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

Abstract

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 ( Tae PRXs) 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 Tae PRXs were consistent with the confocal microscopy results. We predicted that some Tae PRXs 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.

Genome-wide identification, phylogeny and expression analysis of the SPL gene family in wheat

“…However, the number of TaSPLs is higher than that of the above species; in particular, there are threefold as many TaSPLs than TuSPLs and AetSPLs. This relationship of TaSPL with TuSPL and AetSPL is consistent with previous studies on the Prx and PK gene family in wheat, T.urartu, and A. tauschii [30]. It is that wheat is allohexaploid, whose origin involved two polyploidization events, and it appears that many gene duplication events occurred in the wheat genome, allowing the number of TaSPLs to increase compared to other species.…”

A member of wheat class III peroxidase gene family, TaPRX-2A, enhanced the tolerance of salt stress

“…Interestingly, we found that TaPRX-2A was localized in the nucleus with NLSs. Some reports have shown that PRX genes such as TaPRXs, AtGPX8, and GPX in mammals and LjGpx1 were located in the cell nuclei [52][53][54][55][56]. It was reported that a barely PRX possess a putative nuclear localization signal, which is located in the nucleus [57].…”

CsPrx25, a class III peroxidase in Citrus sinensis, confers resistance to citrus bacterial canker through the maintenance of ROS homeostasis and cell wall lignification

“…CIII Prxs are heme-binding proteins that are ubiquitously expressed in all plants and comprise large multigene families [18][19][20][21] . For example, a total of 73 CIII Prxs are present in Arabidopsis thaliana 22,23 , and 138, 374, 93, 94 and 72 have been found in Oryza sativa 24 , Triticum aestivum 25 , Populus trichocarpa 26 , Pyrus bretschneideri 27 and Citrus sinensis 28 , respectively. CIII Prxs regulate the loosening of cell walls, lignification and suberization [29][30][31][32] and participate in ROS and RNS metabolism during abiotic and biotic stress responses [33][34][35] .…”