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Genome‑wide identification and expression analysis of GeBP transcription factor gene family in moso bamboo
SHAN Xuemeng, YANG Kebin, SHI Jingjing, ZHU Chenglei, GAO Zhimin
JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2020, Vol. 44 ›› Issue (3) : 41-48.
PDF(2190 KB)
PDF(2190 KB)
Genome‑wide identification and expression analysis of GeBP transcription factor gene family in moso bamboo
Molecular characteristics and expression pattern of GeBP transcription factors (TFs) in moso bamboo (Phyllostachys edulis) were studied in order to help reveal the role of GeBP TFs involved in the formation of trichomes.
Bioinformatic tools were used for systematic analyses of GeBP TFs in moso bamboo, including the online software GSDS 2.0 to examine gene structure, ExPaSy to investigate basic physicochemical properties, and Plant mPLoc to study protein structural characteristics and their subcellular locations. Phylogenetic analyses were performed using MEGA6.0 and amino acid sequences of GeBPs of different species. Transcriptome data generated from different tissues such as rhizome roots, stem roots, shoots, leaves and sheath blades were used to analyze expression patterns of GeBP genes in moso bamboo. Quantitative reverse?transcription PCR (qRT?PCR) was performed to assess expression patterns of GeBP genes using cDNA of different amounts of trichome tissue.
A total of 16 members of the GeBP gene family were identified in the genome of moso bamboo (PeGeBP1 to PeGeBP16). Only three PeGeBPs (PeGeBP3, PeGeBP4 and PeGeBP5) contained introns (n = 1， n = 1， n = 5, respectively). The molecular weight of proteins encoded by PeGeBPs ranged from 23.37 to 62.17 ku, and the theoretical isoelectric points ranged from 5.02 to 10.14. Predictions of subcellular locations showed that five PeGeBPs are located in both nucleus and cytoplasm, ten PeGeBPs are in nucleus, and one occurs only in the cytoplasm. Phylogenetic analyses suggested four clades of PeGeBPs with five, four, three and four members, respectively; they appeared to be closely related to those of Oryza sativa and Brachypodium distachyum and distantly related to those of Arabidopsis thaliana and Populus trichocarpa. Transcriptome data indicated that all PeGeBPs are expressed in rhizome roots, stem roots, shoots, leaves and sheath blades, at certain differences, apart from PeGeBP5 which was not expressed in leaves. qRT?PCR results showed that 16 PeGeBPs occurred in leaves, shoots, sheaths, sheath blades and cilia, and significant differences between tissue types were observed. Expression levels of 12 PeGeBPs in tissues containing trichomes such as leaves, sheaths, sheath blades and cilia were higher than those in shoots without trichomes. Only PeGeBP16 showed higher expression levels in shoots than that in other tissues. Moreover, expression levels of the other three genes in bamboo shoots were also low.
Sixteen GeBP genes were identified in moso bamboo, and their expression levels differed significantly between tissues, suggesting functional diversity. Expression levels of 12 out of 16 PeGeBPs were higher in tissues containing trichomes than that in tissues without trichomes, suggesting that these genes may be involved in the regulation of trichome formation.
Phyllostachys edulis / GeBP transcription factor genes / expression pattern / trichome
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