Genome-wide identification and expression analysis of the CLC gene family in pomegranate (Punica granatum) reveals its role in salt resistance

Abstract

BackgroundsPomegranate (Punica granatum L.) is an important commercial fruit tree, with moderate tolerance to salinity. The balance of Cl− and other anions in pomegranate tissues are affected by salinity, however, the accumulation patterns of anions are poorly understood. The chloride channel (CLC) gene family is involved in conducting Cl−, NO3−, HCO3− and I−, but its characteristics have not been reported on pomegranate.ResultsIn this study, we identified seven PgCLC genes, consisting of four antiporters and three channels, based on the presence of the gating glutamate (E) and the proton glutamate (E). Phylogenetic analysis revealed that seven PgCLCs were divided into two clades, with clade I containing the typical conserved regions GxGIPE (I), GKxGPxxH (II) and PxxGxLF (III), whereas clade II not. Multiple sequence alignment revealed that PgCLC-B had a P [proline, Pro] residue in region I, which is suspected to be a NO3–/H+ exchanger, while PgCLC-C1, PgCLC-C2, PgCLC-D and PgCLC-G contained a S [serine, Ser] residue, with a high affinity to Cl−. We were determined the content of Cl−, NO3−, H2PO4−, and SO42− in pomegranate tissues after 18 days of salt treatments (0, 100, 200 and 300 mM NaCl). Compared with control, the Cl− content increased sharply in tissues and was ranked as leaf > stem > root. The uptake of NO3− and SO42− was inhibited by high salinity, while that of H2PO4− increased. The results of real-time reverse transcription PCR (qRT-PCR) revealed that PgCLC genes had tissue-specific expression patterns. The high expression levels of PgCLC-C1, PgCLC-C2 and PgCLC-D in leaves suggested they played roles in sequestrating Cl− into the vacuoles. However, the low expression levels of PgCLCs in roots might be contributed to the exclusion of Cl− from root cells. Also, the non-significantly changed concentration of NO3− in leaves and the up-regulated PgCLC-B indicated an acceleration of transporting NO3− into leaves to mitigate the nitrogen deficiency.ConclusionsOur findings suggested that PgCLC genes played important roles in balance of Cl− and NO3− in pomegranate tissues under salt stress. This study establishes a theoretical foundation for the further functional characterization of CLC genes in pomegranate.

Transcriptional profiling of long non-coding RNAs regulating fruit cracking in Punica granatum L. under bagging

“…Pomegranate possesses an outstanding ornamental and medicinal value and has become an emerging functional fruit due to the richness of ellagitannin-based compounds in the peel and aril, which have antioxidant, antibacterial, anti-inflammatory, anticancer, antidiabetic and cardiovascular health promoting properties ( Vlachojannis et al., 2015 ; Baghel et al., 2021 ). At present, the research on pomegranate mainly focuses on evolution, ovule, flower, seed coat, fruit development ( Saminathan et al., 2016 ; Yuan et al., 2017 ; Zhao et al., 2020 ; Qin et al., 2020 ), natural product biosynthesis ( Ono et al., 2011 ), pericarp color synthesis ( Zhao et al., 2015 ) and salt stress response ( Liu et al., 2020 ). Few studies have focused on the quality of pomegranate peel appearance and its regulation mechanism.…”