scholarly journals Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
P. Vignesh ◽  
C. Mahadevaiah ◽  
R. Parimalan ◽  
R. Valarmathi ◽  
S. Dharshini ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Plasma Membrane ◽  
Transcriptome Analysis ◽  
Metabolic Pathways ◽  
De Novo ◽  
Biological Processes ◽  
Wild Relative ◽  
De Novo Transcriptome ◽  
Membrane Bound ◽  
And Control

AbstractErianthus arundinaceus [Retzius] Jeswiet, a wild relative of sugarcane has a high biomass production potential and a reservoir of many genes for superior agronomic traits and tolerance to biotic and abiotic stresses. A comparative physiological, anatomical and root transcriptome analysis were carried out to identify the salt-responsive genes and metabolic pathways associated with salt-tolerant E. arundinaceus genotype IND99-907 and salinity-sensitive sugarcane genotype Co 97010. IND99-907 recorded growth of young leaves, higher proline content, higher relative water content, intact root anatomical structures and lower Na+/K+, Ca2+/K+ and Mg2+/K+ ratio as compared to the sugarcane genotype Co 97010. We have generated four de novo transcriptome assemblies between stressed and control root samples of IND99-907 and Co 97010. A total of 649 and 501 differentially expressed genes (FDR<0.01) were identified from the stressed and control libraries of IND99-907 and Co 97010 respectively. Genes and pathways related to early stress-responsive signal transduction, hormone signalling, cytoskeleton organization, cellular membrane stabilization, plasma membrane-bound calcium and proton transport, sodium extrusion, secondary metabolite biosynthesis, cellular transporters related to plasma membrane-bound trafficking, nucleobase transporter, clathrin-mediated endocytosis were highly enriched in IND99-907. Whereas in Co 97010, genes related to late stress-responsive signal transduction, electron transport system, senescence, protein degradation and programmed cell death, transport-related genes associated with cellular respiration and mitochondrial respiratory chain, vesicular trafficking, nitrate transporter and fewer secondary metabolite biosynthetic genes were highly enriched. A total of 27 pathways, 24 biological processes, three molecular functions and one cellular component were significantly enriched (FDR≤ 0.05) in IND99-907 as compared to 20 pathways, two biological processes without any significant molecular function and cellular components in Co 97010, indicates the unique and distinct expression pattern of genes and metabolic pathways in both genotypes. The genomic resources developed from this study is useful for sugarcane crop improvement through development of genic SSR markers and genetic engineering approaches.

scholarly journals De Novo Transcriptome Analysis of Medicinally Important Plantago ovata Using RNA-Seq

PLoS ONE ◽  
2016 ◽  
Vol 11 (3) ◽  
pp. e0150273 ◽  
Author(s):  
Shivanjali Kotwal ◽  
Sanjana Kaul ◽  
Pooja Sharma ◽  
Mehak Gupta ◽  
Rama Shankar ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
De Novo ◽  
Rna Seq ◽  
Plantago Ovata ◽  
De Novo Transcriptome

scholarly journals Cell Secretion: Current Structural and Biochemical Insights

2010 ◽  
Vol 10 ◽  
pp. 2054-2069 ◽  
Author(s):  
Saurabh Trikha ◽  
Elizabeth C. Lee ◽  
Aleksandar M. Jeremic
Keyword(s):  
Plasma Membrane ◽  
Secretory Vesicles ◽  
Intercellular Signaling ◽  
Cell Secretion ◽  
Membrane Structures ◽  
Calcium Dependent ◽  
Cell Plasma ◽  
Membrane Bound ◽  
And Control ◽  
Fusion Pores

Essential physiological functions in eukaryotic cells, such as release of hormones and digestive enzymes, neurotransmission, and intercellular signaling, are all achieved by cell secretion. In regulated (calcium-dependent) secretion, membrane-bound secretory vesicles dock and transiently fuse with specialized, permanent, plasma membrane structures, called porosomes or fusion pores. Porosomes are supramolecular, cup-shaped lipoprotein structures at the cell plasma membrane that mediate and control the release of vesicle cargo to the outside of the cell. The sizes of porosomes range from 150nm in diameter in acinar cells of the exocrine pancreas to 12nm in neurons. In recent years, significant progress has been made in our understanding of the porosome and the cellular activities required for cell secretion, such as membrane fusion and swelling of secretory vesicles. The discovery of the porosome complex and the molecular mechanism of cell secretion are summarized in this article.

scholarly journals De novo transcriptome analysis of halotolerant bacterium Staphylococcus sp. strain P-TSB-70 isolated from East coast of India: In search of salt stress tolerant genes

PLoS ONE ◽  
2020 ◽  
Vol 15 (2) ◽  
pp. e0228199 ◽  
Author(s):  
Priyanka Das ◽  
Bijay Kumar Behera ◽  
Soumendranath Chatterjee ◽  
Basanta Kumar Das ◽  
Trilochan Mohapatra
Keyword(s):  
Salt Stress ◽  
Transcriptome Analysis ◽  
East Coast ◽  
De Novo ◽  
De Novo Transcriptome ◽  
East Coast Of India ◽  
Halotolerant Bacterium

scholarly journals De novo transcriptome analysis of the critically endangered alpine Himalayan herb Nardostachys jatamansi reveals the biosynthesis pathway genes of tissue-specific secondary metabolites

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Nisha Dhiman ◽  
Anil Kumar ◽  
Dinesh Kumar ◽  
Amita Bhattacharya
Keyword(s):  
Secondary Metabolites ◽  
Transcriptome Analysis ◽  
Vegetative Growth ◽  
De Novo ◽  
Biosynthesis Pathway ◽  
De Novo Transcriptome ◽  
Tissue Specific ◽  
Nardostachys Jatamansi ◽  
Secondary Metabolite Biosynthesis

Abstract The study is the first report on de novo transcriptome analysis of Nardostachys jatamansi, a critically endangered medicinal plant of alpine Himalayas. Illumina GAIIx sequencing of plants collected during end of vegetative growth (August) yielded 48,411 unigenes. 74.45% of these were annotated using UNIPROT. GO enrichment analysis, KEGG pathways and PPI network indicated simultaneous utilization of leaf photosynthates for flowering, rhizome fortification, stress response and tissue-specific secondary metabolites biosynthesis. Among the secondary metabolite biosynthesis genes, terpenoids were predominant. UPLC-PDA analysis of in vitro plants revealed temperature-dependent, tissue-specific differential distribution of various phenolics. Thus, as compared to 25 °C, the phenolic contents of both leaves (gallic acid and rutin) and roots (p-coumaric acid and cinnamic acid) were higher at 15 °C. These phenolics accounted for the therapeutic properties reported in the plant. In qRT-PCR of in vitro plants, secondary metabolite biosynthesis pathway genes showed higher expression at 15 °C and 14 h/10 h photoperiod (conditions representing end of vegetative growth period). This provided cues for in vitro modulation of identified secondary metabolites. Such modulation of secondary metabolites in in vitro systems can eliminate the need for uprooting N. jatamansi from wild. Hence, the study is a step towards effective conservation of the plant.

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