Department Of Botany

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    Transcriptome characterization and generation of marker resource for Himalayan vulnerable species, Ulmus wallichiana
    (Springer Science and Business Media B.V., 2021-01-14T00:00:00) Singh, Amandeep; Majeed, Aasim; Bhardwaj, Pankaj
    Ulmus wallichiana is a traditional medicinal plant listed as a vulnerable in the IUCN red list data. Genomic and transcriptomic resources for this species are lacking, hindering its genetic exploration. Further, no polymorphic marker resource is available for this species, thus limiting the elucidation of its underlying genetic diversity, which is a pre-requisite for its conservation. This study was therefore aimed to generate a functionally annotated transcriptomic resource and screen it for SSR regions. We used paired-end Illumina based RNAseq technology and trinity based de novo assembly approach to generate full length transcripts, which were screened for SSR regions and functionally annotated. Around 6.6 million raw reads were de novo assembled transcripts, which were clustered into 146,083 unigenes. 19,909 transcripts were provided with 3986 unique KEGG ids, 70,519 transcripts with 6621 unique Pfam domains, and 45,125 transcripts with 7302 unique INTERPRO domains. 1456 transcripts were identified as transcriptions factors (TFs). Further, 8868 unique GO terms were obtained for the unigenes. The transcripts mapped to 23,056 known pre-determined orthology clusters in the eggNOG database. A total of 16,570 SSRs were identified from the unigenes. Out of the 90 SSRs selected for characterization on 20 genotypes, 28 were polymorphic. Mean effective alleles (Ne) of 2.53, mean observed heterozygosity (Ho) of 0.77, and average polymorphic information content (PIC) of 0.57 were found. This study may facilitate the genetic exploration of this species. The polymorphic SSRs would prove useful to explore its genetic diversity patterns, required for its conservation. � 2021, The Author(s), under exclusive licence to Springer Nature B.V. part of Springer Nature.
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    Transcriptome characterization and generation of marker resource for Himalayan vulnerable species, Ulmus wallichiana
    (Springer Science and Business Media B.V., 2021-01-14T00:00:00) Singh, Amandeep; Majeed, Aasim; Bhardwaj, Pankaj
    Ulmus wallichiana is a traditional medicinal plant listed as a vulnerable in the IUCN red list data. Genomic and transcriptomic resources for this species are lacking, hindering its genetic exploration. Further, no polymorphic marker resource is available for this species, thus limiting the elucidation of its underlying genetic diversity, which is a pre-requisite for its conservation. This study was therefore aimed to generate a functionally annotated transcriptomic resource and screen it for SSR regions. We used paired-end Illumina based RNAseq technology and trinity based de novo assembly approach to generate full length transcripts, which were screened for SSR regions and functionally annotated. Around 6.6 million raw reads were de novo assembled transcripts, which were clustered into 146,083 unigenes. 19,909 transcripts were provided with 3986 unique KEGG ids, 70,519 transcripts with 6621 unique Pfam domains, and 45,125 transcripts with 7302 unique INTERPRO domains. 1456 transcripts were identified as transcriptions factors (TFs). Further, 8868 unique GO terms were obtained for the unigenes. The transcripts mapped to 23,056 known pre-determined orthology clusters in the eggNOG database. A total of 16,570 SSRs were identified from the unigenes. Out of the 90 SSRs selected for characterization on 20 genotypes, 28 were polymorphic. Mean effective alleles (Ne) of 2.53, mean observed heterozygosity (Ho) of 0.77, and average polymorphic information content (PIC) of 0.57 were found. This study may facilitate the genetic exploration of this species. The polymorphic SSRs would prove useful to explore its genetic diversity patterns, required for its conservation. � 2021, The Author(s), under exclusive licence to Springer Nature B.V. part of Springer Nature.
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    Comparative transcriptome profiling reveals the reprogramming of gene networks under arsenic stress in Indian mustard
    (Canadian Science Publishing, 2019) Thakur S.; Choudhary S.; Dubey P.; Bhardwaj P.
    Arsenic is a widespread toxic metalloid that is classified as a class I carcinogen known to cause adverse health effects in humans. In the present study, we investigated arsenic accumulation potential and comparative gene expression in Indian mustard. The amount of arsenic accumulated in shoots varied in the range of 15.99–1138.70 mg/kg on a dry weight basis among five cultivars. Comparative expression analysis revealed 10 870 significantly differentially expressed genes mostly belonging to response to stress, metabolic processes, signal transduction, transporter activity, and transcription regulator activity to be up-regulated, while most of the genes involved in photosynthesis, developmental processes, and cell growth were found to be down-regulated in arsenic-treated tissues. Further, pathway analysis using the KEGG Automated Annotation server (KAAS) revealed a large-scale reprogramming of genes involved in genetic and environmental information processing pathways. Top pathways with maximum KEGG orthology hits included carbon metabolism (2.5%), biosynthesis of amino acids (2.1%), plant hormone signal transduction (1.4%), and glutathione metabolism (0.6%). A transcriptomic investigation to understand the arsenic accumulation and detoxification in Indian mustard will not only help to improve its phytoremediation efficiency but also add to the control measures required to check bioaccumulation of arsenic in the food chain.
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    Gene and metabolite profiling reveals flowering and survival strategies in Himalayan Rhododendron arboreum
    (Elsevier, 2019) Choudhary, Shurti; Thakur, Sapna; Jaitak, Vikas; Bhardwaj, Pankaj
    Rhododendron arboreum inhabits the Himalayan climate otherwise detrimental to many species, though the underlying survival mechanism remains unclear. Such temperate species have an inherent endurance towards freezing temperature which is prerequisite for an initiation and transition to flowering phase. Orchestrating the molecular architecture is vital towards managing distinct abiotic signals. To determine the molecular factors directing growth, development, and tolerance under environmental extremes in the species, the high-throughput transcriptome and metabolome data from vegetative as well as cold-acclimatized flowering season tissues were generated. Firstly, the de novo assembly pertaining to the foliar and floral tissues comprising of 157,427 unigenes was examined for a comparative analysis. 4149 of 12,577 transcripts observed with a significant fluctuating expression corresponded to seasonal retorts. Following the interactive network, 525 genes were distinguished as the epicenters of sense, response, and tolerance. Secondly, liquid chromatography coupled to mass spectrometry was adopted to profile the extent of metabolite richness across the tissues of two seasons. Taking into account the formula-based mappings offered by MetaboSearch tool, 421 unique ions obtained were annotated to 173 KEGG compounds, especially secondary metabolites. Moreover, by integrating the transcript and metabolite annotations, it was found that right from active metabolism, signaling, development, and their regulations, supplementary response to abiotic/biotic stimuli was induced. A multifaceted response displayed during flowering not only sponsored the climatic encounters but brought the shift from vegetative to reproductive growth. Overall, this comprehensive approach following transcriptome and non-targeted metabolome elucidated the contribution of genetic and metabolic factors in environmental responses