Evolutionary Divergence of Arabidopsis thaliana Classical Peroxidases

Analysis of Arabidopsis thaliana Redox Gene Network Indicates Evolutionary Expansion of Class III Peroxidase in Plants

Reactive oxygen species (ROS) are byproducts of aerobic metabolism and may cause oxidative damage to biomolecules. Plants have a complex redox system, involving enzymatic and non-enzymatic compounds. The evolutionary origin of enzymatic antioxidant defense in plants is yet unclear. Here, we describe the redox gene network for A. thaliana and investigate the evolutionary origin of this network. We gathered from public repositories 246 A. thaliana genes directly involved with ROS metabolism and proposed an A. thaliana redox gene network. Using orthology information of 238 Eukaryotes from STRINGdb, we inferred the evolutionary root of each gene to reconstruct the evolutionary history of A. thaliana antioxidant gene network. We found two interconnected clusters: one formed by SOD-related, Thiol-redox, peroxidases, and other oxido-reductase; and the other formed entirely by class III peroxidases. Each cluster emerged in different periods of evolution: the cluster formed by SOD-related, Thiol-redox, peroxidases, and other oxido-reductase emerged before opisthokonta-plant divergence; the cluster composed by class III peroxidases emerged after opisthokonta-plant divergence and therefore contained the most recent network components. According to our results, class III peroxidases are in expansion throughout plant evolution, with new orthologs emerging in each evaluated plant clade divergence.

Genome-wide and evolutionary analysis of the class III peroxidase gene family in wheat and Aegilops tauschii reveals that some members are involved in stress responses

Background

The class III peroxidase (PRX) gene family is a plant-specific member of the PRX superfamily that is closely related to various physiological processes, such as cell wall loosening, lignification, and abiotic and biotic stress responses. However, its classification, evolutionary history and gene expression patterns are unclear in wheat and Aegilops tauschii.

Results

Here, we identified 374, 159 and 169 PRXs in Triticum aestivum, Triticum urartu and Ae. tauschii, respectively. Together with PRXs detected from eight other plants, they were classified into 18 subfamilies. Among subfamilies V to XVIII, a conserved exon-intron structure within the “001” exon phases was detected in the PRX domain. Based on the analysis, we proposed a phylogenetic model to infer the evolutionary history of the exon-intron structures of PRX subfamilies. A comparative genomics analysis showed that subfamily VII could be the ancient subfamily that originated from green algae (Chlamydomonas reinhardtii). Further integrated analysis of chromosome locations and collinearity events of PRX genes suggested that both whole genome duplication (WGD) and tandem duplication (TD) events contributed to the expansion of T. aestivum PRXs (TaePRXs) during wheat evolution. To validate functions of these genes in the regulation of various physiological processes, the expression patterns of PRXs in different tissues and under various stresses were studied using public microarray datasets. The results suggested that there were distinct expression patterns among different tissues and PRXs could be involved in biotic and abiotic responses in wheat. qRT-PCR was performed on samples exposed to drought, phytohormone treatments and Fusarium graminearum infection to validate the microarray predictions. The predicted subcellular localizations of some TaePRXs were consistent with the confocal microscopy results. We predicted that some TaePRXs had hormone-responsive cis-elements in their promoter regions and validated these predicted cis-acting elements by sequencing promoters.

Conclusion

In this study, identification, classification, evolution, and expression patterns of PRXs in wheat and relative plants were performed. Our results will provide information for further studies on the evolution and molecular mechanisms of wheat PRXs.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-6006-5) contains supplementary material, which is available to authorized users.