Genome-wide identification of MADS-box family genes in moso bamboo (Phyllostachys edulis) and a functional analysis of PeMADS5 in flowering

Yuting Zhang,Zaikang Tong,Mingquan Ding,Dingqin Tang,Xinchun Lin

doi:10.1186/s12870-018-1394-2

Abstract

BackgroundMADS-box genes encode a large family of transcription factors that play significant roles in plant growth and development. Bamboo is an important non-timber forest product worldwide, but previous studies on the moso bamboo (Phyllostachys edulis) MADS-box gene family were not accurate nor sufficiently detailed.ResultsHere, a complete genome-wide identification and characterization of the MADS-box genes in moso bamboo was conducted. There was an unusual lack of type-I MADS-box genes in the bamboo genome database (http://202.127.18.221/bamboo/index.php), and some of the PeMADS sequences are fragmented and/or inaccurate. We performed several bioinformatics techniques to obtain more precise sequences using transcriptome assembly. In total, 42 MADS-box genes, including six new type-I MADS-box genes, were identified in bamboo, and their structures, phylogenetic relationships, predicted conserved motifs and promoter cis-elements were systematically investigated. An expression analysis of the bamboo MADS-box genes in floral organs and leaves revealed that several key members are involved in bamboo inflorescence development, like their orthologous genes in Oryza. The ectopic overexpression of one MADS-box gene, PeMADS5, in Arabidopsis triggered an earlier flowering time and the development of an aberrant flower phenotype, suggesting that PeMADS5 acts as a floral activator and is involved in bamboo flowering.ConclusionWe produced the most comprehensive information on MADS-box genes in moso bamboo. Additionally, a critical PeMADS gene (PeMADS5) responsible for the transition from vegetative to reproductive growth was identified and shown to be related to bamboo floral development.

Highlights

MADS-box genes encode a large family of transcription factors that play significant roles in plant growth and development
To acquire the maximum number of MADS-box domain containing sequences in moso bamboo, we built three different Hidden Markov Models (HMM) profiles to search the P. edulis protein dataset based on Arabidopsis, Oryza, and Brachypodium, respectively
The transcriptome reads were indexed as the references, and the incomplete PeMADS sequences were used as query in BLAST algorithm-based searches of the reads database

Summary

Introduction

MADS-box genes encode a large family of transcription factors that play significant roles in plant growth and development. Several MADS-box genes have been reported to control the vegetative to reproductive phase transition in plants and developmental processes in plant organs, such as fruit, root, stem, and leaf [2,3,4]. Functional studies of type-I MADS-box genes have revealed their crucial roles during plant reproduction and development, especially in determining female gametophyte, embryo, and endosperm development in Arabidopsis [22]

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Conclusion