Institutional Publications
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Item Genome-wide analysis and expression profiling suggest diverse roles of GH3 genes during development and abiotic stress responses in legumes(Frontiers Media S.A., 2015) Singh, Vikash K.; Jain, Mukesh; Garg, RohiniGrowth hormone auxin regulates various cellular processes by altering the expression of diverse genes in plants. Among various auxin-responsive genes, GH3 genes maintain endogenous auxin homeostasis by conjugating excess of auxin with amino acids. GH3 genes have been characterized in many plant species, but not in legumes. In the present work, we identified members of GH3 gene family and analyzed their chromosomal distribution, gene structure, gene duplication and phylogenetic analysis in different legumes, including chickpea, soybean, Medicago, and Lotus. A comprehensive expression analysis in different vegetative and reproductive tissues/stages revealed that many of GH3 genes were expressed in a tissue-specific manner. Notably, chickpea CaGH3-3, soybean GmGH3-8 and -25, and Lotus LjGH3-4, -5, -9 and -18 genes were up-regulated in root, indicating their putative role in root development. In addition, chickpea CaGH3-1 and -7, and Medicago MtGH3-7, -8, and -9 were found to be highly induced under drought and/or salt stresses, suggesting their role in abiotic stress responses. We also observed the examples of differential expression pattern of duplicated GH3 genes in soybean, indicating their functional diversification. Furthermore, analyses of three-dimensional structures, active site residues and ligand preferences provided molecular insights into function of GH3 genes in legumes. The analysis presented here would help in investigation of precise function of GH3 genes in legumes during development and stress conditions.Item Transcriptome profiling for discovery of genes involved in shoot apical meristem and flower development(Elsevier B.V., 2014) Singh, Vikash K.; Jain, MukeshFlower development is one of the major developmental processes that governs seed setting in angiosperms. However, little is known about the molecular mechanisms underlying flower development in legumes. Employing RNA-seq for various stages of flower development and few vegetative tissues in chickpea, we identified differentially expressed genes in flower tissues/stages in comparison to vegetative tissues, which are related to various biological processes and molecular functions during flower development. Here, we provide details of experimental methods, RNA-seq data (available at Gene Expression Omnibus database under GSE42679) and analysis pipeline published by Singh and colleagues in the Plant Biotechnology Journal (Singh et al., 2013), along with additional analysis for discovery of genes involved in shoot apical meristem (SAM) development. Our data provide a resource for exploring the complex molecular mechanisms underlying SAM and flower development and identification of gene targets for functional and applied genomics in legumes.Item A global view of transcriptome dynamics during flower development in chickpea by deep sequencing(John Wiley & Sons Ltd, 2013) Singh, Vikash K.; Garg, Rohini; Jain, MukeshMeasurement of gene expression can provide important clues about gene function and molecular basis of developmental processes. Here, we have analysed the chickpea transcriptome in vegetative and flower tissues by exploiting the potential of high-throughput sequencing to measure gene expression. We mapped more than 295 million reads to quantify the transcript abundance during flower development. We detected the expression of more than 90% genes in at least one tissue analysed. We found quite a large number of genes were differentially expressed during flower development as compared to vegetative tissues. Further, we identified several genes expressed in a stage-specific manner. Various transcription factor families and metabolic pathways involved in flower development were elucidated. The members of MADS-box family were most represented among the transcription factor genes up-regulated during various stages of flower development. The abundant expression of several well-known genes implicated in flower development in chickpea flower development stages confirmed our results. In addition, we detected the expression specificities of lineage-specific genes during flower development. The expression data presented in this study is the most comprehensive dataset available for chickpea as of now and will serve as resource for unraveling the functions of many specific genes involved in flower development in chickpea and other legumes.Item RNA-seq for transcriptome analysis in non-model plants(Springer, 2013) Garg, Rohini; Jain, MukeshSequencing of mRNA using next-generation sequencing (NGS) technologies (RNA-seq) has the potential to reveal unprecedented complexity of the transcriptomes. The transcriptome sequencing of an organism provides quick insights into the gene space, opportunity to isolate genes of interest, development of functional markers, quantitation of gene expression, and comparative genomic studies. Although becoming cheaper, transcriptome sequencing still remains an expensive endeavor. Further, the assembly of millions and billions of RNA-seq reads to construct the complete transcriptome poses great informatics challenges. Here, first we outline various important issues from experimental design to data analysis, including various strategies of transcriptome assembly, which need substantial consideration for a successful RNA-seq experiment. Further, we describe a method for using RNA-seq to characterize the transcriptome of a plant species, taking the example of a legume crop plant chickpea. Our aim is to provide a quick start guide to the nonexpert researchers for NGS-based transcriptome analysis.Item Next-generation sequencing technologies for gene expression profiling in plants(Oxford University Press, 2012) Jain, MukeshNext-generation sequencing (NGS) provides a better approach to gene expression profiling with several advantages. The power of NGS along with novel molecular techniques and computational tools allow the researchers to perform the gene expression profiling to reveal transcriptional complexity of an organism and answering several biological questions. Although many studies for gene expression profiling related to various aspects have been performed in animal systems revealing unprecedented levels of complexity of transcriptomes, their use is still limited in plant biology. This review describes the use of NGS technologies with respect to gene expression profiling, bioinformatics challenges associated with data analysis and advances made so far in the plant biology research. We anticipate many more studies in recent future, which will surely advance our understanding of the complexity of plant genomes.Item Pyrosequencing data reveals tissue-specific expression of lineage-specific transcripts in chickpea(Landes Bioscience, 2011) Garg, Rohini; Jain, MukeshChickpea is a very important crop legume plant, which provides a protein-rich supplement to cereal-based diets and has the ability to fix atmospheric nitrogen. Despite its economic importance, the functional genomic resources for chickpea are very limited. Recently, we reported the complete transcriptome of chickpea using next generation sequencing technologies. We analyzed the tissue-specific expression of chickpea transcripts based on RNA-seq data. In addition, we identified two sets of lineage-specific genes, including a total of 3,632 chickpea-specific and 741 as legume-specific transcripts based on sequence comparison with other species within plant kingdom. The study of lineage-specific genes provides insights into the species-/lineage-specific functions and evolutionary processes. In this study, we further analyze the expression profiles of legume- and chickpea-specific transcripts in various tissue samples. Several legume- and chickpea-specific transcripts showed preferential and/or specific expression in the tissue samples analyzed. Our analysis provides evidence for the role of legume- and chickpea-specific transcripts in various tissues and opens an important area of future research to elucidate the exact role of these genes.