Genomic characterization, phylogenetic comparison and differential expression of the cyclic nucleotide-gated channels gene family in pear (Pyrus bretchneideri Rehd.)

• Identify 21 CNGC genes and could be divided into five groups (I, II, III, IVA and IVB) in pear.
• Domain analyses found IQ motif is more conserved than CaMBD for CaM-binding domain on all CNGCs near to the CNBD.
• In pear, segment duplication accounted for the majority of the gene duplications identified.
• The P-S6 and PBC & hinge domains had co-evolved during the CNGC genes evolution.

The cyclic nucleotide-gated channel (CNGC) family is involved in the uptake of various cations, such as Ca2+, to regulate plant growth and respond to biotic and abiotic stresses. However, there is far less information about this family in woody plants such as pear. Here, we provided a genome-wide identification and analysis of the CNGC gene family in pear. Phylogenetic analysis showed that the 21 pear CNGC genes could be divided into five groups (I, II, III, IVA and IVB). The majority of gene duplications in pear appeared to have been caused by segmental duplication and occurred 32.94–39.14 million years ago. Evolutionary analysis showed that positive selection had driven the evolution of pear CNGCs. Motif analyses showed that Group I CNGCs generally contained 26 motifs, which was the greatest number of motifs in all CNGC groups. Among these, eight motifs were shared by each group, suggesting that these domains play a conservative role in CNGC activity. Tissue-specific expression analysis indicated that functional diversification of the duplicated CNGC genes was a major feature of long-term evolution. Our results also suggested that the P-S6 and PBC & hinge domains had co-evolved during the evolution. These results provide valuable information to increase our understanding of the function, evolution and expression analyses of the CNGC gene family in higher plants.