Dataset Information

Genome-Wide Identification and Expression Analysis of the NHX (Sodium/Hydrogen Antiporter) Gene Family in Cotton.

ABSTRACT: The sodium/hydrogen antiporter (NHX) gene family with the Na⁺/H⁺ exchange protein domain is a transporter of sodium and hydrogen ions and plays an important role in the response of plants to salt stress. Studying the response of cotton to salt stress through comprehensive identification and analysis of NHX genes in several species and their roles in salt tolerance mechanisms is of great significance. In this study, 23, 24, 12, and 12 NHX genes were identified from Gossypium hirsutum (Gh), G. barbadense, G. arboreum and G. raimondii, respectively. Phylogenetic analysis showed that these genes were mainly divided into three clades with significant subcellular localization, namely, endosome (Endo-class), plasma membrane (PM-class) and vacuole (Vac-class). By analyzing the structure of NHX genes and proteins, each branch of the NHX gene family was found to be structurally conserved, and collinearity analysis showed that NHX genes were mainly expressed through whole genome and segmental duplication. The non-synonymous (Ka)/synonymous (Ks) values showed that the NHX gene family experienced strong purifying selection during long-term evolution. Cis-acting element analysis showed that the NHX gene family may be related to the regulation of abscisic acid (ABA) and methyl jasmonate (MeJA) hormones. Additionally, transcriptomic data analysis and qRT-PCR showed that GhNHXs exhibited different expression patterns in each tissue and under different salinities. These results provide an important reference for us to further understand and analyze the molecular regulation mechanism of cotton NHX genes.

SUBMITTER: Fu X

PROVIDER: S-EPMC7461838 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:BackgroundDehydration responsive element-binding (DREB) transcription factors are widely present in plants, and involve in signalling transduction, plant growth and development, and stress response. DREB genes have been characterized in multiple species. However, only a few DREB genes have been studied in cotton, one of the most important fibre crops. Herein, the genome‑wide identification, phylogeny, and expression analysis of DREB family genes are performed in diploid and tetraploid cotton species.ResultsIn total, 193, 183, 80, and 79 putative genes containing the AP2 domain were identified using bioinformatics approaches in G. barbadense, G. hirsutum, G. arboretum, and G. raimondii, respectively. Phylogenetic analysis showed that based on the categorization of Arabidopsis DREB genes, 535 DREB genes were divided into six subgroups (A1-A6) by using MEGA 7.0. The identified DREB genes were distributed unevenly across 13/26 chromosomes of A and/or D genomes. Synteny and collinearity analysis confirmed that during the evolution, the whole genome duplications, segmental duplications, and/or tandem duplications occurred in cotton DREB genes, and then DREB gene family was further expanded. Further, the evolutionary trees with conserved motifs, cis-acting elements, and gene structure of cotton DREB gene family were predicted, and these results suggested that DREB genes might be involved in the hormone and abiotic stresses responses. The subcellular localization showed that in four cotton species, DREB proteins were predominantly located in the nucleus. Further, the analysis of DREB gene expression was carried out by real-time quantitative PCR, confirming that the identified DREB genes of cotton were involved in response to early salinity and osmotic stress.ConclusionsCollectively, our results presented a comprehensive and systematic understanding in the evolution of cotton DREB genes, and demonstrated the potential roles of DREB family genes in stress and hormone response.

Project description:Soil salinization, which is the accumulation of salt in soil, can have a negative impact on crop growth and development by creating an osmotic stress that can reduce water uptake and cause ion toxicity. The NHX gene family plays an important role in plant response to salt stress by encoding for Na+/H+ antiporters that help regulate the transport of sodium ions across cellular membranes. In this study, we identified 26 NHX genes in three cultivars of Cucurbita L., including 9 Cucurbita moschata NHXs (CmoNHX1-CmoNHX9), 9 Cucurbita maxima NHXs (CmaNHX1-CmaNHX9) and 8 Cucurbita pepo NHXs (CpNHX1-CpNHX8). The evolutionary tree splits the 21 NHX genes into three subfamilies: the endosome (Endo) subfamily, the plasma membrane (PM) subfamily, and the vacuole (Vac) subfamily. All the NHX genes were irregularly distributed throughout the 21 chromosomes. 26 NHXs were examined for conserved motifs and intron-exon organization. These findings suggested that the genes in the same subfamily may have similar functions while genes in other subfamilies may have functional diversity. The circular phylogenetic tree and collinearity analysis of multi-species revealed that Cucurbita L. had a substantially greater homology relationship than Populus trichocarpa and Arabidopsis thaliana in terms of NHX gene homology. We initially examined the cis-acting elements of the 26 NHXs in order to investigate how they responded to salt stress. We discovered that the CmoNHX1, CmaNHX1, CpNHX1, CmoNHX5, CmaNHX5, and CpNHX5 all had numerous ABRE and G-box cis-acting elements that were important to salt stress. Previous transcriptome data showed that in the mesophyll and veins of leaves, many CmoNHXs and CmaNHXs, such as CmoNHX1, responded significantly to salt stress. In addition, we heterologously expressed in A. thaliana plants in order to further confirm the response of CmoNHX1 to salt stress. The findings demonstrated that during salt stress, A. thaliana that had CmoNHX1 heterologously expression was found to have decreased salt tolerance. This study offers important details that will aid in further elucidating the molecular mechanism of NHX under salt stress.

Dataset Information

Genome-Wide Identification and Expression Analysis of the NHX (Sodium/Hydrogen Antiporter) Gene Family in Cotton.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets