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Background  Cyclic nucleotide-gated channels ( CNGCs ) are Ca 2+ -permeable cation transport channels, which are present in both animal and plant systems. They have been implicated in the uptake of both essential and toxic cations, Ca 2+  signaling, pathogen defense, and thermotolerance in plants. To date there has not been a genome-wide overview of the  CNGC  gene family in any economically important crop, including rice ( Oryza sativa  L.). There is an urgent need for a thorough genome-wide analysis and experimental verification of this gene family in rice.    Results  In this study, a total of 16 full length rice  CNGC  genes distributed on chromosomes 1–6, 9 and 12, were identified by employing comprehensive bioinformatics analyses. Based on phylogeny, the family of  OsCNGCs  was classified into four major groups (I-IV) and two sub-groups (IV-A and IV- B). Likewise, the  CNGCs  from all plant lineages clustered into four groups (I-IV), where group II was conserved in all land plants. Gene duplication analysis revealed that both chromosomal segmentation ( OsCNGC1  and  2, 10  and  11 ,  15  and  16 ) and tandem duplications ( OsCNGC1  and  2 ) significantly contributed to the expansion of this gene family. Motif composition and protein sequence analysis revealed that the CNGC specific domain “cyclic nucleotide-binding domain (CNBD)” comprises a “phosphate binding cassette” (PBC) and a “hinge” region that is highly conserved among the OsCNGCs. In addition, OsCNGC proteins also contain various other functional motifs and post-translational modification sites. We successively built a stringent motif: (LI-X(2)-[GS]-X-[FV]-X-G-[1]-ELL-X-W-X(12,22)-SA-X(2)-T-X(7)-[EQ]-AF-X-L) that recognizes the rice CNGCs specifically. Prediction of cis-acting regulatory elements in 5′ upstream sequences and expression analyses through quantitative qPCR demonstrated that  OsCNGC  genes were highly responsive to multiple stimuli including hormonal (abscisic acid, indoleacetic acid, kinetin and ethylene), biotic ( Pseudomonas fuscovaginae  and  Xanthomonas oryzae  pv.  oryzae ) and abiotic (cold) stress.    Conclusions  There are 16  CNGC  genes in rice, which were probably expanded through chromosomal segmentation and tandem duplications and comprise a PBC and a “hinge” region in the CNBD domain, featured by a stringent motif. The various cis-acting regulatory elements in the upstream sequences may be responsible for responding to multiple stimuli, including hormonal, biotic and abiotic stresses.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-853) contains supplementary material, which is available to authorized users.

bmc genomics

Cyclic nucleotide-gated ion channel gene family in rice, identification, characterization and experimental analysis of expression response to plant hormones, biotic and abiotic stresses