School Of Basic And Applied Sciences

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Author: search.filters.author.Singh, Amandeep

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    Transcriptome Analysis Revealed Behavior Complexity of Senescence Responses in Himalayan Tree Species Ulmus wallichiana
    (Springer, 2023-05-17T00:00:00) Singh, Amandeep; Majeed, Aasim; Sharma, Vikas; Gadri, Hari Shankar; Chowdhary, Md. Asif; Bhardwaj, Pankaj
    The Himalayas present a highly contrasting environment for the organisms that inhabit it, with summer and winter being the most disparate seasons. As winter approaches, the temperature drops, and deciduous plants, such as Ulmus wallichiana Planch., undergo senescence. In this study, we used the RNA-seq approach to generate a de novo transcriptome assembly of U. wallichiana, consisting of 300,067 unigenes. We investigated the differential expression pattern of these unigenes under changing climatic conditions, with a focus on the contrast between winter and summer. We observed that 2746 unigenes were differentially expressed, with a fold change of ? 2 and an FDR-adjusted p-value of ? 0.001. Among these unigenes, 37 were found to be related to senescence. We also identified nine DREB unigenes in the U. wallichiana transcriptome, which exhibited more or less contrasting patterns between summer and winter. These DREB unigenes may play an important role in regulating the plant�s tolerance to cold and/or drought stress. Our findings shed light on the complex and dynamic process of transcriptomic reprogramming that enables U. wallichiana to cope with seasonal changes. Furthermore, this study highlights the urgent need for further research on U. wallichiana, as this endangered plant species remains largely unexplored at the genomic level. � 2023, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, 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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    Transcribing molecular and climatic data into conservation management for the Himalayan endangered species, Taxus contorta (Griff.)
    (Springer Science and Business Media B.V., 2020-11-12T00:00:00) Majeed, Aasim; Singh, Amandeep; Bhardwaj, Pankaj
    Owing to the changing climatic scenario globally, and human overexploitation, the risk of extinction of Himalayan endangered species has increased many folds. Taxus contorta, an endangered gymnosperm has reached a decisive state in the Western Himalayas, thus, demands immediate attention to rescue it. This study aims to elucidate population and landscape genetics of T. contorta to plan a successful conservation strategy. We used SSR genotyping to identify genetic diversity hotspots, and ecological niche modeling to reveal climatic hotspots of T. contorta in the Indian Western Himalayas. We observed a substantial genetic diversity, and a negligible level of inbreeding among T. contorta populations. A genetic bottleneck was observed in several populations. We propose that changing climate can cause a failure of an entire conservation management plan if the shift produces a degraded environment in the future, at the sites of conservation. Further, the conservation management is futile if it fails to enhance or conserve the genetic diversity. We propound that use of germplasm from genetic diversity hotspots for propagation in climatic hotspots, and prioritization of these hotspot patches for conservation would ensure greater genetic variability under a safe environment. This integrative approach of translating molecular and climatic data into conservation planning would save our efforts, time, and capital investment, and ensure greater success in managing the revival of T. contorta in the Western Himalayas. � 2020, Springer Nature B.V.
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    Transcriptome Analysis Revealed Behavior Complexity of Senescence Responses in Himalayan Tree Species Ulmus wallichiana
    (Springer, 2023-05-17T00:00:00) Singh, Amandeep; Majeed, Aasim; Sharma, Vikas; Gadri, Hari Shankar; Chowdhary, Md. Asif; Bhardwaj, Pankaj
    The Himalayas present a highly contrasting environment for the organisms that inhabit it, with summer and winter being the most disparate seasons. As winter approaches, the temperature drops, and deciduous plants, such as Ulmus wallichiana Planch., undergo senescence. In this study, we used the RNA-seq approach to generate a de novo transcriptome assembly of U. wallichiana, consisting of 300,067 unigenes. We investigated the differential expression pattern of these unigenes under changing climatic conditions, with a focus on the contrast between winter and summer. We observed that 2746 unigenes were differentially expressed, with a fold change of ? 2 and an FDR-adjusted p-value of ? 0.001. Among these unigenes, 37 were found to be related to senescence. We also identified nine DREB unigenes in the U. wallichiana transcriptome, which exhibited more or less contrasting patterns between summer and winter. These DREB unigenes may play an important role in regulating the plant�s tolerance to cold and/or drought stress. Our findings shed light on the complex and dynamic process of transcriptomic reprogramming that enables U. wallichiana to cope with seasonal changes. Furthermore, this study highlights the urgent need for further research on U. wallichiana, as this endangered plant species remains largely unexplored at the genomic level. � 2023, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, 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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    Transcribing molecular and climatic data into conservation management for the Himalayan endangered species, Taxus contorta (Griff.)
    (Springer Science and Business Media B.V., 2020-11-12T00:00:00) Majeed, Aasim; Singh, Amandeep; Bhardwaj, Pankaj
    Owing to the changing climatic scenario globally, and human overexploitation, the risk of extinction of Himalayan endangered species has increased many folds. Taxus contorta, an endangered gymnosperm has reached a decisive state in the Western Himalayas, thus, demands immediate attention to rescue it. This study aims to elucidate population and landscape genetics of T. contorta to plan a successful conservation strategy. We used SSR genotyping to identify genetic diversity hotspots, and ecological niche modeling to reveal climatic hotspots of T. contorta in the Indian Western Himalayas. We observed a substantial genetic diversity, and a negligible level of inbreeding among T. contorta populations. A genetic bottleneck was observed in several populations. We propose that changing climate can cause a failure of an entire conservation management plan if the shift produces a degraded environment in the future, at the sites of conservation. Further, the conservation management is futile if it fails to enhance or conserve the genetic diversity. We propound that use of germplasm from genetic diversity hotspots for propagation in climatic hotspots, and prioritization of these hotspot patches for conservation would ensure greater genetic variability under a safe environment. This integrative approach of translating molecular and climatic data into conservation planning would save our efforts, time, and capital investment, and ensure greater success in managing the revival of T. contorta in the Western Himalayas. � 2020, Springer Nature B.V.
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    RNAseq-based phylogenetic reconstruction of Taxaceae and Cephalotaxaceae
    (Wiley, 2018) Majeed, Aasim; Singh, Amandeep; Choudhary, Shurti; Bhardwaj, Pankaj
    Taxaceae and Cephalotaxaceae are the two economically important conifer families. Over the years there has been much controversy over the issue of merging these families. The position of Amentotaxus and Torreya is also ambiguous. Some authors consider them closer to Taxaceae while others deemed them to fit within Cephalotaxaceae. Still, others prefer to raise them to their own tribe. Different morphological, anatomical, embryological and phylogenetic evidence supports one or the other view, making the precise delineation between them unresolved. Here we used an RNAseq?based approach to obtain orthologous genes across the selected species to reconstruct a more robust phylogeny of these families. A total of 233.123 million raw reads were de novo assembled to generate nine different transcript assemblies for the corresponding species. Of the 940 191 assembled transcripts across nine species, we generated 409 734 unigenes, which were clustered into orthologous groups. A total of 331 single?copy complete orthologous groups were selected for phylogenetic analysis. Maximum?likelihood, maximum?parsimony and Bayesian phylogenetic trees showed a sister relationship between Taxaceae and Cephalotaxaceae. Our analysis supports their distinctiveness at the family level and also shows that Amentotaxus and Torreya fit within Cephalotaxaceae.
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    Genetic diversity and population structure of Melia azedarach in North-Western Plains of India
    (Springer Verlag, 2016) Thakur, Sapna; Choudhary, Shruti; Singh, Amandeep; Ahmad, Kamal; Sharma, Gagan; Majeed, Aasim; Bhardwaj, Pankaj
    Key message: Genetic structure amongM. azedarachpopulations was detected and two subpopulations were present among them. A significant ?isolation by distance? was found inM. azedarachpopulation in North-Western Plains of India. Abstract: Melia azedarach is an important forest tree with pharmaceutical, insecticidal, pesticidal, and commercial significance. It is a good reforestation tree because of its fast growth and drought hardy nature. Genetic variation in a species allows itself to adapt, evolve and respond to environmental stress. It provides the basis for survival of a species and critically influences its evolutionary potential. Assessment of genetic diversity is necessary for improvement and conservation of a species. For this, microsatellite markers are of particular interest given the attributes like co-dominance, reproducibility, hyper variability and abundance throughout the genome. In the present study, we analyzed the genetic diversity and population structure of M. azedarach, an ecologically imperative species growing in the North-Western Plains of India. We developed 43 microsatellite markers, of which 20 were subsequently employed for analysis of diversity and population structure among 33 populations encompassing 318 genotypes representing North-Western Plains of India. A moderate level of diversity (Na?=?5.1, Ho?=?0.506, He?=?0.712, I?=?1.386) was assessed. The highest value of ?K estimated using STRUCTURE indicated 2 subpopulations (K?=?2). AMOVA exhibited 73?% variation within populations and 12?% variation was found among regions. Significant positive correlation between geographical and genetic distance was found (Rxy?=?0.365, P?=?0.010). The present study lays a foundation on a better understanding of genetic dynamics of the species and reveals its diversity and population structure in North-Western Plains of India. ? 2016, Springer-Verlag Berlin Heidelberg.