Phylogeny and evolution of plant Phytochrome Interacting Factors (PIFs) gene family and functional analyses of PIFs in Brachypodium distachyon

Evolutionary studies of the basic helix–loop–helix (bHLH) IVc gene family in plants and the role of AtILR3 in Arabidopsis response to ABA stress

“…To confirm the subcellular localization of the AtILR3 , a transient transformation assay of 35S : AtILR3 ‐GFP constructs was executed in N. benthamiana leaves and green fluorescent signals were surveyed at 48 hours post‐incubation (hpi) by confocal microscopy. The control cells expressing GFP alone were distributed throughout the entire cell without specific compartment, while the AtILR3 ‐GFP green fluorescence signal was symmetrically observed in the nuclei (Figure 6A), suggesting that the AtILR3 could be a nucleus‐localized protein, as in accordance with the predicted results (Table S6) and similar to the localization of other bHLH proteins in A. thaliana (Aparicio & Pallas 2017; Jiang et al, 2022).…”

“…The control cells expressing GFP alone were distributed throughout the entire cell without specific compartment, while the AtILR3-GFP green fluorescence signal was symmetrically observed in the nuclei (Figure 6A), suggesting that the AtILR3 could be a nucleus-localized protein, as in accordance with the predicted results (Table S6) and similar to the localization of other bHLH proteins in A. thaliana (Aparicio & Pallas 2017;Jiang et al, 2022).…”

Evolution of the WRKY66 Gene Family and Its Mutations Generated by the CRISPR/Cas9 System Increase the Sensitivity to Salt Stress in Arabidopsis

“…The ancestral genes of the WRKY66 homologs had been duplicated in angiosperm genomes, prior to the radiation of extent flowering plants. Strictly speaking, the WRKY66 orthologs were angiosperm-specific because they were all derived from the angiosperm-specific duplication events ( Figure 1 B), similar to the divergence pattern of the PIF , BEL1 and ANT [ 38 , 39 ]. Then, the whole genome duplication giving rise to modern angiosperms [ 40 ], together with additional tandem duplications [ 41 ], thus created the genetic substrate for the structural and functional diversification of genes.…”

Genome-Wide Identification of Phytochrome-Interacting Factor (PIF) Gene Family in Potatoes and Functional Characterization of StPIF3 in Regulating Shade-Avoidance Syndrome

“…Phytochrome-interacting factors have been discovered as regulatory hubs that integrate environmental cues into transcriptional scenarios, and functional characterizations have shown that PIF proteins are widely involved in plant growth, development, and stress response biological processes [30,31]. Several PIF genes have been identified in many species; for example, eight candidate PIF genes have been reported in Arabidopsis [9], tomatoes [12], maize [11,32], apples [13,33], and Brachypodium distachyon [15]; six have been reported in rice [10] and Physcomitrella patens [17]; and only one has been reported in Marchantia polymorpha [16]. However, the PIF genes have been insufficiently identified in potatoes to date.…”

“…PIF proteins are encoded by a subfamily of bHLH transcription factors with two conserved domains, bHLH and APB (active phyB-binding) [8], that are widely distributed from bryophytes to higher plants and have been identified from bryophytes to angiosperms, such as Arabidopsis (Arabidopsis thaliana, eight members) [9], rice (Oryza sativa, six members) [10], maize (Zea mays, eight members) [11], tomatoes (Solanum lycopersicum, eight members) [12], apples (Malus domestica, eight members) [13], grapes (Vitis vinifera, four members) [14], Brachypodium distachyon (eight members) [15], Marchantia polymorpha (one member) [16], and Physcomitrella patens (six members) [17]. Previous studies have demonstrated that PIFs are diffusely involved in many processes of plant development and growth, such as seed germination, embryo shaft elongation, chlorophyll biosynthesis, shade-avoidance responses, circadian clock, and so on [18].…”