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

Dan Hou,Lihua Xie,Xiangyu Li,Juan Li,Shaohua Mu,Jian Gao,Zhanchao Cheng

doi:10.3389/fpls.2018.00738

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.

Highlights

The MYB gene family, one of the largest transcription factor (TF) families in plants, is defined by a highly conserved MYB DNA binding domain (DBD) at the N-terminus (Lipsick, 1996)
Numerous studies have shown that R2R3MYB TF is involve in physiological and biochemical processes, especially in responses to the various biotic and abiotic stresses, and participate in hormone synthesis and signal transduction (Dubos et al, 2010; Du et al, 2012a; Katiyar et al, 2012; Baldoni et al, 2015; Wang et al, 2015), such as AtMYB15, AtMYB30, AtMYB60 and AtMYB96 from Arabidopsis (Cominelli et al, 2005; Raffaele et al, 2008; Li et al, 2009; Seo et al, 2009; Seo and Park, 2010), the OsMYB4, OsMYB30, OsMYB2, and OsMYB3R-2 from rice (Agarwal et al, 2006; Dai et al, 2007; Yang et al, 2012; Lv et al, 2017)
The amino acid sequences of Arabidopsis and rice were obtained from The Arabidopsis Information Resource (TAIR) and Rice Genome Annotation Project database7,8, while the protein sequences of Brachypodium R2R3MYBs were download from the Phytozome version 11.0 database9

Summary

Introduction

The MYB gene family, one of the largest transcription factor (TF) families in plants, is defined by a highly conserved MYB DNA binding domain (DBD) at the N-terminus (Lipsick, 1996). OsMYB4 is strongly induced by cold treatment in rice, its overexpression in Arabidopsis significant increased chilling and freezing tolerance of transgenic plants by affecting cold-related genes expressions (Vannini et al, 2004). An MYB gene from Betula platyphylla (BplMYB46) improved salt and osmotic tolerance of transgenic birch plants It increased lignin deposition and secondary cell wall thickness by directly activating the expression of genes involved secondary cell wall biosynthesis (Guo et al, 2017). In Eucalyptus, “EgMYB1, which is known to repress lignin biosynthesis, interacts with a linker histone variant, EgH1.3 They integrate developmental signals to prevent premature or inappropriate lignification of secondary cell walls, providing a mechanism to fine-tune the differentiation of xylem cells in time and space” (Soler et al, 2017)

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Conclusion