Genome-wide identification and expression analysis of the IQD gene family in moso bamboo (Phyllostachys edulis)

Abstract

Members of the plant-specific IQ67-domain (IQD) protein family are involved in various aspects of normal plant growth and developmental processes as well as basal defence response. Although hundreds of IQD proteins have been identified, only a small number of IQDs have been functionally characterized. Moreover, no systematic study has been performed on moso bamboo. In this study, we performed for the first time a genome-wide identification and expression analysis of the IQD gene family in moso bamboo. We identified 29 non-redundant PeIQD encoding genes. Analysis of the evolutionary patterns and divergence revealed that the IQD genes underwent a large-scale event around 12 million years ago and the division times of IQD family genes between moso bamboo and rice, and, between moso bamboo and Brachypodium, were found to be 20–35 MYA and 25–40 MYA, respectively. We surveyed the putative promoter regions of the PeIQD genes, which showed that largely stress-related cis-elements existed in these genes. The expression profiles of the IQD genes shed light on their functional divergence. Additionally, a yeast two-hybrid assay proved that PeIQD8 can interact with PeCaM2 and that IQ or I in the IQ motif is required for PeIQD8 to combine with CaM2.

Genome-wide identification and expression analysis of the GhIQD gene family in upland cotton (Gossypium hirsutum L.)

“…In this study, the expression levels of all 20 selected GhIQD genes were increased ( Fig. 6) in response to MeJA treatment, which is consistent with previous studies showing that most of the IQD genes in P. trichocarpa and moso bamboo are induced by MeJA treatment [8,18]. These results imply that the IQD gene family plays an important role in tolerance to MeJA abiotic stress in plants.…”

“…A number of IQD genes have been reported in different plants; there are 33 AtIQD genes in A. thaliana, 28 OsIQD genes in Oryza sativa [16], 38 PtIQD genes in Populus trichocarpa [8], 29 PeIQD genes in Phyllostachys edulis (moso bamboo) [18], 67 GmIQD genes in Glycine max [19], and 34 SlSUN/IQD genes in Solanum lycopersicum [20]. In this study, a total of 102 GhIQD genes were identified in G. hirsutum L. The number of IQD genes in G. hirsutum L. is greater than that found in other plant species, possibly because G. hirsutum L. is an allotetraploid cotton species that originated from the hybridization of G. arboreum and G. raimondii and subsequent polyploidization 1-2 million years ago [25].…”

“…Plant-specific IQD gene families have been analyzed in Populus trichocarpa [8], Arabidopsis thaliana, Oryza sativa [16], Phyllostachys edulis [18], Glycine max [19], and Solanum lycopersicum [20], and the functions of a few IQD genes have been reported. In tomato, the SUN genes and other members of the IQD gene family exert their effects on organ shape by interacting with microtubules [15].…”

The IQD Family of Calmodulin-Binding Proteins Links Calcium Signaling to Microtubules, Membrane Subdomains, and the Nucleus

“…Knowledge of the CaM/CML targets and of their biochemical functions and underlying biological processes will be imperative for deciphering CaM-mediated Ca 2+ signal transduction in plants (Yang and Poovaiah, 2003). Plant-specific IQD gene families, first annotated in Arabidopsis and rice and more recently in five additional species (Filiz et al, 2013;Huang et al, 2013;Feng et al, 2014;Ma et al, 2014;Wu et al, 2016), possibly encode the largest class of CaMBPs in plants. Although the roles of a few IQD members are beginning to emerge, the precise molecular functions and mechanisms of action are still elusive for any IQD protein .…”

“…The 33 IQD proteins of Arabidopsis are highly diverse in length (103-794 amino acids) and cluster in four major phylogenetic clades that differ mainly in the presence and distribution of family-specific motifs flanking the central IQ67 domain . Extensive IQD families (23-67 genes) have been annotated in rice (Oryza sativa; Abel et al, 2005) and recently in purple falsebrome (Brachypodium distachyon; Filiz et al, 2013), tomato (Solanum lycopersicum; Huang et al, 2013), soybean (Glycine max; Feng et al, 2014), poplar (Populus trichocarpa; Ma et al, 2014), and moso bamboo (Phyllostachys edulis; Wu et al, 2016). Thus, IQD proteins are possibly the largest class of CaMBPs in plants; however, their precise biological roles and biochemical functions remain to be elucidated van der Knaap et al, 2014).…”