Browsing by Author "Suvajit Basu"

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Bryophytes as Modern Model Plants: An Overview of Their Development, Contributions, and Future Prospects
(Springer, 2023) Sandhya Yadav; Suvajit Basu; Akanksha Srivastava; Subhankar Biswas; Raju Mondal; Vishal Kumar Jha; Sushil Kumar Singh; Yogesh Mishra
Model organisms are commonly employed in research as convenient tools for studying diverse biological processes. Plant research relied on several non-model plants until the Arabidopsis thaliana was developed as powerful model for identifying genes and determining their functions. To study the genetics of unique processes in different species, few other model photosynthetic organisms have recently been established, including Synechocystis sp. PCC 6803, Anabaena sp. PCC 7120, Chlamydomonas reinhardatii, Oryza sativa, Zea mays, Triticum dicoccoides, Populus trichocarpa, and Picea abies. However, when it comes to answering different biological problems, each of the current model plants has its own set of advantages and disadvantages, and many questions about land plant adaptation strategies at the level of morpho-physiology, development, and stress mitigation could not be adequately answered using these models. Furthermore, the high occurrence of embryo lethal mutations rendered studying the molecular basis of 3-dimensional (3-D) growth and gametogenesis unfeasible. Since bryophytes have a low cellular complexity and a dominant haploid gametophytic phase, they could be useful models not only for avoiding the aforementioned drawbacks, but also for functional genomics research and understanding the chronology of land plant evolution. These distinguishing characteristics and the advancement of sequencing technology have led to the development of some bryophytes as modern model plants, including Physcomitrium patens, Marchantia polymorpha, Anthoceros agrestis. Here, we review at how bryophytes became model plants, and how they have been able to answer crucial plant biology-related concerns like stress tolerance and evolutionary developmental (evo-devo) biology that other model plants have not been able to. © 2023, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
In silico analysis and expression profiling of S-domain receptor-like kinases (SD-RLKs) under different abiotic stresses in Arabidopsis thaliana
(BioMed Central Ltd, 2021) Raju Mondal; Subhankar Biswas; Akanksha Srivastava; Suvajit Basu; Maitri Trivedi; Sunil Kumar Singh; Yogesh Mishra
Background: S-domain receptor-like kinases (SD-RLKs) are an important and multi-gene subfamily of plant receptor-like/pelle kinases (RLKs), which are known to play a significant role in the development and immune responses of Arabidopsis thaliana. The conserved cysteine residues in the extracellular domain of SD-RLKs make them interesting candidates for sensing reactive oxygen species (ROS), assisting oxidative stress mitigation and associated signaling pathways during abiotic stresses. However, how closely SD-RLKs are interrelated to abiotic stress mitigation and signaling remains unknown in A. thaliana. Results: This study was initiated by examining the chromosomal localization, phylogeny, sequence and differential expression analyses of 37 SD-RLK genes using publicly accessible microarray datasets under cold, osmotic stress, genotoxic stress, drought, salt, UV-B, heat and wounding. Out of 37 SD-RLKs, 12 genes displayed differential expression patterns in both the root and the shoot tissues. Promoter structure analysis suggested that these 12 SD-RLK genes harbour several potential cis-regulatory elements (CREs), which are involved in regulating multiple abiotic stress responses. Based on these observations, we investigated the expression patterns of 12 selected SD-RLKs under ozone, wounding, oxidative (methyl viologen), UV-B, cold, and light stress at different time points using semi-qRT-PCR. Of these 12 SD-SRKs, the genes At1g61360, At1g61460, At1g61380, and At4g27300 emerged as potential candidates that maintain their expression in most of the stress treatments till exposure for 12 h. Expression patterns of these four genes were further verified under similar stress treatments using qRT-PCR. The expression analysis indicated that the gene At1g61360, At1g61380, and At1g61460 were mostly up-regulated, whereas the expression of At4g27300 either up- or down-regulated in these conditions. Conclusions: To summarize, the computational analysis and differential transcript accumulation of SD-RLKs under various abiotic stresses suggested their association with abiotic stress tolerance and related signaling in A. thaliana. We believe that a further detailed study will decipher the specific role of these representative SD-RLKs in abiotic stress mitigation vis-a-vis signaling pathways in A. thaliana. © 2021, The Author(s).
Seasonal Changes in the Antioxidative Defence System of a Liverwort Dumortiera hirsuta
(Springer, 2022) Sandhya Yadav; Akanksha Srivastava; Subhankar Biswas; Suvajit Basu; Sushil Kumar Singh; Yogesh Mishra
Liverworts are influenced by several ecological factors, such as photoperiod, temperature, precipitation, and nutrient availability. These factors vary in different seasons of the Indian calendar year, divisible into pre-monsoon (March–May), monsoon (June–August), post-monsoon (September–November), and fruiting (December–February) seasons. Seasonality causes disturbance in cellular homeostasis, which may trigger ROS formation. To restore the threshold level of ROS, liverworts must be equipped with complex antioxidant defence machinery. Thus, in this study, we analysed the effect of seasonal changes on oxidative stress markers [malondialdehyde (MDA) and total peroxide (H2O2 content)], total protein and pigment contents, and enzymatic and non-enzymatic antioxidants activities/contents in a liverwort, Dumortiera hirsuta, during its four distinct growing seasons. During the fruiting season, the results revealed the highest level of MDA and H2O2 with the lowest level during the pre-monsoon/monsoon seasons. The protein and pigment contents were maximal during the monsoon season and minimal during the fruiting season. With the exception of few [ascorbate peroxidase (APX) and ascorbic acid (ASC)], enzymatic [superoxide dismutase (SOD), catalase (CAT), and glutathione reductase (GR)] and non-enzymatic antioxidants (total thiol, proline, and carotenoids) activities/contents were correspondingly high during the fruiting season and low during the pre-monsoon/monsoon seasons, indicating their defensive role in neutralizing/suppressing the increased ROS during the fruiting season when the temperature was very low and the nutrient availability was less. These results therefore suggest that the antioxidative defence machinery plays a potential role in the adaptation of D. hirsuta against oxidative stress, naturally imposed by seasonal climatic changes. © 2021, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
Two Evolutionary Diverged Liverworts that Shared the Same Habitats Developed a Few Distinct Seasonal Adaptive Strategies: Insights from a Transcriptomic Approach
(Springer, 2025) Suvajit Basu; Sandhya Yadav; Vishal Kumar Jha; Subhankar Biswas; Akanksha Srivastava; Kritika Tripathi; Raju Mondal; Neha Chaurasia; Sushil Kumar Singh; Yogesh Mishra
Since liverworts are among the earliest land plants to undergo seasonal fluctuations, they hold the secret to the molecular mechanism behind seasonal adaptation. Depending on their evolutionary histories, different liverwort species may have relatively distinct adaptive mechanisms. We therefore, performed a seasonal transcriptome analysis of two Indian liverworts, Dumortiera hirsuta and Plagiochasma appendiculatum, during their four different growing seasons (pre-monsoon, monsoon, post-monsoon, and fruiting season). These two species diverged at different points in their evolutionary history but coexist in the same habitat. Phylogenetic trees and evolutionary timescale analyses showed that D. hirsuta is primitive than P. appendiculatum. The RNA-seq analysis showed that D. hirsuta primarily modifies its transcriptome by differentially regulating growth, metabolism, and stress-responsive genes and related TFs in the post-monsoon but mainly induces specific stress-responsive genes in the fruiting season. This is likely to develop reproductive organs in the post-monsoon season and to strategically adapt to the harsh environmental conditions of both seasons by conserving energy during the fruiting season. Conversely, P. appendiculatum exhibited significant transcriptome variability by modulating the expression of genes with similar functions during both the fruiting and post-monsoon seasons, albeit to a lesser degree than D. hirsuta. This suggests that P. appendiculatum strategically modulated its necessary gene expression levels over an extended period of time while taking energy conservation into consideration in order to survive the harsh conditions of both seasons. This study offers the first comprehensive view of seasonal adaptive strategies employed by two evolutionary diverged liverworts that coexist in the same habitat. © The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2025.