Genomic survey, expression profile and co-expression network analysis of OsWD40 family in rice

Jialing Yao,Xiaolong Huang,Yidan Ouyang,Zhanhua Lu

doi:10.1186/1471-2164-13-100

Abstract

BackgroundWD40 proteins represent a large family in eukaryotes, which have been involved in a broad spectrum of crucial functions. Systematic characterization and co-expression analysis of OsWD40 genes enable us to understand the networks of the WD40 proteins and their biological processes and gene functions in rice.ResultsIn this study, we identify and analyze 200 potential OsWD40 genes in rice, describing their gene structures, genome localizations, and evolutionary relationship of each member. Expression profiles covering the whole life cycle in rice has revealed that transcripts of OsWD40 were accumulated differentially during vegetative and reproductive development and preferentially up or down-regulated in different tissues. Under phytohormone treatments, 25 OsWD40 genes were differentially expressed with treatments of one or more of the phytohormone NAA, KT, or GA3 in rice seedlings. We also used a combined analysis of expression correlation and Gene Ontology annotation to infer the biological role of the OsWD40 genes in rice. The results suggested that OsWD40 genes may perform their diverse functions by complex network, thus were predictive for understanding their biological pathways. The analysis also revealed that OsWD40 genes might interact with each other to take part in metabolic pathways, suggesting a more complex feedback network.ConclusionsAll of these analyses suggest that the functions of OsWD40 genes are diversified, which provide useful references for selecting candidate genes for further functional studies.

Highlights

WD40 proteins represent a large family in eukaryotes, which have been involved in a broad spectrum of crucial functions
Collection and identification of the OsWD40 genes in rice In order to identify the OsWD40 genes in the rice, the consensus protein sequence which is characteristic of WD40 genes in eukaryotes, GECKXVLXGHTSTVTCVAFSPDGPLLASGSRDGTIKIWD, was generated by hmmemit from Hidden Markov Model (HMM) profile (PF00400)
A total of 342 sequences were identified as putative OsWD40 genes

Summary

Introduction

WD40 proteins represent a large family in eukaryotes, which have been involved in a broad spectrum of crucial functions. WD40 proteins are a group of proteins that are highly conserved in evolution and are extremely abundant across a wide range of eukaryotic organisms [1] These proteins are characterized by the presence of approximately 40 amino acids core region, which contains a glycine-histidine (GH) dipeptide at the N terminus and a tryptophan-aspartate (WD) dipeptide at the C terminus separated by a region of variable lengths [2]. Biochemical and structural studies have recognized WD40 proteins to be a broader spectrum of components in cytoplasm and nucleoplasm They participate in important cellular pathways, including signal transduction, RNA processing, cytoskeleton dynamics, vesicular trafficking, nuclear export, regulation of cell division, and are especially prevalent in chromatin modification and transcriptional regulation [2,4,5]. The results suggested that these proteins played key roles in plant-specific processes, with diversity in function conferred at least in part by divergence in upstream signaling pathways, downstream regulatory targets and/or structure outside of the WD 40 regions [5]

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