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The cytochrome P450 (CYP) is a large and complex eukaryotic gene superfamily with enzymatic activities involved in several physiological and regulatory processes. As an objective, an in-silico genome-wide DNA methylation (5mC) analysis was performed in rice (Oryza sativa cv. Zhonghua11), and the epigenetic role of CYPs in two abiotic stresses was observed. Being a stable representative mark, DNA-methylation alters the gene expression under stressful environmental conditions. Rice plants under salinity and drought stresses were analyzed through MeDIP-chip hybridization, and 14 unique genes of the CYP family were identified in the rice genome with varying degrees of methylation. The gene structure, promoter sequences, and phylogenetic analysis were performed. Furthermore, the responses of CYPs to various abiotic stresses, including salinity, drought, and cold were revealed. Similarly, the expression profile of potential CYPs was also investigated under various phytohormone stresses, which revealed the potential involvement of CYPs to hormone regulations. Overall, the current study provides evidence for CYP's stress regulation and fundamental for further characterization and understanding their epigenetic roles in gene expression regulation and environmental stress regulation in higher plants. [ABSTRACT FROM AUTHOR]

Abstract The ubiquitous phosphoenolpyruvate carboxylase enzymes in plants play pivotal role during carbon metabolism in photosynthesis, physicochemical processes, and tolerance to various abiotic or chemical stresses. We are presenting a bioinformatics identification of PEPC gene family in tomato and its phylogenetic classification into PTPC and BTPC sub families. Tomato PEPC genes are distributed in four different chromosomes with a unique motif and gene structure that strengthen their classification into two sub families. Identification of twelve different cis-regulatory elements related to abiotic and exogenous phytohormones showed their diverse role. Moreover, RNA-seq and qRT-PCR based tissues specific analysis revealed their role in its growth and development. In tomato, PEPC genes exhibited a diverse temporal expression under salt, cold and exogenous phytohormones. For an instance, SlPEPC1 , SlPEPC4 , and SlPEPC5 was upregulated under salt, drought, ABA, and JA in shoots. While, SlPEPC3 , SlPEPC4 , and SlPEPC5 was induced in root tissues upon exposure to drought, cold, and GA. Similarly, the enzyme activity of tomato PEPC was significantly upregulated under all these stresses but peaked under salt and IAA in roots and under GA in leaves. All tomato PEPC predicted in cytoplasm and the transient expression assay validate it. Our study insight into unique features of PEPC gene family in tomato and may sever as foundation for functional their studies. Highlights • Five PEPC identified in tomato genome are classified into two subfamilies by phylogenetic analysis. • All PEPC genes display a unique characteristic genes motif and gene structure features validating its classification. • Tomato PEPC genes show tissue specific expression pattern. • The expression level of tomato PEPCs were affected by exogenous phytohormone stress. [ABSTRACT FROM AUTHOR]

Abstract FK506-protein also called FKBP protein belongs to PPIase (peptidylprolylcis-trans isomerase) super family of immune suppressive drugs that act as molecular protein chaperones. In plants, FKBPs are ubiquitous and involved in various biological and physiological processes like plant germination, development, stress response and hormonal signaling. Here, we identified 24 FKBP family genes in tomato by using different tools and bioinformatic approaches. The specific structure, domain organisation, cis-regulatory elements, phylogenetic analysis, multiple sequence alignment, tissue-specific expression patterns and expression under abiotic and phytohormone stresses of all genes were investigated. The genes are clustered on ten tomato chromosomes and are categorised into two sub-classes; single and multiple domains protein gene. One of the main features of tomato FKBPs is their large fractions localized in chloroplast (in silico analysis) and clustered together phylogenetically. Tissue-specific expression analysis using available RNA-seq data revealed the spatiotemporal expression of the FKBPs , but few genes were observed with relatively high expressions in certain developmental stages. However, the quantitative expression profile of all genes under hormone stress provided a supporting evidence for their potential role in hormone signal pathways. Our prediction not only providing the foundation for better understanding the complex physiological regulation of FKBP gene family in tomato but also providing the potential aids to accelerate tolerance and survival in tomato under stressful condition. Highlights • A total of 24 tomato FKBP genes were identified. • Bioinformatics analysis of FKBP gene family in tomato plant • The transcript levels in seedlings revealed that several genes involved in abiotic stress • Expression profiling of 24 candidate tomato FKBP genes in various tissues [ABSTRACT FROM AUTHOR]