Genome-wide investigation and expression analyses of WD40 protein family in the model plant foxtail millet (Setaria italica L.).
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 WD40 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 WD40 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. In silico comparative mapping with sorghum, maize and rice demonstrated the orthologous relationships and chromosomal rearrangements including duplication, inversion and deletion of WD40 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 SiWD40 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.
National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi.
Awdhesh Kumar
AK
Mishra
National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi.
Mehanathan
M
Muthamilarasan
National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi.
Yusuf
Y
Khan
National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi.
Swarup Kumar
SK
Parida
National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi.
Manoj
M
Prasad
D015415:Biomarkers / Q000378:metabolism*; D002874:Chromosome Mapping; D020869:Gene Expression Profiling; D017343:Genes, Plant; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D035683:MicroRNAs; D058977:Molecular Sequence Annotation; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics; D010802:Phylogeny; D011401:Promoter Regions, Genetic; D012333:RNA, Messenger / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction; D032983:Setaria Plant / Q000235:genetics* / Q000254:growth & development; D045868:Sorghum / Q000235:genetics; D003313:Zea mays / Q000235:genetics
D015415:Biomarkers; D035683:MicroRNAs; D012333:RNA, Messenger