Institutional Publications
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Item Identification, evolutionary profiling, and expression analysis of F-box superfamily genes under phosphate deficiency in tomato(Elsevier B.V., 2021) Akash; Parida, Adwaita Prasad; Srivastava, Alok; Mathur, Saloni; Sharma, Arun Kumar; Kumar, RahulF-box genes are an integral component of the Skp1-cullin-F-box (SCF) complex in eukaryotes. These genes are primarily involved in determining substrate specificities during cellular proteolysis. Here we report that 410 members constitute the F-box superfamily in tomato. Based on the incidence of C-terminal domains, these genes fell into ten subfamilies, leucine-rich repeat domain-containing F-box members constituting the largest subfamily. The F-box genes are present on all 12 chromosomes with varying gene densities. Both segmental and tandem duplication events contribute significantly to their expansion in the tomato genome. The syntenic analysis revealed close relationships among F-box homologs within Solanaceae species genomes. Transcript profiling of F-box members identified several ripening-associated genes with altered expression in the ripening mutants. RNA-sequencing data analysis showed that phosphate (Pi) deficiency affected 55 F-box transcripts in the Pi-deficient seedlings compared to their control seedlings. The persistent up-regulation of eight members, including two phloem protein 2B (PP2–B) genes, PP2–B15, and MATERNAL EFFECT EMBRYO ARREST 66 (MEE66) homologs, at multiple time-points in the roots, shoot, and seedling, point towards their pivotal roles in Pi starvation response in tomato. The attenuation of such upregulation in sucrose absence revealed the necessity of this metabolite for robust activation of these genes in the Pi-deficient seedlings. Altogether, this study identifies novel F-box genes with potential roles in fruit ripening and Pi starvation response and unlocks new avenues for functional characterization of candidate genes in tomato and other related species.Item Genomic survey, gene expression, and interaction analysis suggest diverse roles of ARF and Aux/IAA proteins in Solanaceae(Springer, 2015) Kumar, Rahul; Agarwal, Priyanka; Pareek, Amit; Tyagi, Akhilesh K.; Sharma, Arun K.Auxin response factor (ARF) and Auxin/INDOLE-3-ACETIC ACID (Aux/IAA) proteins are the foremost regulators of auxin action and play an essential role in the coordination of many aspects of plant growth and development. Though many members of both ARF and Aux/IAA gene families have been identified and characterized in tomato, they are less studied in other Solanaceae species. In the present study, we focused on gaining insights into their functional conservation as well as diversification during auxin-mediated responses in Solanaceae. First, we identified their full complement in tomato, potato, pepper, Nicotiana benthamiana, eggplant, and petunia and found that both the gene families have expanded in N. benthamiana. We also looked into the structural variations associated with all the members of these two classes of genes in tomato and showed that huge natural variation exists in their sequence in wild relatives. The comprehensive gene expression analysis provided evidence of high conservation in the expression of orthologous ARFs and Aux/IAAs during fruit development and ripening in tomato and pepper. Furthermore, the molecular changes caused by exogenous plant hormones and abiotic stress conditions on their transcript levels were investigated which showed that many members of both the gene families may participate in various hormone- and stress-mediated responses in tomato and potato. Some of these genes may play a role in linking the hormone-controlled plant growth and stress-related signaling pathways. Finally, we demonstrate that single tomato ARF can interact with multiple Aux/IAA proteins and vice versa. Overall, our study will be very helpful in establishing both conserved as well as non-conserved functions of these genes in Solanaceae.Item Genome-wide investigation and expression analysis suggest diverse roles of auxin-responsive GH3 genes during development and response to different stimuli in tomato (Solanum lycopersicum)(Springer Science, 2012) Kumar, Rahul; Agarwal, Priyanka; Tyagi, Akhilesh K.; Sharma, Arun K.In plants, auxin-mediated responses are regulated by diverse proteins. One such class of proteins, i.e. GH3, is involved in the conjugation of IAA to amino acids and provides a negative feedback loop to control auxin homoeostasis. In order to have a better understanding of the mechanism of the auxin action, 15 genes encoding GH3 members were identified using existing EST databases of tomato. Their orthologs were identified from tobacco, potato, N. benthemiana, pepper, and petunia. Phylogenetic analysis of AtGH3, SlGH3, and their Solanaceae orthologs provided insights into various orthologous relationships among these proteins. These genes were found to be responsive to a variety of signals including, phytohormones and environmental stresses. Analysis of AuxRE elements in their promoters showed variability in the sequence as well as number of this element. Up-regulation of only 11 SlGH3 genes, in response to exogenous auxin, suggested possible relationship between the diversity in the sequence and number of AuxRE element with the auxin inducibility. Expression analysis of SlGH3 genes in different vegetative and reproductive tissues/stages suggested limited or no role for most of the SlGH3 genes at the initiation of fruit ripening. However, up-regulation of SlGH3-1 and -2 at the onset of fruit ripening indicates that these genes could have a role in fruit ripening. The present study characterizes GH3 gene family of tomato and its evolutionary relationship with members of this family from other Solanaceae species and Arabidopsis. It could help in the identification of GH3 genes and revelation of their function during vegetative/reproductive development stages from other Solanaceae members.Item Genome-wide analysis of auxin response factor (ARF) gene gamily from tomato and analysis of their role in flower and fruit development(Springer Science, 2011) Kumar, Rahul; Tyagi, Akhilesh K.; Sharma, Arun K.Auxin response transcription factors have been widely implicated in auxin-mediated responses during various developmental processes ranging from root and shoot development to flower and fruit development in plants. In order to use them for improvement of agronomic traits related to fruit, we need to have better understanding of their role during fruit development. In this study, 17 SlARF genes have been identified from tomato (Solanum lycopersicum), using various publically available tomato EST databases. Phylogenetic analysis of the 23 AtARF and 17 SlARF proteins results in formation of three major classes and a total of 14 sister pairs, including seven SlARF-AtARF, four SlARF-SlARF and three AtARF-AtARF sister pairs, providing insights into various orthologous relationships between AtARFs and SlARFs. Further, search for orthologs of these SlARFs resulted in identification of nine, ten, four and three ARF genes from potato, tobacco, N. benthemiana and pepper, respectively. A phylogenetic analysis of these genes, along with their orthologs from Solanaceae species, suggests the presence of a common set of the ARF genes in this family. Comparison of the expression of these SlARF genes in wild type and rin mutant provides an insight into their role during different stages of flower and fruit development. This study suggests that ARF genes may play diverse role during flower and fruit development. Comprehensive data generated here will provide a platform for identification of ARF genes and elucidation of their function during reproductive development stages in Solanaceae in general and fruit development in tomato, in particular.