Biology subjects

Debnath, M.

Publications and source records attributed to Debnath, M..

7 recordsLinked to original sources

bioRxiv2022

Molecular evolution and characterization of domestic duck (Anas platyrynchos) and Goose (Anser indicus) with reference to its wild relatives through whole mitochondrial genome sequencing

It is important to study the evolution and domestication of the domesticated duck (Anas platyrynchos) population from the wide range of wild relatives of Anas spp. Whole mitochondrial genome sequencing was attempted for Anas platyrynchos (Bengal duck) and Anser indicus (goose) from same geographical region. The study deals with the Molecular evolution of domestic duck based on mitochondrial gene due to its sequence variability, and to find out the phylogenetic relationships among Anas platyrynchos and its wild relatives. In this study we have used 45 wild species of Anas spp to study the mitochondrial genes and phylogenomics. Our result signifies that duck species were effectively discriminated with respect to mitochondrial genes, which could then be used for an appropriate genetic conservation program for the wild duck and domestic duck breeds. The DNA sequences from any unknown sample of the mitochondrial gene may be determined and can compare with those on a DNA database and can do blast for phylogenetic analysis of unknown wild duck, which gives its future scope. In silico analysis for 3D structure for Anas platyrynchos with the closest relative as Anas poecilorhyncha (Indian spot-billed duck) was attempted. Anas platyrynchos was also compared with Anser indicus. Therefore, this experiment was conducted to investigate the genetic diversity of West Bengal wild ducks with reference to its wild relatives based on mitochondrial gene.

genomics↗

bioRxiv2022

Whole mitochondrial genome sequencing- a novel approach for studying Phylogenomics for Anas platyrynchos

The evolution of duck and its distribution across the globe has been an interesting aspect. Domestication of duck and its evolution was also important to analyze if domesticated duck has migrated to other region of the globe or separate domestication process has occurred in particular region of the world. Mitochondrial genes as D-loop or cytochrome B had been used for studying evolution or molecular phylogeny. In current study, we aim to study phylogenomics for Anas platyrynchos across the globe. Whole mitochondrial genome sequencing for Bengal duck (indigenous duck from West Bengal, India) was performed on illumina platform and gene sequences were analyzed for all 37 mitochondrial genes. Variabilities were observed at nucleotide sequence, but absent in amino acid sequence and corresponding 3D structure of polypeptides coded by mitochondrial genes. We observed Anas platyrynchos from Eurasia (europe and Asia) were clustered together indicating common origin. Extensive variabilities were observed among the chinese duck population. The duck population from US was outgrouped. These ducks might have migrated from China and later bred with wild ducks to evolve as new breed or strain in US.

genomics↗

bioRxiv2022

Genomics for reproduction in Anas platyrynchos-a novel report

Anas platyrynchos (ducks) are reared mostly for egg, which are very nutritious, that fetch better prices, however duck meat possess rich nutrient content. They possess the unique characteristics of disease resistance to the common avian diseases, even asymptomatic to avian influenza, with a scopeto evolve as one of the best poultry species The major limitation encountered is the lowered average egg production as well as higher age at first egg (an indicator for sexual maturity) for the indigenous ducks compared to that of exotic ones. In this current study, we attempt to explore the genes responsible for duck reproduction in terms of sexual maturity,egg production and fertility of the ducks. We had compared the genomic constitution for the Bengal duck with highest egg production with that of non-layer (infertile or sexually immature) ducks. We characterized the genes in indigenous ducks from ovarian tissues, identified important domains for characterized genes for the first time, and studied differential mRNA expression profiling for these genes with respect to layer and non-layer groups. Upregulation was observed for ESR2, DIAPH2, KMT2E, ASCF2 genes for Bengal duck in highest egg producing duck in comparison to non-layer duck, whereas downregulation was observed for KSR1, A2M, BMPR1B, ACVR1. In the next step, we explored the association with the genes which were actually responsible for egg production. Thus, duck may be utilized as a model for studying the molecular aspect of reproduction. Genes upregulated may be utilized for knock in of gene, whereas down regulated genes may be knocked out or knocked down through gene editing technologies for the improvement of reproductive performance of the duck in future. Molecular biomarkers may be developed with these genes for early selection of better reproducing ducks at day of hatch or even earlier.

genomics↗

bioRxiv2022

Role of mucin gene for growth in Anas platyrynchos - a novel report

Mucin gene is expressed at the mucous membrane of the inner layer of the internal organs. Intestinal mucin 2 (MUC2), a major gel-forming mucin, represents a primary barrier component of mucus layers. This is the first report of role of mucin gene in growth traits in animals. In the current study, we had randomly studied Bengal ducks (Anas platyrynchos) reared from day old to 10 weeks of age under organized farm and studied the growth parameters as well as body weight and average daily body weight gain. We had characterized mucin gene for Bengal duck and observed glycosylation and EGF1 (EGF like domain signature) as important domain for growth traits in duck. We observed better expression profile for mucin gene in high growing ducks in comparison to that of lower growing ducks with real time PCR. Hence mucin gene may be employed as a marker for growth traits.

genomics↗

bioRxiv2022

Role of RIGI, MDA5 and interferon alpha of duck in Duck Plague infection, a novel report

Duck Plague (DP) or Duck viral enteritis is an acute contagious and highly fatal disease in water fowl commonly caused by Anatidalphavirus-1 belonging from Herpesviridae family and contains double stranded DNA as genetic material. Pathogen associated molecular pattern (PAMP)s when identified by Pathogen Recognition Receptor (PRR)s acts as effective immunity system action against the pathogen. Melanoma Differentiation-Associated protein 5 (MDA5) and Retionic Acid Inducible Gene I (RIG1) are protein sensor commonly sense for viral double stranded RNA and helps for pro-inflammatory cytokine expression. Gut Associated Lymphoid Tissue (GALT)s have important role in immune response. The current study depicts the important role of three important immune response genes as RIGI, MDA5 and INFalpha in duck plague infestation for the first time. In silico studies followed by differential mRNA expression of RIG1, MDA5 and INFalpha was employed to detect effectiveness of gut associated immune responsiveness in liver, where kupfer cells are the major immune response cells. This was further confirmed through histological section of liver, kupfer cell and immunohistochemistry. This will be helpful to identify molecular mechanism of host innate immunity through duck plague virus infection in indigenous duck. This information may be helful for production of duck with the inherent resistance against duck plague virus infection through suitable biotechnological approaches as gene editing.Due to this inherent nature of better immunity in terms of resistance to other common avian diseases, duck will evolve as one of the major sustainable poultry species.The current study explores the scope to study host immunity against herpes virus in animal model.

genomics↗

bioRxiv2020

Antimicrobial Resistance Profile and mcr-1 gene Detection in Salmonella Isolates from Poultry in Bangladesh: Molecular and Bioinformatics Characterization

Antimicrobial resistance gene mcr-1 has been disseminated globally since its first discovery in Southern China in late 2015. However, the mcr-1 gene had not been identified previously in Salmonella isolates from poultry in Bangladesh. Here, we aimed to explore antimicrobial resistance gene mcr-1 in Salmonella isolates. Eighty two Salmonella isolates were isolated and characterized from suspected poultry specimens received from different zones of the country. A phenotypic disc diffusion assay with 15 antimicrobial agents was performed following CLSI standard. The disk diffusion assay showed that, all of the isolates presented high resistance to colistin (92.68%), oxytetracycline (86.59%), co-trimoxazole (76.83%), ciprofloxacin (73.17%) and enrofloxacin (65.85%). Further, randomly selected 10 Salmonella isolates were analyzed by polymerase chain reaction (PCR) targeting genus-specific invA and antimicrobial (colistin) resistance mcr-1 genes. Five were confirmed for the presence of the mcr-1 gene belonging to Salmonella spp. Further, sequencing followed by phylogenetic analysis revealed divergent evolutionary relation between the LptA and MCR proteins rendering them resistant to colistin. Three-dimensional homology structures of MCR-1 proteins were constructed and verified using different bioinformatics tools. Moreover, molecular docking interactions suggested that, MCR-1 and LptA share a similar substrate binding cavity which could be validated for the functional analysis. The results represent here is the first molecular and in silico analysis of colistin resistance mcr-1 gene of Salmonella in poultry in Bangladesh, which may emphasize the importance of the study on antibiotic resistance genes requiring for national monitoring and strategic surveillance in the country.

microbiology↗

bioRxiv2018

The Complete Chloroplast Genome of Dendrobium nobile, an endangered medicinal orchid from Northeast India and its comparison with related chloroplast genomes of Dendrobium species.

The medicinal orchid genus Dendrobium belonging to the Orchidaceae family is the largest genus comprising about 800-1500 species. To better illustrate the species status in the genus Dendrobium, a comparative analysis of 33 newly sequenced chloroplast genomes retrieved from NCBI Refseq database was compared with that of the first complete chloroplast genome of D. nobile from north-east India based on next-generation sequencing methods (Illumina HiSeq 2500-PE150). Our results provide comparative chloroplast genomic information for taxonomical identification, alignment-free phylogenomic inference and other statistical features of Dendrobium plastomes, which can also provide valuable information on their mutational events and sequence divergence.

evolutionary biology↗