Botany - Research Publications

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Author: search.filters.author.Sharma, Vikas

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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 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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    Identification and cross-species amplification of microsatellite markers derived from expressed sequence data of rose species
    (Springer India, 2015) Sharma, Ram Kumar; Chaudhary, Anil; Sharma, Himanshu; Bhardwaj, Pankaj; Sharma, Vikas; Kumar, Rahul; Ahuja, Paramveer Singh
    Genic SSR markers derived from public expressed sequence tags (ESTs) data are valuable and cost effective marker resources for genome mapping and diversity studies. Owing to their derivation from the transcribed regions which often have putative functions, these markers can be easily associated with desired trait. In the present study, 19 novel SSR markers were identified from 450 non redundant unigenes derived from 3,726 public ESTs of two rose species. Among SSRs, tri-repeats (61.3?%) were most abundant followed by di-repeat (29?%). Newly identified EST-SSR markers recorded significant homology with the known/putative proteins of Arabidopsis thaliana. The cross transferability to 12 rose species ranged from 63.2 to 100?%. Novel SSR loci found to be moderately to highly polymorphic with locus wise average number of alleles and polymorphism information content (PIC) were 4.1 and 0.33, respectively. Cloning and sequencing of EST-SSR size variant amplicons of marker locus Rches12 revealed that the variation in the number of SSR repeat-units was the main source of fragment polymorphism. The high polymorphic potential coupled with high cross-transferability rate demonstrates wider applicability of novel SSR markers in genetic diversity, genome mapping and evolutionary studies in various rose species. ? 2014, Society for Plant Biochemistry and Biotechnology.