Genome-Wide Analysis of the MYB Transcription Factor Superfamily in Physcomitrella patens

Abstract

MYB transcription factors (TFs) are one of the largest TF families in plants to regulate numerous biological processes. However, our knowledge of the MYB family in Physcomitrella patens is limited. We identified 116 MYB genes in the P. patens genome, which were classified into the R2R3-MYB, R1R2R3-MYB, 4R-MYB, and MYB-related subfamilies. Most R2R3 genes contain 3 exons and 2 introns, whereas R1R2R3 MYB genes contain 10 exons and 9 introns. N3R-MYB (novel 3RMYB) and NR-MYBs (novel RMYBs) with complicated gene structures appear to be novel MYB proteins. In addition, we found that the diversity of the MYB domain was mainly contributed by domain shuffling and gene duplication. RNA-seq analysis suggested that MYBs exhibited differential expression to heat and might play important roles in heat stress responses, whereas CCA1-like MYB genes might confer greater flexibility to the circadian clock. Some R2R3-MYB and CCA1-like MYB genes are preferentially expressed in the archegonium and during the transition from the chloronema to caulonema stage, suggesting their roles in development. Compared with that of algae, the numbers of MYBs have significantly increased, thus our study lays the foundation for further exploring the potential roles of MYBs in the transition from aquatic to terrestrial environments.

Comprehensive analysis of the Ppatg3 mutant reveals that autophagy plays important roles in gametophore senescence in Physcomitrella patens

“…Full length coding sequence (lacking the stop codon) of PpATG3 was PCR amplified from P. patens cDNA template using the primers PpATG3-F and PpATG3-R (Additional file 10 ). The resulting 921-bp PCR fragment was cloned using KpnI and XbaI restriction enzymes (Thermo Scientific FastDigest, FD0524 and FD0684) into the vector pM999 [ 55 ] by sticky end ligation. The pM999 contains the eGFP coding sequence driven by a 35S promoter.…”

Expression of MYB transcription factor gene ZmMYB59 affects seed germination in Nicotiana tabacum and Oryza sativa

“…In T 2 generation transgenic tobacco, compared to WT lines, the contents of endogenous GA 1 , GA 3 , GA 4 , IAA, CTK were reduced by 21.1~39.2%, 18.7~29.9%, 3.3~15.4%, 3.4~7.5% and 27.9~44.8%, whereas the content of ABA was increased by 23.8~43.9% (Table 5). In T 2 generation transgenic rice, the contents of endogenous GA 1 , GA 3 , GA 4 , IAA and CTK were decreased by 29.4~47.6%, 14.9~22.3%, 15.4~24.3%, 5.7~10.0% and 15.7~37.8%, whereas the content of ABA was increased by 17.9~26.9% (Table 5). Among them, the changes of endogenous GA 1 , CTK and ABA reached significant level while there were no significant changes in those of endogenous GA 3 , GA 4 and IAA.…”

“…Depending on the number of conserved motifs, the superfamily is divided into four classes: R1-MYB, R2R3-MYB, R1R2R3-MYB and 4R-MYB [12]. The functions of MYB proteins have been probed in plentiful plant species such as Arabidopsis, maize, rice, petunia, snapdragon, grapevine, poplar and apple [9], involving the regulation of cell differentiation, plant development, organ morphogenesis, phytohormone response, stress tolerance, secondary metabolism [13,14].…”

Expression of MYB transcription factor gene ZmMYB59 affects seed germination in Nicotiana tabacum and Oryza sativa

“…Depending on the number of conserved motifs, the superfamily is divided into four classes: R1-MYB, R2R3-MYB, R1R2R3-MYB and 4R-MYB [12]. The functions of MYB proteins have been probed in plentiful plant species such as Arabidopsis, maize, rice, petunia, snapdragon, grapevine, poplar and apple [9], involving the regulation of cell differentiation, plant development, organ morphogenesis, phytohormone response, stress tolerance, secondary metabolism [13,14].…”