Dataset Information

Genome-wide characterization of MATE gene family and expression profiles in response to abiotic stresses in rice (Oryza sativa).

ABSTRACT: Multidrug and toxic compound extrusion (MATE) proteins are involved in many physiological functions of plant growth and development. Although an increasing number of MATE proteins have been identified, the understanding of MATE proteins is still very limited in rice. In this study, 46 MATE proteins were identified from the rice (Oryza sativa) genome by homology searches and domain prediction. The rice MATE family was divided into four subfamilies based on the phylogenetic tree. Tandem repeats and fragment replication contribute to the expansion of the rice MATE gene family. Gene structure and cis-regulatory elements reveal the potential functions of MATE genes. Analysis of gene expression showed that most of MATE genes were constitutively expressed and the expression patterns of genes in different tissues were analyzed using RNA-seq. Furthermore, qRT-PCR-based analysis showed differential expression patterns in response to salt and drought stress. The analysis results of this study provide comprehensive information on the MATE gene family in rice and will aid in understanding the functional divergence of MATE genes.

SUBMITTER: Du Z

PROVIDER: S-EPMC8268253 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature

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Genome-wide characterization of MATE gene family and expression profiles in response to abiotic stresses in rice (Oryza sativa).

Du Zhixuan Z Su Qitao Q Wu Zheng Z Huang Zhou Z Bao Jianzhong J Li Jianbin J Tu Hang H Zeng Chuihai C Fu Junru J He Haohua H

BMC ecology and evolution 20210709 1

Multidrug and toxic compound extrusion (MATE) proteins are involved in many physiological functions of plant growth and development. Although an increasing number of MATE proteins have been identified, the understanding of MATE proteins is still very limited in rice. In this study, 46 MATE proteins were identified from the rice (Oryza sativa) genome by homology searches and domain prediction. The rice MATE family was divided into four subfamilies based on the phylogenetic tree. Tandem repeats an ...[more]

PMID: 34243710

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Project description:The cation-proton antiporter (CPA) superfamily plays pivotal roles in regulating cellular ion and pH homeostasis in plants. To date, the regulatory functions of CPA family members in rice (Oryza sativa L.) have not been elucidated. In this study, we use rice public data and information techniques, 29 OsCPA candidate genes were identified in the rice japonica variety (referred to as OsCPA) and phylogenetically categorized into K+ efflux antiporter (KEA), Na+/H+ exchanger (NHX), and cation/H+ exchanger (CHX) groups containing 4, 7, and 18 OsCPA genes. The OsCPA proteins were predominantly localized in the plasma membrane and unevenly scattered on 11 chromosomes. The structural analysis of OsCPA proteins revealed higher similarities within groups. Prediction of selection pressure, collinearity, and synteny analysis indicated that all duplicated OsCPA genes had undergone strong purifying selection throughout their evolution. The cis-acting regulatory elements (CAREs) analysis identified 56 CARE motifs responsive to light, tissue, hormones, and stresses. Additionally, 124 miRNA families were identified in the gene promoters, and OsNHX7 was targeted by the highest number of miRNAs (43 miRNAs). Gene Ontology analysis demonstrated the numerous functions of OsCPA genes associated with biological processes (57.14%), cellular components (7.94%), and molecular functions (34.92%). A total of 12 transcription factor families (TFFs), including 40 TFs were identified in gene promoters, with the highest numbers of TFFs (5TFFs) linked to OsCHX13, and OsCHX15. Protein-protein interaction analysis suggested maximum functional similarities between rice and Arabidopsis CPA proteins. Based on expression analysis, OsKEA1, OsKEA2, OsNHX3, and OsNHX7 were frequently expressed in rice tissues. Furthermore, OsNHX3, OsNHX4, OsNHX6, OsNHX7, OsCHX8, and OsCHX17 in abscisic acid, OsKEA1, OsNHX3, and OsCHX8 in gibberellic acid, OsKEA1, OsKEA3, OsNHX1, and OsNHX3 in indole-3-acetic acid treatment were demonstrated as potential candidates in response to hormone. These findings highlight potential candidates for further characterization of OsCPA genes, which may aid in the development of rice varieties.

Dataset Information

Genome-wide characterization of MATE gene family and expression profiles in response to abiotic stresses in rice (Oryza sativa).

Publications

Genome-wide characterization of MATE gene family and expression profiles in response to abiotic stresses in rice (Oryza sativa).

Similar Datasets

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