Browsing by Author "Majeed, Aasim"

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Adaptability of Rhododendrons in high altitude habitats
(Northeast Forestry University, 2020-01-03T00:00:00) Choudhary, Shruti; Thakur, Sapna; Majeed, Aasim; Bhardwaj, Pankaj
Tree species dominate many ecosystems throughout the world and their response to climate, in light of global warming, is a matter of primary concern. This review describes past and ongoing research in Rhododendron, an ecologically important and well-adapted genus of more than 1000 species, occupying diverse habitats. Research to date indicates survival ability and mechanisms, with an emphasis on cold tolerance. The capability of long-distance gene flow in these species increases their genetic variability which in turn enhances their adaptability to newer niches as well as to environmental gradients (mainly temperature). Attempts to explain the molecular basis of morphological and behavioural changes in Rhododendron against cold-induced damage has been made. Gradual advances in �omics� have led to an enriched genomic resource dissecting the role and interaction of multiple molecular factors participating in cold adaptability. However, fewer genetic studies are available on species with an inherent or a default cold-tolerance ability. Considering this fact, understanding specific features of an adapted species can provide insights on overriding the effects of desiccation and determining phase transitions in other plants as well. We propose to integrate ecological and evolutionary studies with functional genomics to improve predictions of tree responses to their environment. � 2020, Northeast Forestry University.
Adaptability of Rhododendrons in high altitude habitats
(Northeast Forestry University, 2020-01-03T00:00:00) Choudhary, Shruti; Thakur, Sapna; Majeed, Aasim; Bhardwaj, Pankaj
Tree species dominate many ecosystems throughout the world and their response to climate, in light of global warming, is a matter of primary concern. This review describes past and ongoing research in Rhododendron, an ecologically important and well-adapted genus of more than 1000 species, occupying diverse habitats. Research to date indicates survival ability and mechanisms, with an emphasis on cold tolerance. The capability of long-distance gene flow in these species increases their genetic variability which in turn enhances their adaptability to newer niches as well as to environmental gradients (mainly temperature). Attempts to explain the molecular basis of morphological and behavioural changes in Rhododendron against cold-induced damage has been made. Gradual advances in �omics� have led to an enriched genomic resource dissecting the role and interaction of multiple molecular factors participating in cold adaptability. However, fewer genetic studies are available on species with an inherent or a default cold-tolerance ability. Considering this fact, understanding specific features of an adapted species can provide insights on overriding the effects of desiccation and determining phase transitions in other plants as well. We propose to integrate ecological and evolutionary studies with functional genomics to improve predictions of tree responses to their environment. � 2020, Northeast Forestry University.
Codon usage pattern in Gnetales evolved in close accordance with the Gnetifer hypothesis
(Oxford University Press, 2021-01-06T00:00:00) Majeed, Aasim; Kaur, Harpreet; Kaur, Amitozdeep; Das, Sreemoyee; Joseph, Josepheena; Bhardwaj, Pankaj
The evolution of Gnetales is ambiguous, and their phylogenetic position is still debated. The biological and molecular processes may evolve with the evolutionary history of a species or a clade. The molecular/biological processes of phylogenetically similar lineages closely follow their evolutionary pattern. If Gnetales evolved as a sister to Pinaceae, cupressophytes or Coniferales as a whole, then it is expected that the molecular or biological processes may reflect this pattern of evolution. In light of this, we deciphered the codon usage pattern of Gnetales, compared it with angiosperms, Pinaceae, cupressophytes and Coniferales as a whole. We evaluated whether this important molecular process has evolved in agreement with the Anthophyte, Gnepine, Gnecup or Gnetifer hypothesis. We observed that Gnetales prefer A/U-ending codons to G/C-ending codons like other lineages. Natural selection plays a dominant role in governing the codon usage bias (CUB). The CpA/CpT dinucleotides were over-represented, whereas the CpG dinucleotide was suppressed. Hierarchical clustering (HC) and correspondence analysis (CA) on relative synonymous codon usage values of 59 synonymous codons showed Gnetales as a sister clade to Coniferales as a whole and revealed that the codon usage pattern in Gnetales has evolved in close accordance with the Gnetifer hypothesis. � 2021 The Linnean Society of London, Botanical Journal of the Linnean Society.
Codon usage pattern in Gnetales evolved in close accordance with the Gnetifer hypothesis
(Oxford University Press, 2021-01-06T00:00:00) Majeed, Aasim; Kaur, Harpreet; Kaur, Amitozdeep; Das, Sreemoyee; Joseph, Josepheena; Bhardwaj, Pankaj
The evolution of Gnetales is ambiguous, and their phylogenetic position is still debated. The biological and molecular processes may evolve with the evolutionary history of a species or a clade. The molecular/biological processes of phylogenetically similar lineages closely follow their evolutionary pattern. If Gnetales evolved as a sister to Pinaceae, cupressophytes or Coniferales as a whole, then it is expected that the molecular or biological processes may reflect this pattern of evolution. In light of this, we deciphered the codon usage pattern of Gnetales, compared it with angiosperms, Pinaceae, cupressophytes and Coniferales as a whole. We evaluated whether this important molecular process has evolved in agreement with the Anthophyte, Gnepine, Gnecup or Gnetifer hypothesis. We observed that Gnetales prefer A/U-ending codons to G/C-ending codons like other lineages. Natural selection plays a dominant role in governing the codon usage bias (CUB). The CpA/CpT dinucleotides were over-represented, whereas the CpG dinucleotide was suppressed. Hierarchical clustering (HC) and correspondence analysis (CA) on relative synonymous codon usage values of 59 synonymous codons showed Gnetales as a sister clade to Coniferales as a whole and revealed that the codon usage pattern in Gnetales has evolved in close accordance with the Gnetifer hypothesis. � 2021 The Linnean Society of London, Botanical Journal of the Linnean Society.
Exploring microRNA profiles for circadian clock and flowering development regulation in Himalayan Rhododendron
(Elsevier, 2018) Choudhary, Shruti; Thakur, Sapna; Majeed, Aasim; Bhardwaj, Pankaj
miRNA is a non-coding, yet crucial entity in remodeling the genetic architecture. Rhododendron arboreum of Himalayas grows and even flower under fluctuating climate. sRNA from leaves of vegetative and reproductive periods was sequenced to elucidate its seasonal associations. Conserved (256) and novel (210) miRNAs and their precursors were located based on homology with plant databases and transcriptome of the species. 27,139 predicted targets were involved with metabolism, reproduction, and response to abiotic stimuli. A comparative analysis showed differential expression of 198 miRNAs with season-specific abundance of 103 miRNAs. Specific isoforms of 11 miRNA families exhibited a temporal expression and targeted different genes implying a complex regulation. The variable miRNA expression among the tissues of different conditions can be associated with the adaptability of the species, which will prove essential for further study on miRNAs mediating seasonal response. Moreover, exogenous cues also mediate phase transition via networking of flowering pathways and their components. In this context, 18 known families and 77 novel miRNAs modulating 117 genes crucial in circadian entrainment were filtered. A negative correlation was obtained between the expression of 18 of these miRNAs and their targets when tested through quantitative-PCR. It highlighted the role of miRNA-target pairs in perceiving environmental variabilities and monitoring flowering growth. Furthermore, a phylogenetic clustering was performed, which supported the lineage-specific evolution and function of putative miR156 sequence in the species. This documentation of genome-wide profiling of miRNA, their targets, and expression will enhance the understanding of developmental and climate-tolerance strategies in high-altitude trees.
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.
Large-Scale Characterization of the Soil Microbiome in Ancient Tea Plantations Using High-Throughput 16S rRNA and Internal Transcribed Spacer Amplicon Sequencing
(Frontiers Media S.A., 2021-10-16T00:00:00) Kui, Ling; Xiang, Guisheng; Wang, Ya; Wang, Zijun; Li, Guorong; Li, Dawei; Yan, Jing; Ye, Shuang; Wang, Chunping; Yang, Ling; Zhang, Shiyu; Zhang, Shuangyan; Zhou, Ling; Gui, Heng; Xu, Jianchu; Chen, Wei; Zhang, Jun; Huang, Tingyuan; Majeed, Aasim; Sheng, Jun; Dong, Yang
There is a special interaction between the environment, soil microorganisms, and tea plants, which constitute the ecosystem of tea plantations. Influenced by environmental factors and human management, the changes in soil microbial community affected the growth, quality, and yield of tea plants. However, little is known about the composition and structure of soil bacterial and fungal communities in 100-year-old tea plantations and the mechanisms by which they are affected. In this regard, we characterized the microbiome of tea plantation soils by considering the bacterial and fungal communities in 448 soil samples from 101 ancient tea plantations in eight counties of Lincang city, which is one of the tea domestication centers in the world. 16S and Internal Transcribed Spacer (ITS) rRNA high-throughput amplicon sequencing techniques were applied in this study. The results showed that the abundance, diversity, and composition of the bacterial and fungal communities have different sensitivity with varying pH, altitude, and latitude. pH and altitude affect soil microbial communities, and bacterial communities are more sensitive than fungi in terms of abundance and diversity to pH. The highest ?-diversity of bacterial communities is shown in the pH 4.50�5.00 and 2,200-m group, and fungi peaked in the pH 5.00�5.50 and 900-m group. Because of environmental and geographical factors, all microbes are similarly changing, and further correlations showed that the composition and structure of bacterial communities are more sensitive than fungal communities, which were affected by latitude and altitude. In conclusion, the interference of anthropogenic activities plays a more important role in governing fungal community selection than environmental or geographical factors, whereas for the bacterial community, it is more selective to environment adaptation than to adaptation to human activities. � Copyright � 2021 Kui, Xiang, Wang, Wang, Li, Li, Yan, Ye, Wang, Yang, Zhang, Zhang, Zhou, Gui, Xu, Chen, Zhang, Huang, Majeed, Sheng and Dong.
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.
Selection constraints determine preference for A/U-ending codons in Taxus contorta
(Canadian Science Publishing, 2020) Majeed, Aasim; Kaur, Harpreet; Bhardwaj, Pankaj
Unequal utilization of synonymous codons is a well-known phenomenon among living organisms. This phenomenon plays a major role in the enhancement of the accuracy and efficiency of translation. Gymnosperms are rarely paid attention in this aspect. Understanding the degree of and determining the forces influencing codon usage bias (CUB) in Taxus contorta, an endangered Himalayan gymnosperm, will prove useful in interpreting the evolutionary characteristics of this species. Using RNAseq data, 93?790 assembled transcripts were clustered into 32?701 unigenes. Around 13?061 full-length sequences were utilized for the analysis of CUB. Compositional properties showed that GC-content ranged from 28.76% to 65.22%, with an average value of 44.28%, suggesting an AT-rich genome. The mean effective number of codons (ENC) value revealed that CUB is not strong in T. contorta. The preferred codons tended to be A/U ending, whereas the avoided codons tended to be G/C ending. A P2 index of 0.54 and a Mutation Responsive Index (MRI) value of-0.02 in addition to the results revealed by the neutrality, ENC, and parity plots showed that natural selection is a predominating factor governing CUB. Mutational pressure, gene length, hydropathiciy, aromaticity, and nucleotide composition influence CUB weakly
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.
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.
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.
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.
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.
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.