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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]

Cytosine DNA methylation (5mC) is an epigenetic mark that regulates gene expression in plant responses to environmental stresses. Zinc-finger protein (ZFP) is the largest family of DNA-binding transcription factors that also plays an essential role in eukaryote. In plant we have already identified and characterized different useful ZFP-genes. While, the main objective of this research was to observe and identify more targeted stress responsive genes of ZFPs epigenetically throughout genome in rice for the first time. A comprehensive correlation analysis was performed through methylated DNA immunoprecipitation (MeDIP)-chip hybridization in rice under salt and osmotic stresses. High salinity and drought are two major abiotic hazards that are destroying the crop world-wide. As a result, Through-out genome 14 unique stress responsive transcription factors of ZFP-genes with varying level of methylation and expression under two conditions (control vs. stress) were isolated. All the identified genes were confirmed from different databases for their specific structure, cis-regulatory elements, phylogenetic analysis, and synteny analysis. Moreover, the tissue-specific expression patterns, and expression under abiotic and phytohormones stresses were also investigated. Phylogenetically all the genes were divided into 6 distinct subgroups with Arabidopsis and orthologous proteins were find-out through synteny analysis. Available RNA-seq data in response to various phytohormones provided hormone inducible gene expression profile. Through Reverse Transcriptase qPCR (RT-qPCR) analysis tissue-specific expression in shoot and root over various time points against salt and osmotic stresses exhibited the diverse expression patterns of identified genes. Overall, the present study providing a foundation for in-depth characterization of identified genes and to further understand the epigenetic role of DNA methylation for genes expression and environmental stresses regulation in higher plant. • 14 unique OsZFP genes partially or fully methylated were identified through MeDIP-chip. • All OsZFPs were clustered in three clades. • RNA-seq data in response to various phytohormones provided hormone specific genes expression profiles. • The candidate rice ZFP genes exhibited diverse expression patterns under salinity and drought stresses. [ABSTRACT FROM AUTHOR]