The IQD gene family in soybean: structure, phylogeny, evolution and expression.

Lin Feng,Xue Chen,Yuan Li,Yiyi Wang,Yan Xiang,Zhu Chen,Hui Ma,Marc Robinson-Rechavi

doi:10.1371/journal.pone.0110896

Abstract

Members of the plant-specific IQ67-domain (IQD) protein family are involved in plant development and the basal defense response. Although systematic characterization of this family has been carried out in Arabidopsis, tomato (Solanum lycopersicum), Brachypodium distachyon and rice (Oryza sativa), systematic analysis and expression profiling of this gene family in soybean (Glycine max) have not previously been reported. In this study, we identified and structurally characterized IQD genes in the soybean genome. A complete set of 67 soybean IQD genes (GmIQD1–67) was identified using Blast search tools, and the genes were clustered into four subfamilies (IQD I–IV) based on phylogeny. These soybean IQD genes are distributed unevenly across all 20 chromosomes, with 30 segmental duplication events, suggesting that segmental duplication has played a major role in the expansion of the soybean IQD gene family. Analysis of the Ka/Ks ratios showed that the duplicated genes of the GmIQD family primarily underwent purifying selection. Microsynteny was detected in most pairs: genes in clade 1–3 might be present in genome regions that were inverted, expanded or contracted after the divergence; most gene pairs in clade 4 showed high conservation with little rearrangement among these gene-residing regions. Of the soybean IQD genes examined, six were most highly expressed in young leaves, six in flowers, one in roots and two in nodules. Our qRT-PCR analysis of 24 soybean IQD III genes confirmed that these genes are regulated by MeJA stress. Our findings present a comprehensive overview of the soybean IQD gene family and provide insights into the evolution of this family. In addition, this work lays a solid foundation for further experiments aimed at determining the biological functions of soybean IQD genes in growth and development.

Highlights

Ca2 + is a pivotal cytosolic second messenger involved in many physiological processes such as plant growth [1], plant-pathogen interactions [2], photosynthetic electron transport and photophosphorylation [3], regulation of stomatal aperture [4], hormonal regulation [5] and so on
Through removing redundant sequences and pattern identificating, a total of 67 IQD genes were identified in the soybean genome, which is twice that of Arabidopsis (Table 1 and 2)
Structural characteristics of IQD proteins The plant-specific IQD gene family has previously been comprehensively analyzed in Arabidopsis, rice, tomato and Brachypodium distachyon, this gene family has not been previously identified and annotated in soybean

Summary

Introduction

Ca2 + is a pivotal cytosolic second messenger involved in many physiological processes such as plant growth [1], plant-pathogen interactions [2], photosynthetic electron transport and photophosphorylation [3], regulation of stomatal aperture [4], hormonal regulation [5] and so on. Plants produce calcium signals by adjusting cytoplasm Ca2+ levels at specific times, places and concentrations [6], responding to numerous extracellular stimuli including physical signals (light, temperature, gravity, etc.) and chemical signals (plant hormones, pathogenic bacteria inducing factors, etc.) [7]. The transmission of these intracellular calcium signals relies on the oscillation signal generated by voltage- and ligand-gated Ca2+ -permeable channels (influx) and by Ca2+-ATPases and antiporters (efflux) to return to resting Ca2+ levels [8,9].

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Results

Conclusion