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

Abstract

Backgrounds Pomegranate (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. Results In 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 was 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 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 pomegranate tissues. Salinity inhibited the uptake of NO3− and SO42−, but accelerated H2PO4− uptake. The results of real-time reverse transcription PCR (qRT-PCR) revealed that PgCLC genes had tissue-specific expression patterns. The high expression levels of three antiporters PgCLC-C1, PgCLC-C2 and PgCLC-D in leaves might be contributed to sequestrating Cl− into the vacuoles. However, the low expression levels of PgCLCs in roots might be associated with the exclusion of Cl− from root cells. Also, the up-regulated PgCLC-B in leaves indicated that more NO3− was transported into leaves to mitigate the nitrogen deficiency. Conclusions Our findings suggested that the PgCLC genes played important roles in balancing of Cl− and NO3− in pomegranate tissues under salt stress. This study established a theoretical foundation for the further functional characterization of the CLC genes in pomegranate.

Comparative transcriptomic and physiological analyses of weedy rice and cultivated rice to identify vital differentially expressed genes and pathways regulating the ABA response

“…RNA-Seq data demonstrated that three genes were enriched after ABA treatment and seven after the application of diniconazole. Similar results have been previously observed in Dendrobium officinale 52 and Poa pratensis 53 exposed to abiotic stress conditions. These results indicate that WR04-6 can respond to ABA by actively regulating glycolysis and TCA cycle pathway-related genes and enzyme activities.…”

Genome-Wide Identification and Functional Characterization of the Chloride Channel TaCLC Gene Family in Wheat (Triticum aestivum L.)

“…In pomegranate ( Punica granatum ), the expression level of the PgCLC genes under salt stress was high in leaves and low in roots. Moreover, PgCLC genes have been shown to affect the accumulation of Cl − , SO 4 2− , and NO 3 − in pomegranate tissues under salt stress ( Liu C. et al, 2020 ). Our results showed that all TaCLC genes were expressed under low nitrogen stress conditions over the short term.…”

“…Later, it was discovered that the CLC family genes also existed in most plants, including Arabidopsis thaliana , Nicotiana tabacum , Oryza sativa (L.), Poncirus trifoliata (L.) Raf., Zea mays (L.), and Glycine max ( Lurin et al, 1996 ; Diedhiou and Golldack, 2006 ; Lv et al, 2009 ; Wang et al, 2015 ; Wei et al, 2015 ). Plants CLC proteins play important roles in turgor maintenance, stomatal movement, ion homeostasis, as well as enhancing drought and salt tolerance, and increasing nitrate accumulation ( Wei et al, 2015 ; Zhang et al, 2018 ; Liu C. et al, 2020 ).…”

Genome and Transcriptome Sequencing of Populus × sibirica Identified Sex-Associated Allele-Specific Expression of the CLC Gene

“…CLC genes participate in Cl – and NO 3 – transport, are involved in response to salt stress, and are related to the efficiency of nitrogen use in plants ( Liao et al, 2018 ; Liu et al, 2020 ; Subba et al, 2020 ). Therefore, differences in CLC expression in vegetative tissues of P. × sibirica could be of interest in terms of determination of the possible role of sex in adaptation to particular environments.…”