Botany - Research Publications
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Item 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, PankajUlmus 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.Item 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, PankajUlmus 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.Item Transcriptomic investigations of gene networks in response to arsenic accumulation in Brassica juncea (L.) Czern & Coss(Central University of Punjab, 2019) Thakur, Sapna; Bhardwaj, PankajArsenic (As), a widespread toxic metalloid is class I carcinogen known to cause adverse health effects in human. In the present study, As accumulation potential and differential gene expression in B. juncea is investigated. The amount of arsenic accumulated varied in the range of 15.99 to 1138.70 mg/Kg on dry weight basis in five cultivars. A decrease in chlorophyll content and increase in membrane damage and enzymatic activities of antioxidants was observed with increase in As concentration in the B. juncea cultivars. Using maximum As accumulating cultivar (RLM514), a total of 10,870 significantly differentially expressed transcripts in response to As treatment were identified. Further, the pathway analysis revealed a large scale reprogramming of genes involving carbon metabolism (2.5%), plant hormone signaling (1.4%), and glutathione metabolism (0.6%). Moreover, a comparative account of Cd toxicity revealed a total of 11,294 transcripts to be significantly differentially expressed. The genes related to response to chemical, oxidative stress, transport, and secondary metabolism were upregulated whereas multicellular organismal development, developmental process, photosynthesis were downregulated by Cd treatment. Furthermore, 616 membrane transport proteins were found to be significantly differentially expressed. Cd-related transporters such as metal transporter (Nramp1), metal tolerance protein (MTPC2, MTP11), cadmiumtransporting ATPase, and plant cadmium resistance protein (PCR2, PCR6) were upregulated while cadmium/zinc- transporting ATPase (HMA2, HMA3, HMA4), highaffinity calcium antiporter (CAX1), and iron transport protein (IRT1) were downregulated by Cd treatment. Pathway analysis revealed signaling cascades including plant hormones signaling, MAPK signaling and Ca signaling was modulated suggesting their role in Cd-stress tolerance. The regulation overview using MapMan also revealed gene expression related to plant hormones, calcium regulation and MAP kinases were altered under Cd-stress.Item 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.Item Transcriptome characterization and development of functional polymorphic SSR marker resource for Himalayan endangered species, Taxus contorta (Griff)(Elsevier, 2019) Majeed, A; Singh, A; Choudhary, S; Bhardwaj, PankajTaxus contorta is an important medicinal plant currently listed as endangered in IUCN Red Data List. It produces an anticancer drug, paclitaxel which is well known in the industrial sector. Due to habitat destruction and overexploitation, it is at the verge of extinction. Genomic and transcriptomic data for this species is scarce which has hampered its genomic studies. Moreover, large scale polymorphic informative codominant marker resource is also scarce which hinders its population and landscape genetic analysis. Here, we generated a reference transcriptome for this species which would facilitate the understanding of the functional elements and promote genomic research in this species. Also, a robust polymorphic SSR marker resource was characterized which can be used in conservation of this species. More than 100 million paired end raw reads were obtained through Illumina sequencing. A total of 129,869 unigenes with mean sequence length of 1244 nt were obtained from 209,860 de novo assembled transcripts. Of these, 35,752 transcripts were assigned 5971 unique GO terms. Around 40,386 transcripts were found to have 2163 unique Pfam Ids. Pathway analysis against KEGG database yielded 3721 unique enzyme numbers. Screening of the transcripts for microsatellite regions yielded 7041 SSRs. Among the 100 SSRs selected for characterization on 30 genotypes, 37 polymorphic markers showed a total of 214 alleles with mean of 5.78 alleles per locus. Mean effective number of alleles (Ne) was found to be 3.64 and average PIC value of 0.64 was observed. Observed heterozygosity (0.57) was found to be lower than expected (0.69). This effective polymorphic SSR marker resource will act as valuable tool for deciphering its genetic diversity. © 2019 Elsevier B.V.Item Gene and metabolite profiling reveals flowering and survival strategies in Himalayan Rhododendron arboreum(Elsevier, 2019) Choudhary, Shurti; Thakur, Sapna; Jaitak, Vikas; Bhardwaj, PankajRhododendron 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 responsesItem Comparative Transcriptome Profiling Under Cadmium Stress Reveals the Uptake and Tolerance Mechanism in Brassica juncea(Springer, 2019) Thakur, Sapna; Choudhary, Shurti; Bhardwaj, PankajCadmium (Cd) is a biologically non-essential and phytotoxic heavy metal pollutant. In this study, we estimated the Cd accumulation potential of Indian mustard and identified factors responsible for Cd uptake, tolerance, and detoxification. Eight transcriptomic libraries were sequenced and ??230 million good quality reads were generated. The alignment rate against B. juncea reference genome V1.5 varied in the range of 85.03-90.06%. Comparative expression analysis using DESeq2 revealed 11,294 genes to be significantly differentially expressed under Cd treatment. The agriGO singular enrichment analysis revealed genes related to response to chemical, oxidative stress, transport, and secondary metabolic process were upregulated, whereas multicellular organismal development, developmental process, and photosynthesis were downregulated by Cd treatment. Furthermore, 616 membrane transport proteins were found to be significantly differentially expressed. Cd-related transporters such as metal transporter (Nramp1), metal tolerance protein (MTPC2, MTP11), cadmium-transporting ATPase, and plant cadmium resistance protein (PCR2, PCR6) were upregulated whereas cadmium/zinc-transporting ATPase (HMA2, HMA3, HMA4), high-affinity calcium antiporter (CAX1), and iron transport protein (IRT1) were downregulated by Cd treatment. A total of 332 different gene-networks affected by Cd stress were identified using KAAS analysis. Various plant hormones signaling cascades were modulated suggesting their role in Cd stress tolerance. The regulation overview using MapMan analysis also revealed gene expression related to plant hormones, calcium regulation, and MAP kinases were altered under Cd stress.