Genome-wide characterization of Major Intrinsic Protein (MIP) gene family in Brachypodium distachyon

Abstract

Background: Major intrinsic proteins (MIPs) are membrane channel proteins which maintain water homeostasis and permeable to small molecules across the membrane.

Objective: Genome analysis of Brachypodium MIPs (BdMIPs) gene family and in silico studies are based on available bioinformatic tools. Further comparison and evolutionary study of MIPs members were performed within grass family.

Method: MIPs sequences were retrieved from Gramene database, aligned and weblogo was generated. Physio-chemical analysis was performed and phylogenetic tree was constructed by neighbor-joining. In silico expression profile of BdMIP genes was searched and image maps were generated by CIMMiner web-based server.

Result: Genome wide analysis of B. distachyon identified 33MIP genes and classified into four major groups. Analysis of motifs and transmembrane domains strongly supported their identity as a member of the MIP super family. Duplication analysis revealed that 4 genes were tandemly duplicated and no segmental duplication events in BdMIPs were observed. Prediction of cis-elements in BdMIP promoter region gave more insight into regulation mechanism under hormonal and stress conditions. In silico expression profile under development stages provided insight into expression pattern of BdMIP genes.

Conclusion: Total 33 MIPs were predicted in Brachypodium genome. Tandem duplication event was dominant phenomenon over segmental duplication in BdMIPs. Orthology analysis revealed Brachypodium MIP members were close to grass family MIP members compared to Arabidopsis. Compilation of this work will significantly contribute to the understanding of an evolutionary and biological importance of MIP genes in grass family and thus provide a set up for functional genomics studies in Brachypodium.