relationships. To trace the origin and divergence of ZAR1 and ZRK immune gene families across the plant kingdom, we performed phylogenomic analyses using an extended set of plant genomes. Results Genome-wide identification of ZAR1 and ZRK immune gene families by blast similarity searches combined with phylogenetic analysis showed that these two gene families have experienced frequent gene losses in massive lineages. Gene distribution patterns across the plant kingdom revealed that ZAR1 and ZRK emerged after the divergence of most angiosperms from Amborella and before the split of magnoliids, monocots, and eudicots. Co-occurrence of ZAR1-A and ZRKs was found in various plant species belonging to different angiosperm orders, but both genes were found to be absent in chlorophyta, bryophytes, lycophytes, ferns, and gymnosperms. We also detected a large number of concerted gene losses in angiosperms, especially within the orders Fabales, Cucurbitales, Asterales, and Apiales. All analysed monocot genomes thus far examined, except for the aroid Colocasia esculenta, were previously reported to lack both ZAR1-A and ZRKs. Here we now report other exceptions on the concerted ZAR1-A–ZRKs presence-absence pattern within several early diverging monocot lineages, including the genome of Acorus tatarinowii—a species representing the first branching monocot lineage. We also revealed strong variation in ZAR1-A–ZRKs co-occurrence within the asterid order Ericales, suggesting patterns of de-coevolution in angiosperms. Our research further shows that both gene families experienced significant diversification through various duplication events. Additionally, their evolutionary paths have been shaped by frequent gene losses and lineage-specific transposition. Conclusion This study provides novel findings on the evolution of ZAR1 and ZRK immune gene families across a wide range of plant species, suggesting that more potential exceptions can be expected when expanding the list of sequenced genomes from distinct orders. Our results provide new hypotheses about the origin and diversification of these critical immune genes for future functional studies.https://doi.org/10.1186/s12870-025-06099-4Immune genesPhylogenomicsEvolutionary relationshipsGene conservationGene synteny |
| spellingShingle | Li Yang Shengyi Liu M. Eric Schranz Klaas Bouwmeester Phylogenomic analysis reveals exceptions to the co-evolution of ZAR1 and ZRK immune gene families in plants BMC Plant Biology Immune genes Phylogenomics Evolutionary relationships Gene conservation Gene synteny |
| title | Phylogenomic analysis reveals exceptions to the co-evolution of ZAR1 and ZRK immune gene families in plants |
| title_full | Phylogenomic analysis reveals exceptions to the co-evolution of ZAR1 and ZRK immune gene families in plants |
| title_fullStr | Phylogenomic analysis reveals exceptions to the co-evolution of ZAR1 and ZRK immune gene families in plants |
| title_full_unstemmed | Phylogenomic analysis reveals exceptions to the co-evolution of ZAR1 and ZRK immune gene families in plants |
| title_short | Phylogenomic analysis reveals exceptions to the co-evolution of ZAR1 and ZRK immune gene families in plants |
| title_sort | phylogenomic analysis reveals exceptions to the co evolution of zar1 and zrk immune gene families in plants |
| topic | Immune genes Phylogenomics Evolutionary relationships Gene conservation Gene synteny |
| url | https://doi.org/10.1186/s12870-025-06099-4 |
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