Structure of representative SiWD40 proteins from each subfamily.

<p>The protein structure is based on the presence of WD40 and other additional domains as identified by SMART and pfam. This categorizes the SiWD40 in 12 Subfamilies (A–L).</p

The relative expression ratio of 13 candidate <i>SiWD40</i> genes analyzed using qRT-PCR under (A) dehydration stress, (B) salinity stress, (C) ABA treatment (D) Cold stress for 0, 1, 3, 6, 12, 24 and 48 h.

<p>The relative expression ratio of each gene was calculated relative to its expression in control sample (0 h). <i>Act2</i> was used as an internal control to normalize the data. The error bars representing standard deviation were calculated based on three technical replicates for each biological duplicates.</p

A summary of comparative mapping of foxtail millet <i>SiWD40</i> genes on sorghum, maize and rice.

<p>A summary of comparative mapping of foxtail millet <i>SiWD40</i> genes on sorghum, maize and rice.</p

Genome-Wide Investigation and Expression Analyses of WD40 Protein Family in the Model Plant Foxtail Millet (<i>Setaria italica</i> L.)

<div><p>WD40 proteins play a crucial role in diverse protein-protein interactions by acting as scaffolding molecules and thus assisting in the proper activity of proteins. Hence, systematic characterization and expression profiling of these <i>WD40</i> genes in foxtail millet would enable us to understand the networks of WD40 proteins and their biological processes and gene functions. In the present study, a genome-wide survey was conducted and 225 potential <i>WD40</i> genes were identified. Phylogenetic analysis categorized the WD40 proteins into 5 distinct sub-families (I–V). Gene Ontology annotation revealed the biological roles of the WD40 proteins along with its cellular components and molecular functions. <i>In silico</i> comparative mapping with sorghum, maize and rice demonstrated the orthologous relationships and chromosomal rearrangements including duplication, inversion and deletion of <i>WD40</i> genes. Estimation of synonymous and non-synonymous substitution rates revealed its evolutionary significance in terms of gene-duplication and divergence. Expression profiling against abiotic stresses provided novel insights into specific and/or overlapping expression patterns of <i>SiWD40</i> genes. Homology modeling enabled three-dimensional structure prediction was performed to understand the molecular functions of WD40 proteins. Although, recent findings had shown the importance of WD40 domains in acting as hubs for cellular networks during many biological processes, it has invited a lesser research attention unlike other common domains. Being a most promiscuous interactors, WD40 domains are versatile in mediating critical cellular functions and hence this genome-wide study especially in the model crop foxtail millet would serve as a blue-print for functional characterization of WD40s in millets and bioenergy grass species. In addition, the present analyses would also assist the research community in choosing the candidate WD40s for comprehensive studies towards crop improvement of millets and biofuel grasses.</p></div

Predicated structures of SiWD40 proteins.

<p>The structure of 24 SiWD40 proteins with >90% confidence level were shown. Active sites are highlighted in blue colour.</p

Phylogenetic relationships of foxtail millet WD40 proteins.

<p>The sequences were aligned by CLUSTALW at MEGA5 and the unrooted phylogenetic tree was deduced by neighbor-joining method with 1000 bootstrap replicates. The evolutionary distances were computed using p-distance method. The bootstrap values are shown at the nodes. The tree was divided into five phylogenetic cluster designated as I to V. The members of the SiWD40 were distinctly coloured to represent respective WD40 subfamilies.</p

Distribution of segmentally duplicated <i>SiWD40</i> genes on foxtail millet chromosomes.

<p>Grey lines indicate collinear blocks in whole foxtail millet genome, and black lines indicate duplicated <i>SiWD40</i> gene pairs.</p

Gene Ontology (GO) distributions for the SiWD40 protein.

<p>The Blast2Go program defines the gene ontology under three categories, (A) biological processes, (B) molecular functions and (C) cellular component.</p

Distribution of 225 <i>SiWD40</i> genes onto nine foxtail millet chromosomes.

<p>(A) Percentage of <i>SiWD40</i> genes on each the foxtail millet chromosome to show their distribution abundance. (B) Graphical (scaled) representation of physical locations for each <i>SiWD40</i> gene on foxtail millet chromosomes (numbered 1–9). Tandem duplicated genes on a particular chromosome are depicted by black boxes. Chromosomal distances are given in Mb.</p

Time of duplication and divergence (MYA) based on synonymous substitution rate (Ks) estimated using duplicated <i>SiWD40</i> gene pairs of foxtail millet and orthologous <i>SiWD40</i> gene pairs between foxtail millet and rice or maize or sorghum.

<p>Time of duplication and divergence (MYA) based on synonymous substitution rate (Ks) estimated using duplicated <i>SiWD40</i> gene pairs of foxtail millet and orthologous <i>SiWD40</i> gene pairs between foxtail millet and rice or maize or sorghum.</p