The R2R3MYB Gene Family in Phyllostachys edulis: Genome-Wide Analysis and Identification of Stress or Development-Related R2R3MYBs

Abstract

The MYB transcription factor (TF) is one of the largest gene families in plants and involved to multiple biological processes. However, little is known about the MYB family and its functional role in the genome of moso bamboo. In the present study, a total of 114 R2R3MYB genes were first identified from moso bamboo genome and full-length non-chimeric (FLNC) reads. Phylogenetic analysis coupled with gene structure analysis and motif determination resulted in the division of these PheR2R3MYBs into 17 subgroups. The position of eight proteins along an external branch in the phylogenetic tree suggested their relatively ancient origin. The genes in this group were all substituted by (Met, M)/(Arg, R) at conservative W residues in both R2 and R3 repeats, and half were found to possess no transcriptional activation activity. The analysis of evolutionary patterns and divergence suggests that the expansion of PheMYBs was mainly attributable to whole genome duplication (WGD) under different selection pressures. Expressional analysis based on microarray and qRT-PCR data performed diverse expression patterns of R2R3MYBs in response to both various abiotic stimuli and flower development. Furthermore, the co-expression analysis of R2R3MYBs suggested an intricate interplay of growth- and stress-related responses. Finally, we found a hub gene, PheMYB4, was involved in a complex proteins interaction network. Further functional analysis indicated that ectopic overexpression of its homologous gene, PheMYB4-1, could increase tolerance to cold treatment and sensitivity to drought and salt treatment of transgenic Arabidopsis seedlings. These findings provide comprehensive insights into the MYB family members in moso bamboo and offer candidate MYB genes for further studies on their roles in stress resistance.

Genome-wide analysis of GATA factors in moso bamboo (Phyllostachys edulis) unveils that PeGATAs regulate shoot rapid-growth and rhizome development

“…Moreover, bamboo is known for its fast-growing shoots and widespread rhizomes [2]. It has been reported that several gene families are involved in flower development and abiotic stress [30–32, 41], the rapid-growth associated transcription factors remain elusive. The genome sequences of moso bamboo[33] and transcriptome studies [2, 27, 28, 40] provide important platforms for the identification of rapid-growth shoot and rhizome development associated gene families.…”

“…Recently, large-scale transcriptome analysis has shown that light and phytohormones may play important roles in the rapid-growth of bamboo [27–29]. In addition, a large number of transcription factor families are involved in the abiotic stress response and flower development have been studied in moso bamboo [30–32]. Although our group has functionally characterized rapid-growth associated key gene- PeGSK1 , the rapid-growth associated transcription factor families are largely unexplored in moso bamboo.…”

Genome-Wide Analysis and Expression Profiling of the Heat Shock Factor Gene Family in Phyllostachys edulis during Development and in Response to Abiotic Stresses

“…For more accurate identification of Hsf genes in Moso bamboo, multiple database searches were performed according Hou et al [33]. First, Hsf mRNA sequences of Oryza sativa and Brachypodium distachyon, obtained from NCBI Nucleotide database (https://www.ncbi.nlm.nih.gov/) as query sequences to blast against the moso bamboo genome database.…”

Overexpression of PheNAC3 from moso bamboo promotes leaf senescence and enhances abiotic stress tolerance in Arabidopsis

“…To observe the effects of NaCl or mannitol on seed germination and phenotypic differences between WT and OE-PheNAC3 plants, three independent PheNAC3 overexpressing lines (T 3 ) and WT Arabidopsis plants were tested according to method previously methord (Hou et al, 2018). WT and PheNAC3 seeds were sown on 1/2 MS medium solid plates with 150 mM NaCl or 200 mM mannitol, stratified at 4 C for 2 days and then transferred to long-day growth conditions (16 h light/8 h dark cycle at 23 ± 2 C) in a growth chamber.…”