Genome-wide identification and analysis of the CNGC gene family in maize.

Lidong Hao,Xiuli Qiao

doi:10.7717/peerj.5816

Abstract

As one of the non-selective cation channel gene families, the cyclic nucleotide-gated channel (CNGC) gene family plays a vital role in plant physiological processes that are related to signal pathways, plant development, and environmental stresses. However, genome-wide identification and analysis of the CNGC gene family in maize has not yet been undertaken. In the present study, twelve ZmCNGC genes were identified in the maize genome, which were unevenly distributed on chromosomes 1, 2, 4, 5, 6, 7, and 8. They were classified into five major groups: Groups I, II, III, IVa, and IVb. Phylogenetic analysis showed that gramineous plant CNGC genes expanded unequally during evolution. Group IV CNGC genes emerged first, whereas Groups I and II appeared later. Prediction analysis of cis-acting regulatory elements showed that 137 putative cis-elements were related to hormone-response, abiotic stress, and organ development. Furthermore, 120 protein pairs were predicted to interact with the 12 ZmCNGC proteins and other maize proteins. The expression profiles of the ZmCNGC genes were expressed in tissue-specific patterns. These results provide important information that will increase our understanding of the CNGC gene family in maize and other plants.

Highlights

Organism evolution has led to the formation of complex nutrient absorption and transport systems, including ion channels, ion pumps, and carriers
The 18 putative ZmCNGC genes were confirmed by using SMART and NCBI CDD to determine whether they contained the cyclic nucleotide-gated channel (CNGC)-specific domains (CNBD and TM)
To further confirm the existence of the ZmCNGCs, we identified all the expressed sequence tags (ESTs) that had aligned to the ZmCNGC genes by using the BLASTN program provided by the NCBI

Summary

Introduction

Organism evolution has led to the formation of complex nutrient absorption and transport systems, including ion channels, ion pumps, and carriers. The cyclic nucleotide-gated channel (CNGC) is a Ca2+-permeable cation transport channel, and it has been suggested that it is one of the fundamental mechanisms in organism systems (Yuen & Christopher, 2013; Nawaz et al, 2014). Secondary messengers, such as cyclic nucleotide monophosphates (3 ,5 -cAMP and 3 ,5 -cGMP) and Ca2+/calmodulin (CaM), can regulate CNGCs by acting as molecular switches. The CNGCs are activated by directly binding cyclic nucleotides and are inhibited when CaM binds to the CaM binding domain (Saand et al, 2015b; Borsics et al, 2007; Defalco et al, 2016; Kaplan, Sherman & Fromm, 2007).

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Conclusion