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Abstract The continuous exposure of chemical pesticides in agriculture, their contamination in soil and water pose serious threat to the environment. Current study used an approach to evaluate various pesticides like Hexaconazole, Mancozeb, Pretilachlor, Organophosphate and λ-cyhalothrin degradation capability of esterase. The enzyme was isolated from Salinicoccus roseus. Genome analysis unveiled the carboxylesterase genes underlying the degradation of pesticides, and was located between 2070Mbp to 2080Mbp region. Herein, partially purified esterase was immobilized into beads by mixing with an equal volume (1:1) of sodium alginate solution [2.5% (w/v)].Scanning electron microscopy (SEM) of the beads showed the microspheres for enhanced enzyme-substrate reaction, wide peak at 3316, 1635 and 696 cm− 1 in Fourier-transform infrared spectroscopy (FTIR) represented intermolecular hydrogen bonding, and thermogravimetric analysis (TGA) reaffirmed the binding of esterase entrapped into the beads. Maximum degradation rate (after 4 days) for free enzyme accounted 83.2% in Hexaconazole. Degradation rate moderately increased 4% in the presence of immobilized esterase. Degradation products were detected by liquid chromatography–mass spectrometry (LC–MS). Cytotoxicity test (root length and mitotic index) revealed differences in various treatments. Enzyme kinetics parameters, Michaëlis-Menten constant (K M) 6.61 mM and maximum velocity (V max) 1.89 µmol/min/mg increased after immobilization. Further, molecular docking results validated that esterase contributed to pesticide degradation by catalytic triad of Ser93-His222-Phe24, ligand interactions, and specific binding pockets. Additionally, molecular dynamics (MD) simulations confirmed the protein-ligand conformational stability. Hence, present study highlighted an effective method for improving the catalytic properties of esterase, and also potential candidate for bioremediation of pesticides.

Background: At present, research on facile, green synthesis of nanoparticles has significantly increased because of its fast, one-step, cost-effective, time-efficient, and non-toxic nature. In this study, we have reported a single-step green synthesis of copper nanoparticles using cell wall polysaccharides of a hot spring origin, thermotolerant Bacillus species. Result: Copper nanoparticles were characterized using UV-visible spectrophotometry, fluorescence and Fourier transform infrared spectroscopy, scanning electron microscopy with energy dispersive spectroscopy, particle size, and zeta potential analyses. UV-visible spectra of synthesized copper nanoparticles exhibited a band cantered between 220–235 nm, characteristic spectra of copper oxide nanoparticles. Infrared spectra showed the band at 490-530 cm−1 corresponding to metal-oxygen or copper nanoparticle vibration, supporting the presence of copper oxide nanoparticles in the monoclinic phase. The energy dispersive spectra of copper nanoparticles exhibited a strong signal from elemental copper. The dynamic Light Scattering pattern confirmed the nanoparticle nature of the studied sample. These nanoparticles showed preferential activity against gram-negative pathogens, Salmonella typhi and Escherichia coli. The thermodynamic nature of the nanoparticles is also established for its antibacterial actions. Conclusions: The antibacterial action and its thermodynamics reinforce the possible use of copper nanoparticles as an alternative to commercially available antimicrobials. This study may open a new path for future studies to treat harmful microorganisms resistant to traditional antibiotics in a greener way.How to cite: Banerjee A, Roy RK, Sarkar S, et al. Synthesis of hot spring origin bacterial cell wall polysaccharide-based copper nanoparticles with antibacterial property. Electron J Biotechnol 2024;68. https://doi.org/10.1016/j.ejbt.2023.11.005.

Abstract Background Microbial community played an essential role in ecosystem processes, be it mangrove wetland or other intertidal ecologies. Several enzymatic activities like hydrolases are effective ecological indicators of soil microbial function. So far, little is known on halophilic bacterial contribution and function on a genomic viewpoint of Indian Sundarban Wetland. Considering the above mentioned issues, the aims of this study was to understand the life style, metabolic functionalities and genomic features of the isolated bacterium, Salinicoccus roseus strain RF1H. A comparative genome-based study of S. roseus has not been reported yet. Henceforth, we have considered the inclusion of the intra-species genome comparison of S. roseus to gain insight into the high degree of variation in the genome of strain RF1H among others. Results Salinicoccus roseus strain RF1H is a pink-red pigmented, Gram-positive and non-motile cocci. The bacterium exhibited high salt tolerance (up to 15% NaCl), antibiotic resistance, biofilm formation and secretion of extracellular hydrolytic enzymes. The circular genome was approximately 2.62978 Mb in size, encoding 574 predicted genes with GC content 49.5%. Presence of genomic elements (prophages, transposable elements, CRISPR-Cas system) represented bacterial virulence and multidrug-resistance. Furthermore, genes associated with salt tolerance, temperature adaptation and DNA repair system were distributed in 17 genomic islands. Genes related to hydrocarbon degradation manifested metabolic capability of the bacterium for potential biotechnological applications. A comparative pangenome analysis revealed two-component response regulator, modified C4-dicarboxylate transport system and osmotic stress regulated ATP-binding proteins. Presence of genes encoding arginine decarboxylase (ADC) enzyme being involved in biofilm formation was reported from the genome. In silico study revealed the protein is thermostable and made up with ~ 415 amino acids, and hydrophilic in nature. Three motifs appeared to be evolutionary conserved in all Salinicoccus sequences. Conclusion The first report of whole genome analysis of Salinicoccus roseus strain RF1H provided information of metabolic functionalities, biofilm formation, resistance mechanism and adaptation strategies to thrive in climate-change induced vulnerable spot like Sundarban. Comparative genome analysis highlighted the unique genome content that contributed the strain’s adaptability. The biomolecules produced during metabolism are important sources of compounds with potential beneficial applications in pharmaceuticals.

Rice is widely cultivated worldwide, and beneficial bactrial colonization are particularly desirable for sustainable agriculture because they promote growth and production by preventing excessive heavy metal contamination. The present study was conducted with the aim of improving the growth of rice seedlings (MTU1010 variety) under copper (Cu) stress by using Cu-tolerant plant growth promoting bacteria (PGPB) Micrococcus yunnanensis GKSM13. Strain GKSM13 was able to produce plant growth promoting factors (PGPFs) such as indole-3-acetic acid (IAA), gibberellin A3 (GA3) and ammonia, accumulate proline, fix N2, and inhibit 2,2-Diphenyl-1-picrylhydrazyl (DPPH). Rice seedlings treated with Cu2+ and co-inoculated with GKSM13 significantly improved their growth in morphological and biochemical aspects. When analysed by field emission scanning electron microscope (FE-SEM), GKSM13 was found to be associated with the root cells in the form of large number of coccoid cells. The uptake of Cu2+ in rice seedlings was reduced to 57.5% in the presence of GKSM13. Strain GKSM13 treatment also reduced Cu-induced oxidative stress of rice seedlings by activating antioxidant enzymes including superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APOX) and glutathione peroxidase (GPOX), which was supported by DPPH inhibition and reduction of malondialdehyde (MDA) accumulation. Insight into the genome of strain GKSM13 reveals the presence of tryptophan (trp), ent-kaurene, cyanase (cyn), phosphate-specific transport (pst), major facilitator superfamily transporter (MFS), sulphate transporter (cys), proline (pro) and SOD (sod) genes, which are responsible for promoting plant growth and alleviating Cu2+ stress. Therefore, the application of strain M. yunnanensis GKSM13 could provide a sustainable agricultural solution for Cu-affected mining areas.

Abstract Background Arsenic, a ubiquitous toxic metalloid, is a threat to the survival of all living organisms. Bioaccumulation of arsenic interferes with the normal physiological pathway. To overcome arsenic toxicity, organisms have developed arsenite methyltransferase enzyme, which methylates inorganic arsenite to organic arsenic MMA (III) in the presence of S-adenosylmethionine (SAM). Bacteria-derived arsM might be horizontally transported to different domains of life as arsM or as3mt (animal ortholog). A systematic study on the functional diversity of arsenite methyltransferase from various sources will be used in arsenic bioremediation. Results Several arsenite methyltransferase protein sequences of bacteria, fungi, fishes, birds, and mammals were retrieved from the UniProt database. In silico physicochemical studies confirmed the acidic, hydrophilic, and thermostable nature of these enzymes. Interkingdom relationships were revealed by performing phylogenetic analysis. Homology modeling was performed by SWISS-MODEL, and that was validated through SAVES-v.6.0. QMEAN values ranged from − 0.93 to − 1.30, ERRAT score (83–96), PROCHECK (88–92%), and other parameters suggested models are statistically significant. MOTIF and PrankWeb discovered several functional motifs and active pockets within the proteins respectively. The STRING database showed protein–protein interaction networks. Conclusion All of our in silico studies confirmed the fact that arsenite methyltransferase is a cytosolic stable enzyme with conserved sequences over a wide range of organisms. Thus, because of its stable and ubiquitous nature, arsenite methyltransferase could be employed in arsenic bioremediation.

Abstract Extracellular polysaccharide (EPS) produced by a deep-sea, psychrotolerant Bacillus altitudinis SORB11 was evaluated by considering physiochemical nature and structural constituents. The productivity of crude EPS was measured ~ 13.17 g L−1. The surface topography of the crude EPS showed a porous, webbed structure along with a branched coil-like configuration. The crystalline crude EPS contained a high amount of sulfur. Further, the crude EPS was subjected for purification. The molecular weight of purified EPS was determined ~ 9.8 × 104 Da. The purified EPS was appeared to show glucomannan-like configuration that is composed of → 4)-β-Manp-(1 → and → 4)-β-Glcp-(1 → residues. So, this polysaccharide was comparable to the structure of plant-derived glucomannan. Subsequently, EPS biosynthesis protein clusters like EpsC, EpsD, EpsE, and glycosyltransferase family proteins were predicted from the genome of strain SORB11, which may provide an insight into the production of glucomannan-type of polysaccharide. This low molecular weight linear form of glucomannan-type EPS might be involved to form a network-like unattached aggregation, and helps in cell-to-cell interaction in deep-sea microbial species.

Abstract Background Halophiles are extremophilic organisms represented by archaea, bacteria and eukaryotes that thrive in hypersaline environment. They apply different osmoadaptation strategies to survive in hostile conditions. Habitat diversity of halophilic microorganisms in hypersaline system provides information pertaining the evolution of life on Earth. Main body The microbiome-gut-brain axis interaction contributes greatly to the neurodegenerative diseases. Gut resident halophilic bacteria are used as alternative medication for chronic brain diseases. Halophiles can be used in pharmaceuticals, drug delivery, agriculture, saline waste water treatment, biodegradable plastic production, metal recovery, biofuel energy generation, concrete crack repair and other sectors. Furthermore, versatile biomolecules, mainly enzymes characterized by broad range of pH and thermostability, are suitable candidate for industrial purposes. Reflectance pattern of halophilic archaeal pigment rhodopsin is considered as potential biosignature for Earth-like planets. Short conclusions This review represents important osmoadaptation strategies acquired by halophilic archaea and bacteria and their potential biotechnological applications to resolve present day challenges. Graphical Abstract

Abstract Contamination of soil by antibiotics and heavy metals originating from hospital facilities has emerged as a major cause for the development of resistant microbes. We collected soil samples surrounding a hospital effluent and measured the resistance of bacterial isolates against multiple antibiotics and heavy metals. One strain BMCSI 3 was found to be sensitive to all tested antibiotics. However, it was resistant to many heavy metals and metalloids like cadmium, chromium, copper, mercury, arsenic, and others. This strain was motile and potentially spore-forming. Whole-genome shotgun assembly of BMCSI 3 produced 4.95 Mb genome with 4,638 protein-coding genes. The taxonomic and phylogenetic analysis revealed it, to be a Bordetella petrii strain. Multiple genomic islands carrying mobile genetic elements; coding for heavy metal resistant genes, response regulators or transcription factors, transporters, and multi-drug efflux pumps were identified from the genome. A comparative genomic analysis of BMCSI 3 with annotated genomes of other free-living B. petrii revealed the presence of multiple transposable elements and several genes involved in stress response and metabolism. This study provides insights into how genomic reorganization and plasticity results in evolution of heavy metals resistance by acquiring genes from its natural environment.

The interaction between microbes and plants in rhizospheric environment is evident regarding sustainable development in agriculture. Microbes are involved in various metabolic activities in plant systems, which in turn help in plant health improvement. Eventually, plant-microbe interactions are connected with biogeochemical cycles. In this context, metagenomic study helps us to survey the microbial diversity in their natural niches, especially in rhizospheric regions. Noticeably, a diverse group of bacteria, fungi, and archaea are likely to be involved in plant growth promoting (PGP) activities. Variation in microbial communities in the rhizosphere depends on various parameters, such as soil organic matter, plant genotype, plant exudates, crop rotation, soil pH, nutrient cycling, etc. Some abiotic factors and chemical fertilizers have negative impact on crop productivity, influencing sustainable development of environment. Despite having negative impacts from climate change, microbes cope with this altered scenario and try to adjust themselves successfully and consequently promote plant growth by nutrient acquisition and stress tolerance approaches. Therefore, climate change has appeared as a big threat to the agricultural sector in recent past and this might be persistent in near future. However, the conservation of microbial diversity in the rhizospheric regions appears as one of the most promising options for long-term environmental sustainability.

Background: Arsenic contamination in the ground water of rural India is a recurrent problem and decontamination is mostly based on the chemical or physical treatments until now. Microbial bioremediation is eco-friendly, cheap, time-efficient and does not produce any toxic by-products. Result: In the present study, a high arsenic tolerant bacteria Brevundimonas aurantiaca PFAB1 was isolated from Panifala hot spring located in West Bengal, India. Previously Panifala was also reported to be an arsenic-rich hot spring. B. aurantiaca PFAB1 exhibited both positive arsenic reductase and arsenite oxidase activity. It was tolerant to arsenite up to 90 mM and arsenate up to 310 mM. Electron microscopy has proved significant changes in cellular micromorphology and stalk appearance under the presence of arsenic in growth medium. Bioaccumulation of arsenic in As (III) treated cells were 0.01% of the total cell weight, while 0.43% in case of As (V) treatment. Conclusions: All experimental lines of evidence prove the uptake/accumulation of arsenic within the bacterial cell. All these features will help in the exploitation of B. aurantiaca PFAB1 as a potent biological weapon to fight arsenic toxicity in the near future.How to cite: Banerjee A, Sarkar S, Gorai S, et al. High arsenic tolerance in Brevundimonas aurantiaca PFAB1 from an arsenic-rich Indian hot spring. Electron J Biotechnol 2021:52. https://doi.org/10.1016/j.ejbt.2021.05.006

Clinically relevant antibiotic-resistant bacteria are appeared to be hard or impossible to treat using conventional antibiotics. In this context, copper oxide nanoparticles (CuO NPs) with latent and flexible character showed remarkable antimicrobial activity against pathogenic Pseudomonas aeruginosa. Minimum inhibitory concentration (

Abstract Background Chitin is one of the most abundant biopolymers on Earth, only trailing second after cellulose. The enzyme chitinase is responsible for the degradation of chitin. Chitinases are found to be produced by wide range of organisms ranging from archaea to higher plants. Though chitin is a major component of fungal cell walls and invertebrate exoskeletons, bacterial chitinase can be industrially generated at low cost, in facile downstream processes at high production rate. Microbial chitinases are more stable, active, and economically practicable compared to the plant- and animal-derived enzymes. Results In the present study, computationally obtained results showed functional characteristics of chitinase with particular emphasis on bacterial chitinase which is fulfilling all the required qualities needed for commercial production. Sixty-two chitinase sequences from four different groups of organisms were collected from the RCSB Protein Data Bank. Considering one suitable exemplary sequence from each group is being compared with others. Primary, secondary, and tertiary structures are determined by in silico models. Different physical parameters, viz., pI, molecular weight, instability index, aliphatic index, GRAVY, and presence of functional motifs, are determined, and a phylogenetic tree has been constructed to elucidate relationships with other groups of organisms. Conclusions This study provides novel insights into distribution of chitinase among four groups and their characterization. The results represent valuable information toward bacterial chitinase in terms of the catalytic properties and structural features, can be exploited to produce a range of chitin-derived products.

Various microorganisms thrive under extreme environments, like hot springs, hydrothermal vents, deep marine ecosystems, hyperacid lakes, acid mine drainage, high UV exposure, and more. To survive against the deleterious effect of these extreme circumstances, they form a network of biofilm where exopolysaccharides (EPSs) comprise a substantial part. The EPSs are often polyanionic due to different functional groups in their structural backbone, including uronic acids, sulfated units, and phosphate groups. Altogether, these chemical groups provide EPSs with a negative charge allowing them to (a) act as ligands toward dissolved cations as well as trace, and toxic metals; (b) be tolerant to the presence of salts, surfactants, and alpha-hydroxyl acids; and (c) interface the solubilization of hydrocarbons. Owing to their unique structural and functional characteristics, EPSs are anticipated to be utilized industrially to remediation of metals, crude oil, and hydrocarbons from contaminated wastewaters, mines, and oil spills. The biotechnological advantages of extremophilic EPSs are more diverse than traditional biopolymers. The present review aims at discussing the mechanisms and strategies for using EPSs from extremophiles in industries and environment bioremediation. Additionally, the potential of EPSs as fascinating biomaterials to mediate biogenic nanoparticles synthesis and treat multicomponent water contaminants is discussed.

Background: Textile industry not only plays a vital role in our daily life but also a prominent factor in improving global economy. One of the environmental concern is it releases huge quantities of toxic dyes in the water leading to severe environmental pollution. Bacterial laccase and azoreductase successfully oxidize complex chemical structure of nitrogen group-containing azo dyes. Additionally, the presence of textile dye infuriates bacterial peroxidase to act as a dye degrading enzyme. Our present study deals with three textile dye degrading enzymes laccase, azoreductase, and peroxidase through analyzing their structural and functional properties using standard computational tools. Result: According to the comparative analysis of physicochemical characteristics, it was clear that laccase was mostly made up of basic amino acids whereas azoreductase and peroxidase both comprised of acidic amino acids. Higher aliphatic index ascertained the thermostability of all these three enzymes. Negative GRAVY value of the enzymes confirmed better water interaction of the enzymes. Instability index depicted that compared to laccase and preoxidase, azoreductase was more stable in nature. It was also observed that the three model proteins had more than 90% of total amino acids in the favored region of Ramachandran plot. Functional analysis revealed laccase as multicopper oxidase type enzyme and azoreductase as FMN dependent enzyme, while peroxidase consisted of α-β barrel with additional haem group. Conclusion: Present study aims to provide knowledge on industrial dye degrading enzymes, choosing the suitable enzyme for industrial set up and to help in understanding the experimental laboratory requirements as well.How to cite: Sarkar S, Banerjee A, Chakraborty N, et al. Structural-functional analyses of textile dye degrading azoreductase, laccase and peroxidase: a comparative in silico study. Electron J Biotechnol 2020;43. https://doi.org/10.1016/j.ejbt.2019.12.004 Keywords: Acidic amino acids, Azo dyes, Azoreductase, Basic amino acids, Dye degradation, Laccase, Peroxidase, Textile industry, Thermostable three enzymes

Marine microalgae has been attracting the researcher’s attention for centuries. Development on microalgal research is majorly favoured by its medicinal, pharmaceutical or cosmeceutical properties. The advancement in the investigation related to microalgal products have been concentrated in the coastal zones because of the greater supply of raw material. The Southern Ocean, highly productive and relatively poorly studied ecosystem, constitutes approximately 10% of the global volume of the oceans. In this study, marine microalgae Chlorella sp. PR-1 was isolated from the Southern Ocean (Indian Sector) for the identification of bioactive antibacterial compounds. The antimicrobial activity of this microalgal extracts was evaluated against three gram positive (Staphylococcus aureus, Bacillus licheniformis, and Bacillus subtilis) and three gram negative bacteria (Pseudomonas aeruginosa, Salmonella typhimurium, and Escherichia coli). The extract showing antibacterial activity was further purified by thin layer and column chromatography. The antimicrobial activity was again evaluated and confirmed with the purified fraction against the same bacteria. The identification of the functional groups in the purified fraction was performed by infrared spectroscopic analysis. Based on gas chromatographic and mass spectroscopic analysis, the principle bioactive compound was proved to be 2,4-bis (1,1-dimethylethyl)- phenol. Thus, the bioactive compound isolated from marine microalga of Southern Ocean origin may be a novel alternative source of antibacterials in the future.

Extremophilic microorganisms often produce novel bioactive compounds to survive under harsh environmental conditions. Exopolysaccharides (EPSs), a constitutive part of bacterial biofilm, are functional biopolymers that act as a protecting sheath to the extremophilic bacteria and are of high industrial value. In this study, we elucidate a new EPS produced by thermophilic Bacillus haynesii CamB6 from a slightly acidic (pH 5.82) Campanario hot spring (56.4 °C) located in the Central Andean Mountains of Chile. Physicochemical properties of the EPS were characterized by different techniques: Scanning electron microscopy- energy dispersive X-ray spectroscopy (SEM-EDS), Atomic Force Microscopy (AFM), High-Performance Liquid Chromatography (HPLC), Gel permeation chromatography (GPC), Fourier Transform Infrared Spectroscopy (FTIR), 1D and 2D Nuclear Magnetic Resonance (NMR), and Thermogravimetric analysis (TGA). The EPS demonstrated amorphous surface roughness composed of evenly distributed macromolecular lumps. GPC and HPLC analysis showed that the EPS is a low molecular weight heteropolymer composed of mannose (66%), glucose (20%), and galactose (14%). FTIR analysis demonstrated the polysaccharide nature (–OH groups, Acetyl groups, and pyranosic ring structure) and the presence of different glycosidic linkages among sugar residues, which was further confirmed by NMR spectroscopic analyses. Moreover, D-mannose α-(1→2) and α-(1→4) linkages prevail in the CamB6 EPS structure. TGA revealed the high thermal stability (240 °C) of the polysaccharide. The functional properties of the EPS were evaluated for food industry applications, specifically as an antioxidant and for its emulsification, water-holding (WHC), oil-holding (OHC), and flocculation capacities. The results suggest that the study EPS can be a useful additive for the food-processing industry.

Xylans are the second most abundant form of hemicelluloses and are the second most abundant polysaccharide in nature after cellulose. To degrade xylan, microbes produce mainly xylanase enzyme. Wide range of microorganisms like fungi, bacteria, yeast, marine algae etc. are capable of producing xylanase. Main source of xylanase is fungi but industrial production of bacterial xylanase is low cost, easy downstream process and high production rate. To understand primary, secondary and tertiary structure of xylanase, in silico composition of amino acids, basic physiological characteristics; viz., pI, molecular weight, instability index, GRAVY, molar extinction coefficient, secondary structure, presence of functional domain and motifs, phylogenetic tree, salt bridge compositions are determined. In silico study of xylanase focused on 36 different bacterial sources are performed by retrieving FASTA and PDB sequences using RCSB PDB. FASTA and PDB files are proceed further in ExPASy-ProtParam, RAMPAGE, QMEAN, MEME, PSIPRED, InterProScan, MOTIF scan, ERRAT, Peptide cutter, ESBRI and MEGA 7. The instability index range (16.90–38.78) clearly indicates that the protein is highly stable. α-helix mean value (27.11%) infers the protein is dominated by α-helix region. The aliphatic index (39.80–90.68) gives information that the protein is highly thermostable, prevalence by alanine amino acid in aliphatic side chain. No transmembrane domain was found in the protein which confirms the enzyme is extracellular in nature. Ancestor chart analysis confirmed that it is a part of carbohydrate metabolic process and more specifically a member of glycoside hydrolase super family. Keywords: Bacterial xylanase, Phylogenetic relationships, Physical parameters, Structural and functional analysis

Deep marine microorganisms survive under extreme ecological settings and harsh environmental conditions of low temperature, high salinity, and high atmospheric pressure making it significant of scientific interest. Southern Ocean (SO) is one such example of deep marine ecosystem and the microorganisms inhabiting in such hostile environment may produce different bioactive secondary metabolites. SO (Indian Sector) is relatively less documented in terms of microbial composition and community dynamics. The present study involves isolation of exopolysaccharides (EPSs) from three potent SO (Indian Sector) bacteria, optimization of the EPS production and partial characterization of them. Three different EPSs show varying structural conformation, that is from porous to strong flakes mimicking polymeric structure with C/N ratio ranging between 4 - 11. FTIR spectra have exhibited the presence of different active groups of carbohydrate moieties, water molecules and protein-associated amides. EPSs produced by marine microorganisms show high biotechnological promises such as drug carrier in pharmaceutical field, emulsifier and cryo- protectant in food-processing industry, detoxification of petrochemical oils and much more. The three bacterial isolates in this study showed potential of producing EPS biopolymer that can be further explored in terms of its proper biotechnological applications.

Introduction: DNA barcode, a molecular marker, is used to distinguish among the closely related species, and it can be applied across a broad range of taxa to understand ecology and evolution. MaturaseK gene ( matK ) and rubisco bisphosphate carboxylase/oxygenase form I gene ( rbcL ) of the chloroplast are highly conserved in a plant system, which are used as core barcode. This present endeavor entails the comprehensive examination of the under threat plant species based on success of discrimination on DNA barcode under selection pressure. Result: The family Dipterocarpaceae comprising of 15 genera is under threat due to some factors, namely, deforestation, habitat alteration, poor seed, pollen dispersal, etc. Species of this family was grouped into 6 clusters for matK and 5 clusters and 2 sub-clusters for rbcL in the phylogenetic tree by using neighbor-joining method. Cluster I to cluster VI of matK and cluster I to cluster V of rbcL genes were analyzed by various codon and substitution bias tools. Mutational pressure guided the codon bias which was favored by the avoidance of higher GC content and significant negative correlation between GC12 and GC3 (in sub-cluster I of cluster I [0.03 0.85) also showed the same result, which possibly could be due to the negative impact of very high and low transition rate than transversion. Conclusion: Through the analysis of inter-generic, inter/intra-specific variation and phylogenetic data, it was found that both selection and mutation played an important role in synonymous codon choice in these genes, but they acted inconsistently on the genes, both matK and rbcL . In vitro stable proteins of both matK and rbcL were selected through natural selection rather than mutational selection. matK gene had higher individual discrimination and barcode success compared with rbcL . These discriminatory approaches may describe the problem related to the extinction of plant species. Hence, it becomes very imperative to identify and detect the under threat plant species in advance.

Commiphora wightii is an endangered, endemic species found in the Thar Desert of Rajasthan, India and adjoining areas of Pakistan. The populations of this plant are rapidly dwindling due to overexploitation for their medicinally important resin. Analysis of nucleotide sequences of the internal transcribed spacer of rDNAs revealed low genetic diversity (π = 0.03905; θw = 0.05418) and high population structure (ϕST = 0.206). Parsimony based assessment and Bayesian analyses were conducted on the dataset. Mantel’s test showed a statistically significant positive correlation between genetic and geographic distance (r2 = 0.3647; p = 0.023). Anthropogenic overexploitation of C. wightii for its natural resources has resulted in population fragmentation. Initiatives should be taken immediately to preserve the diversity of this important plant species.

The present study involves discovery, validation and use of single-nucleotide polymorphisms (SNPs) in bread wheat utilizing 48 EST-contigs (individual contigs having 20-89 ESTs, derived from 2 to 11 different genotypes). In order to avoid a problem due to homoeologous relationships, the ESTs in each contig were classified into 175 sub-contigs (3.7 sub-contigs/EST-contig) using characteristic homoeologue sequence variants (HSVs), which had a density of 1 HSV every 136.7 bp. In silico analysis of sub-contigs led to the discovery of 230 candidate EST-SNPs with a density of 1SNP/273.9 bp. Locus specific primers (each primer pair flanking 1-18 SNPs) were designed utilizing one sub-contig each from 42 EST-contigs that contained SNPs, the remaining 6 contigs having no SNPs. To provide locus specificity to the PCR products, each primer was tagged with an HSV at its 3' end. Only 10 primer pairs, which gave each a characteristic solitary band, were utilized to validate EST-SNPs over 30 diverse bread wheat genotypes; 7 SNPs were validated through resequencing the PCR products. Allele specific primers were designed and utilized for genotyping of 50 diverse bread wheat accessions (including 30 bread wheat genotypes previously used for validation of SNPs), with an aim to test their utility in genotyping and map construction. The allele specific primers allowed the classification of 50 genotypes in two alternative allele groups for each SNP as expected, thus suggesting their utility for genotyping. Of the above 7 validated SNPs, 4 belonged to a solitary locus (PKS37); 7 haplotypes were available at this locus. Altogether, the results suggested that EST-SNPs constitute an important source of molecular markers for studies on wheat genomics.