Biology subjects

Sharma, V. K.

Publications and source records attributed to Sharma, V. K..

At least 19 recordsLinked to original sources

bioRxiv2026

A telomere-to-telomere genome of Manilkara zapota (Chiku) reveals the repeat-mediated genome evolution

Manilkara zapota (Chiku) is a tropical fruit tree in the Sapotaceae family. In this study, we assembled the first Telomere-to-telomere (T2T) genome assembly of M. zapota, spanning 1.6 Gb with high contiguity (N50 = 134 Mb). Comparative analysis revealed a very recent divergence and a shared WGD among Sapotaceae members. A newly constructed Ancestral Sapotaceae Karyotype (ASK) suggests a fusion-dominated chromosome structure in the family. The genome exhibits lineage-specific proliferation of transposable elements (TEs) accompanied by a recent burst of LTR-Gypsy elements (~0.09 mya). Genome-wide methylation profiling revealed elevated CpG and CHG methylation levels and age-dependent reinforcement of TE silencing, suggesting strong epigenetic regulation that stabilises the repeat-rich genome while maintaining gene expression. Collectively, these findings advance our understanding of repeat-rich genome evolution in plants and provide a valuable framework for genomic-assisted breeding in M. zapota.

genomics↗

bioRxiv2026

Next generation protein-corrole bio-assemblies provide effective tumoricidal treatment in a metastatic triple-negative breast cancer model

Assemblies that combine chemotherapeutics with tumor-targeting proteins are promising agents for treating resistant cancers but require full biochemical characterization before therapeutic deployment. We developed and optimized a HER3-targeting capsomere, HPK2.0, which forms stable nanoscale assemblies with cytotoxic corroles via electrostatic neutralization and shape complementarity. These nanocomplexes exhibit durable serum stability, HER3-dependent tumor invasion, and efficient endosomal escape, resulting in potent and selective cytotoxicity in triple-negative breast cancer (TNBC) cells. In an orthotopic metastatic TNBC model, systemic treatment with HPK2.0-corrole assemblies achieved 67-83% tumor regression, near-complete suppression of spontaneous lung metastasis, and a [~]2-fold improvement in survival relative to mock treatment, with minimal off-target toxicity. By integrating tumor specificity with therapeutic potency, this next-generation protein-corrole platform establishes a clinically scalable strategy for treating metastatic HER3-positive TNBC. SignificanceTriple-negative breast cancer (TNBC) is an aggressive disease with high rates of metastasis and mortality, largely because it lacks molecular targets for precision therapy. As a result, patients rely primarily on chemotherapy, which causes systemic toxicity and frequently fails to control metastatic spread. Here, we introduce a targeted therapeutic strategy in which a bioengineered protein selectively recognizes a receptor highly expressed in metastatic TNBC and delivers a potent cytotoxic payload directly into tumor cells. In mouse models, this approach produced robust tumor regression, markedly reduced lung metastases, extended survival, and showed minimal off-target toxicity. These findings establish a versatile platform for targeted treatment of TNBC and highlight a strategy that may be broadly applicable to other HER3-expressing cancers.

cancer biology↗

bioRxiv2025

Mapping Fusarium Wilt and Sterility Mosaic Disease Resistance-Associated Genomic Regions and Haplotype Variants in Pigeonpea

The occurrence of fusarium wilt and sterility mosaic disease in genial conditions causes significant yield losses in pigeonpea. The present genome-wide association study (GWAS) was employed on 176-genotype panel to identify candidate genomic regions associated with FW and SMD resistance in pigeonpea. A total of 869,447 filtered SNP markers were used for GWAS analysis. GWAS analysis identified significant genomic regions for FW on chromosomes 05, 10, and 11 and for SMD on chromosome 09. Four resistant sources, namely, ICP20096, ICP20097, ICPL87119 and ICP13304 were identified as a resistance source for both FW and SMD. Total 12 markers from chromosome 11 for FW and 4 markers from chromosome 09 for SMD were validated using the KASP genotyping approach. We have identified resistant haplotypes for FW on chromosome 10 and 11 and for SMD on chromosome 09. Moreover, we have identified four InDels for FW on chromosome 5 in Two component response regulator gene (Cc_11098) and four InDels for SMD on chromosome 9 in genes, namely, LRR and NB-ARC domain disease resistance protein (Cc_21069), Flavonoid 3, 5-hydroxylase (Cc_21070) respectively. For FW, Cc_10507586 region from chromosome 5 is identified in ICPL87119 and ICPL20096 donors. A region Cc_21637656 from chromosome 11 is identified in the ICPL87119 but not in the ICPL20096. Similarly, a region Cc_4438493 from chromosome 10 is identified in the ICPL20096 but not in the ICPL87119. For SMD, Cc_24131177 region is identified in both the SMD resistance donors (ICPL20096 and ICPL87119). Ccsmd04 region from chromosome 4 has been identified in ICPL87119 but not in the ICPL20096. These genomic regions can be brought together into single elite genetic background with the help of the markers identified in this study. The validated markers and donor lines in this study offer valuable tools and resources for the genetic improvement of pigeonpea cultivars with enhanced FW and SMD resistance.

genomics↗

bioRxiv2025

InDels in an intronic region of gene Ccsmd04 coding for dormancy/auxin-associated protein controls sterility mosaic disease resistance in pigeonpea

Sterility mosaic disease presents a significant challenge to pigeonpea cultivation in the Indian subcontinent, potentially leading to total crop failure. The development of diagnostic molecular markers for SMD resistance can aid in improving SMD-resistant varieties. In this context, a QTL-seq approach identified genomic regions associated with SMD resistance using a recombinant inbred line generated from ICP8863 x ICPL87119. In total, 6,105 high-confidence variants were identified in the genomic region, namely, smdCc04 based on the delta SNP index. A genomic region smdCc04 on chromosome Cc04 spans 3.2 Mb (9.3 - 12.5 Mb) comprised of 6 missense variants and eight indels. A total of 211 candidate genes were identified from this region. 1 bp insertion, 21 bp insertion, 9 bp deletion, and 3 bp insertion at different intronic positions in 22 susceptible line leads to downregulation of Dormancy/auxin associated protein (Ccsmd04) resulting in loss of signaling in disease resistance pathways. The identified sites recognize four important disease and plant growth related transcription factors. A total of 4 Indels and 8 SNPs were validated from smdCc04 genomic regions using whole genome re-sequencing data and KASP genotyping on resistant and susceptible pigeonpea lines respectively. These markers will be used in pigeonpea breeding programs.

genomics↗

bioRxiv2025

Chromosome-level genome assembly of Tamarindus indica

Tamarindus indica is the sole member of the genus Tamarindus of the Leguminosae family. It is a multipurpose horticultural plant, with every part of the plant finding importance in food, medicine, and other industries. To gain an understanding of genome structure and evolution, we reported the first high-quality genome assembly of T. indica anchored to 12 chromosomes with N50 of [~]56 Mb. Supported by comprehensive transcriptome data, we reported >48,000 protein-coding genes. Through phylogenetic and evolutionary analysis, we uncovered an independent whole-genome duplication event in T. indica and highlighted the expression divergence of segmentally duplicated genes and their role in the better adaptivity of the plant. Our study thus provides first insights into its genomic organization, evolutionary history, and WGD event and thus becomes an important resource for future genetic and biotechnological studies to understand essential pathways and assist breeding programs for trait enhancements.

genomics↗

bioRxiv2025

Natural product-mediated reaction hijacking mechanism validates Plasmodium aspartyl-tRNA synthetase as an antimalarial drug target

Malaria poses an enormous threat to human health. With ever-increasing resistance to currently deployed antimalarials, new targets and starting point compounds with novel mechanisms of action need to be identified. Here, we explore the antimalarial activity of the Streptomyces sp natural product, 5'-O-sulfamoyl-2-chloroadenosine (dealanylascamycin, DACM) and compare it with the synthetic adenosine monophosphate (AMP) mimic, 5-O-sulfamoyladenosine (AMS). These nucleoside sulfamates exhibit potent inhibition of P. falciparum growth with an efficacy comparable to that of the current front-line antimalarial dihydroartemisinin. Exposure of P. falciparum to DACM leads to inhibition of protein translation, driven by eIF2 phosphorylation. We show that DACM targets multiple amino acyl tRNA synthetase (aaRS) targets, including the cytoplasmic aspartyl tRNA synthetase (AspRS). The mechanism involves hijacking of the reaction product, leading to the formation of a tightly bound inhibitory amino acid-sulfamate conjugate. We show that recombinant P. falciparum and P. vivax AspRS are susceptible to hijacking by DACM and AMS, generating Asp-DACM and Asp-AMS adducts that stabilize these proteins. By contrast, human AspRS appears less susceptible to hijacking. X-ray crystallography reveals that apo P. vivax AspRS exhibits a stabilized flipping loop over the active site that is poised to bind substrates. By contrast, human AspRS exhibits disorder in an extended region around the flexible flipping loop as well as in a loop in motif II. These structural differences may underpin the decreased susceptibility of human AspRS to reaction-hijacking by DACM and AMS. Our work reveals Plasmodium AspRS as a promising antimalarial target and highlights structural features that underpin differences in the susceptibility of aaRSs to reaction hijacking inhibition.

biochemistry↗

bioRxiv2024

Exploring the microbiome of black soil from Central India and the impacts of agricultural practices on soil microbial communities

BackgroundHealthy microbial communities in soil are indispensable for agricultural productivity. The diversity in physiochemical properties, their geological origins, and local climatic conditions lead to the evolution of diverse soil types with distinct bacterial communities. Despite a global distribution, the microbial composition of black soil remains largely unexplored. Here, we investigate the composition, diversity, and functional potential of bacterial communities in black soils from central India. We also examine how common agricultural disturbances like fertilizer application and the growth of crops impact soil communities in a three-year longitudinal field experiment involving three crops. ResultsThe black soil core microbiome was dominated by phyla Actinobacteriota and Proteobacteria members. Analysis of bacterial composition in vermicompost revealed the presence of plant growth-promoting taxa. Among the assessed cropping practices, crop growth significantly affected microbiome composition in soil. We also observed the impact of crops in selectively enhancing the microbiome in the soil, highlighting the role of plant species in shaping community structure. During this experiment, fertilizer treatment did not influence the microbiome significantly. Overall, the data showed the vulnerability and resilience of soil bacterial communities to agricultural disturbances. ConclusionThe microbial composition of black soil in central India was revealed, and the effects of agricultural management on black soil microbial composition were evaluated. The prominent impact of individual plants showed the role of plant-root microbiome interactions in shaping the composition of soil communities. Fertilizer application did not show significant effects during the field experiment, reflecting the resilience of soil communities to short-term disturbances. We also shed light on the functional metagenomic potential of black soil communities and the effect of common agricultural disturbances in a prominent soil type.

microbiology↗

bioRxiv2024

A High-quality Genome Assembly of Annona squamosa (Custard Apple) Provides Functional Insights into an Emerging Fruit Crop

Annona squamosa, also known as custard apple, is an emerging fruit crop with medicinal significance. We constructed a high-quality genome of A. squamosa along with transcriptome data to gain insights into its phylogeny, evolution and demographic history. The genome has an N50 value of 93.2 Mb assembled into seven pseudochromosomes. The demographic history showed a continuous decline in the effective population size of A. squamosa. Phylogenetic analysis revealed that magnoliids were sister to eudicots, whereas ASTRAL gene trees showed discordance due to incomplete lineage sorting (ILS). Genome syntenic and Ks distribution analyses confirmed the absence of a recent whole genome duplication event in the A. squamosa. Gene families related to photosynthesis, oxidative phosphorylation and plant thermogenesis were found to be highly expanded in the genome. Comparative analysis with other magnoliids revealed the adaptative evolution in the genes of flavonoid biosynthesis pathway, amino sugar, nucleotide sugar and sucrose metabolism, conferring medicinal value and enhanced hexose sugar accumulation. In addition, we performed genome-wide identification of SWEET genes. Our high-quality genome and evolutionary insights of this emerging fruit crop, thus, serve as a valuable resource for advancing studies in functional genomics, evolutionary biology, and crop improvement.

genomics↗

bioRxiv2024

Spectrally Resolved Single Molecule Orientation Imaging Reveals Direct Correspondence between Polarity and Order Experienced by Nile Red in Supported Lipid Bilayer Membrane

Molecular level interaction among lipids, cholesterol and water dictates nanoscale membrane organization of lipid bilayers into liquid ordered (Lo) and liquid disordered (Ld) phases, characterized by different polarity and order. Generally, solvatochromic dyes easily discriminate polarity difference between Lo and Ld phases, whereas molecular flippers and rotors show distinct photophysics depending on membrane order. In spite of progress in single molecule spectral imaging and single molecule orientation mapping, still direct experimental proof linking polarity with order sensed by the same probe eludes us. Here, we demonstrate spectrally resolved single molecule orientation localization microscopy to connect nanoscopic localization of probe on bilayer membrane with its emission spectra, three-dimensional dipole orientation and rotational constraint offered by the local microenvironment and highlights the beautiful correspondence between polarity and order. This technique has the potential to addres nanoscale heterogeneity and dynamics, especially in biology as well as material sciences. TOC GRAPHICS O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=164 SRC="FIGDIR/small/600028v1_ufig1.gif" ALT="Figure 1"> View larger version (75K): org.highwire.dtl.DTLVardef@d3aa13org.highwire.dtl.DTLVardef@42e184org.highwire.dtl.DTLVardef@e3a244org.highwire.dtl.DTLVardef@b25a50_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2023

Genome sequencing of Syzygium cumini (Jamun) reveals adaptive evolution in secondary metabolism pathways associated with its medicinal properties

Syzygium cumini, also known as jambolan or jamun, is an evergreen tree widely known for its medicinal properties, fruits, and ornamental value. To understand the genomic and evolutionary basis of its medicinal properties, we sequenced S. cumini genome, which is the largest genome sequenced for the first time from the worlds largest tree genus Syzygium using Oxford Nanopore and 10x Genomics sequencing technologies. The tetraploid and highly heterozygous draft genome of S. cumini had a total size of 709.9 Mbp with 61,195 coding genes. The phylogenetic position of S. cumini was established using a comprehensive genome-wide analysis including species from 18 Eudicot plant orders. The existence of neopolyploidy in S. cumini was evident from the higher number of coding genes and expanded gene families compared to the other two sequenced species from this genus. Comparative evolutionary analyses showed the adaptive evolution of genes involved in the phenylpropanoid-flavonoid (PF) biosynthesis pathway and other secondary metabolites biosynthesis such as terpenoid and alkaloid in S. cumini, along with genes involved in stress tolerance mechanisms, which was also supported by leaf transcriptome data generated in this study. The adaptive evolution of secondary metabolism pathways is associated with the wide range of pharmacological properties, specifically the anti-diabetic property, of this species conferred by the bioactive compounds that act as nutraceutical agents in modern medicine.

genomics↗

bioRxiv2023

Genome of Phyllanthus emblica: the medicinal plant Amla with super antioxidant properties

Phyllanthus emblica or Indian gooseberry, commonly known as amla, is an important medicinal horticultural plant used in traditional and modern medicines. It bears stone fruits with immense antioxidant properties due to being one of the richest natural sources of vitamin C and numerous flavonoids. This study presents the first genome sequencing of this species performed using 10x Genomics and Oxford Nanopore Technology. The draft genome assembly was 519 Mbp in size and consisted of 4,384 contigs, N50 of 597 Kbp, 98.4% BUSCO score and 37,858 coding sequences. This study also reports the genome-wide phylogeny of this species with 26 other plant species that resolved the phylogenetic position of P. emblica. The presence of three ascorbate biosynthesis pathways including L-galactose, galacturonate and myo-inositol pathways was confirmed in this genome. A comprehensive comparative evolutionary genomic analysis including gene family expansion/contraction and identification of multiple signatures of adaptive evolution provided evolutionary insights into ascorbate and flavonoid biosynthesis pathways and stone fruit formation through lignin biosynthesis. The availability of this genome will be beneficial for its horticultural, medicinal, dietary, and cosmetic applications and will also help in comparative genomics analysis studies.

genomics↗

bioRxiv2023

Comparative Analysis of TG/CA Repeats in Sixteen Primate Genomes Reveals the Dynamics and Role of TG/CA Repeats in the Human Genome

Among the different microsatellite sequences found in the human genome, the dinucleotide TG/CA repeats are one of the most abundant, exhibiting multifaceted functional roles. Availability of several primate genomes offers relevant datasets for studying the evolution and function of these repeats in non-human primates and human genome. Using pairwise genomic alignments, genome-wide analysis of these repeats was performed in human and sixteen other primate genomes. The total number of these repeats and expansion of medium (12[≤] n< 23) and long (n[≥]23) (TG/CA)n repeats was significantly higher in human than other primates. Further, other dinucleotide repeats like TA were found in the orthologous genomic regions in other primates. Thus, selection, elongation and a selective process of conversion of other dinucleotide repeats in primates to TG/CA repeats in humans was apparent and presented in this study as a comprehensive model for the dynamics and role of TG/CA repeats in the human genome.

genomics↗

bioRxiv2023

High-quality genome assemblies provide clues on the evolutionary advantage of blue peafowl over green peafowl

An intriguing example of differential adaptability is the case of two Asian peafowl species, Pavo cristatus (blue peafowl) and Pavo muticus (green peafowl), where the former has a "Least Concern" conservation status and the latter is an "Endangered" species. To understand the genetic basis of this differential adaptability of the two peafowl species, a comparative analysis of these species is much needed to gain the genomic and evolutionary insights. Thus, we constructed a high-quality genome assembly of blue peafowl with an N50 value of 84.81 Mb (pseudochromosome-level assembly), and a high-confidence coding gene set to perform the genomic and evolutionary analyses of blue and green peafowls with 49 other avian species. The analyses revealed adaptive evolution of genes related to neuronal development, immunity, and skeletal muscle development in these peafowl species. Major genes related to axon guidance showed adaptive evolution in peafowl species. However, blue peafowl showed the presence of 42% more coding genes compared to the green peafowl along with a higher number of unique gene clusters, segmental duplicated genes and expanded gene families, and comparatively higher evolution in neuronal and developmental pathways. Blue peafowl also showed longer branch length compared to green peafowl in the species phylogenetic tree. These genomic insights obtained from the high-quality genome assembly of P. cristatus constructed in this study provide new clues on the superior adaptability of the blue peafowl over green peafowl despite having a recent species divergence time.

genomics↗

bioRxiv2022

Novel Peptide Inhibitor of Human Tumor Necrosis Factor-α has Antiarthritic Activity

The inhibition of tumor necrosis factor- (TNF) trimer formation renders it inactive for binding to its receptors thus mitigating the vicious cycle of inflammation. We designed a peptide (PIYLGGVFQ) that simulates a sequence strand of human TNF monomer using a series of in silico methods, such as active site finding (Acsite), protein-protein interaction (PPI), docking studies (GOLD and Modeller) followed by molecular dynamics (MD) simulation studies. The MD studies confirmed the intermolecular interaction of the peptide with the TNF. Fluorescence-activated cell sorting (FACS) and fluorescence microscopy revealed that the peptide effectively inhibited the binding of TNF to the cell surface receptors. The cell culture assays showed that the peptide significantly inhibited the TNF-mediated cell death. In addition, the nuclear translocation of the nuclear factor kappa B (NF{kappa}B) was significantly suppressed in the peptide-treated A549 cells as observed in immunofluorescence and gel mobility-shift assays. Furthermore, peptide protected against joint damage in collagen-induced arthritis (CIA) mouse model as revealed in the microfocal-CT scans. In conclusion, this TNF antagonist would be useful for the prevention and repair of inflammatory bone destruction and subsequent loss in the mouse model of CIA as well as human rheumatoid arthritis (RA) patients. This calls upon further clinical investigation to utilize its potential effect as an anti-arthritic drug.

immunology↗

bioRxiv2022

2D-QSAR and Molecular Docking based virtual screening of the herbal molecules against Alzheimers Disorder: An approach to predict CNS activity

Acetylcholinesterase (AChE) is one of the key enzyme targets that have been used clinically for the management of Alzheimers Disorder (AD). Numerous reports in the literature predict and demonstrate in-vitro, and in-silico anticholinergic activity of synthetic and herbal molecules, however, the majority of them failed to reproduce the results in preclinical or clinical settings. To address these issues, we developed a 2D-QSAR model that could not only efficiently predict the AChE inhibitory activity of herbal molecules but also predicted their potential to cross BBB to exert their beneficial effects during AD. Applying this model, virtual screening of the herbal molecules was performed and amentoflavone, asiaticoside, astaxanthin, bahouside, biapigenin, glycyrrhizin, hyperforin, hypericin, and tocopherol were predicted as the most promising herbal molecules for inhibiting AChE. Results were validated through molecular docking studies against human AChE (PDB ID: 4EY7). To determine whether or not these molecules can cross BBB to inhibit AChE within the CNS for being beneficial for the management of AD, we determined a CNS PPO score, which was found in the range of 1 to 3.76. Overall, the best results were observed for amentoflavone and our results demonstrated a PIC50 value of 7.377 nM, molecular docking score of -11.5 kcal/mol, and CNS MPO score of 3.76. In conclusion, we successfully developed a reliable and efficient 2D-QSAR model and predicted amentoflavone to be the most promising molecule that could inhibit human AChE enzyme within the CNS and could prove beneficial for the management of AD.

bioinformatics↗

bioRxiv2022

Use of Transient Transfection for cGMP Manufacturing of eOD-GT8 60mer, a Self-Assembling Nanoparticle Germline-Targeting HIV-1 Vaccine Candidate

We describe the current Good Manufacturing Practice (cGMP) production and subsequent characterization of eOD-GT8 60mer, a glycosylated self-assembling nanoparticle HIV-1 vaccine candidate germline-targeting priming immunogen. Production was carried out by transient expression in the human embryonic kidney 293 (HEK293) cell line followed by a combination of purification techniques. A large scale cGMP (200 L) production run yielded 354 mg of the purified eOD-GT8 60mer drug product material, which was formulated at 1 mg/mL in 10% sucrose in phosphate-buffered saline (PBS) at pH 7.2. The clinical trial material was comprehensively characterized for purity, antigenicity, glycan composition, amino acid sequence, aggregation, and by several safety-related tests during cGMP lot release. A comparison of purified products produced at 1 L scale and 200 L cGMP scale demonstrated consistency and robustness of the transient transfection upstream process and the downstream purification strategies. The cGMP clinical trial material is being tested in a phase 1 clinical trial (NCT03547245) and is currently stored at -80{degrees}C and on a stability testing program as per regulatory guidelines. The methods described here illustrate the utility of transient transfection for cGMP production of complex products such as glycosylated self-assembling nanoparticles.

biochemistry↗

bioRxiv2022

Phenotypic and genomic comparison of human outbreak and cattle-associated Shiga toxin-producing Escherichia coli O157:H7

Escherichia coli O157:H7 (O157)-adulterated food products, including beef and produce, are associated with disease outbreaks in humans. Although cattle feces are a source for the contamination, it is unclear if diverse O157 human-associated outbreak isolates expressing a specific virulence phenotype can colonize and shed in the feces of cattle at a quantitatively similar levels to non-outbreak isolates. It is also unclear if other phenotypes, such as biofilm, cell attachment, and toxin production, differentiate environmental O157 isolates from O157 isolates associated with human illness. Genomic profiling of O157 isolates acquired through routine surveillance can inform if the isolates encode virulence genes associated with human disease, but many genotype-phenotype relationships remain unclear for O157. Therefore, the objective of this study was to compare a diverse set of O157 isolates, with the intent of identifying potential genotypic differences that could inform phenotypes such as cattle colonization and fecal shedding, in vitro cell attachment, biofilm production, and Shiga toxin production. In addition, the relationship between phenotypes and potential for foodborne illness as it relates to genomic virulence traits was explored. No significant differences in cattle colonization and fecal shedding were detected for the tested isolates, despite broad genomic differences. In addition, the in vitro phenotypic differences noted in biofilm and cell attachment did not associate with one LSPA-6 lineage compared to another. Overall, no differences in cattle shedding were observed, yet variations in genotype and phenotype were identified indicating further work is warranted to better understand the relationship between O157 genome and virulence. ImportanceFoodborne illness has a major impact on the health and wellbeing of the global population, besides creating substantial financial hardships for industry. While many bacteria and viruses are implicated in foodborne illness, Escherichia coli serotype O157:H7 (O157) is a common food adulterant that can cause human disease and food recalls. Cattle feces are a significant source of food-adulterating O157. A greater understanding of O157 genetics and its relation to phenotype is needed to develop mitigation strategies to limit spread of O157 into the food chain. The goal of the research was to identify O157 genomic and phenotypic attributes of O157 associated with cattle colonization and fecal shedding along with other factors involved in environmental persistence and illness in humans. It was observed that variations in biofilm formation and in vitro cellular adherence did not associate with enhanced cattle colonization or fecal shedding, indicating that the processes involved in cattle colonization are complex and not well understood.

microbiology↗

bioRxiv2022

Genome sequencing and de novo and reference-based genome assemblies of Bos indicus breeds

Bos indicus is a domestic cattle species with many indigenous breeds found in India and is important for dairy, draught work, and other household activities. Distinct phenotypic differences are observed among the breeds of this species; however, their whole genome sequences were not available. Therefore, in this study, we performed the whole genome sequencing using Illumina short-read technology to construct draft genome assemblies of four B. indicus breeds; Ongole, Kasargod Dwarf, Kasargod Kapila, and Vechur, of which Vechur is known as the smallest cow of the world. We also report the first de novo genome assemblies of these native B. indicus breeds. Further, we constructed the 18S rRNA marker gene sequences of these B. indicus breeds, which were not yet known. Genomic analysis helped to identify the distinct bovine phenotypic characteristics-related and other biological process-related genes in this species compared to B. taurus, and to gain comparative genomic insights between the dwarf and non-dwarf breeds of this species.

genomics↗