Vinita Joardar
A5052133615- Genomics and Phylogenetic Studies
- Plant-Microbe Interactions and Immunity
- Plant Pathogenic Bacteria Studies
- Plant Disease Resistance and Genetics
- Antifungal resistance and susceptibility
- Plant Pathogens and Fungal Diseases
- Mycotoxins in Agriculture and Food
- Insect symbiosis and bacterial influences
- Legume Nitrogen Fixing Symbiosis
- RNA and protein synthesis mechanisms
- Mosquito-borne diseases and control
- Molecular Biology Techniques and Applications
- Vector-borne infectious diseases
- Infectious Diseases and Mycology
- Fungal and yeast genetics research
- Algal biology and biofuel production
- Microbial Natural Products and Biosynthesis
- Fungal Biology and Applications
- Biocrusts and Microbial Ecology
- RNA modifications and cancer
- Plant pathogens and resistance mechanisms
- Genomics and Rare Diseases
- Plant and Fungal Interactions Research
- Gene expression and cancer classification
- Bacteriophages and microbial interactions
National Center for Biotechnology Information
2015-2024
National Institutes of Health
2015-2024
J. Craig Venter Institute
2006-2018
Virginia Tech
2005
Cornell University
2003
United States Department of Agriculture
2003
University of Nebraska–Lincoln
2003
Washington University in St. Louis
2002
The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). leverages data submitted to International Nucleotide Sequence Database Collaboration (INSDC) against combination computation, manual curation, collaboration produce standard set stable, non-redundant reference sequences. augments these sequences with current...
We report the complete genome sequence of model bacterial pathogen Pseudomonas syringae pathovar tomato DC3000 (DC3000), which is pathogenic on and Arabidopsis thaliana . The (6.5 megabases) contains a circular chromosome two plasmids, collectively encode 5,763 ORFs. identified 298 established putative virulence genes, including several clusters genes encoding 31 confirmed 19 predicted type III secretion system effector proteins. Many were members paralogous families also proximal to mobile...
Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology of developing tools to fight them has been slowed by lack a high-quality genome assembly. Here we combine diverse technologies produce markedly improved, fully re-annotated AaegL5 assembly, demonstrate how it accelerates mosquito science. We anchored physical cytogenetic maps, doubled number...
As an obligatory parasite of humans, the body louse (Pediculus humanus humanus) is important vector for human diseases, including epidemic typhus, relapsing fever, and trench fever. Here, we present genome sequences its primary bacterial endosymbiont Candidatus Riesia pediculicola. The has smallest known insect genome, spanning 108 Mb. Despite status as obligate parasite, it retains a remarkably complete basal repertoire 10,773 protein-coding genes 57 microRNAs. Representing hemimetabolous...
We present the genome sequences of a new clinical isolate important human pathogen, Aspergillus fumigatus, A1163, and two closely related but rarely pathogenic species, Neosartorya fischeri NRRL181 clavatus NRRL1. Comparative genomic analysis A1163 with recently sequenced A. fumigatus Af293 has identified core, variable up to 2% unique genes in each genome. While core are 99.8% identical at nucleotide level, identity for can be as low 40%. The most divergent loci appear contain heterokaryon...
Abstract Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of tick, Ixodes scapularis (Say), which vectors that cause Lyme disease, human granulocytic anaplasmosis, babesiosis diseases. The large reflects accumulation repetitive DNA, new lineages retro-transposons, gene architecture patterns resembling ancient metazoans rather pancrustaceans. Annotation scaffolds representing ∼57% genome, reveals 20,486 protein-coding genes...
Penicillins and derived β-lactam antibiotics are essential in healthcare. To gain more insight into penicillin synthesis van den Berg colleagues sequence analyze the genome transcriptome of filamentous fungus Penicillium chrysogenum. Industrial production with chrysogenum is based on an unprecedented effort microbial strain improvement. synthesis, we sequenced 32.19 Mb P. Wisconsin54-1255 identified numerous genes responsible for key steps production. DNA microarrays were used to compare...
Abstract Comprehensive genome annotation is essential to understand the impact of clinically relevant variants. However, absence a standard for clinical reporting and browser display complicates process consistent interpretation reporting. To address these challenges, Ensembl/GENCODE 1 RefSeq 2 launched joint initiative, Matched Annotation from NCBI EMBL-EBI (MANE) collaboration, converge on human gene transcript jointly define high-value set transcripts corresponding proteins. Here, we...
Pseudomonas syringae pv. phaseolicola, a gram-negative bacterial plant pathogen, is the causal agent of halo blight bean. In this study, we report on genome sequence P. phaseolicola isolate 1448A, which encodes 5,353 open reading frames (ORFs) one circular chromosome (5,928,787 bp) and two plasmids (131,950 bp 51,711 bp). Comparative analyses with phylogenetically divergent pathovar, tomato DC3000, revealed strong degree conservation at gene levels. total, 4,133 ORFs were identified as...
Many plant pathogens suppress antimicrobial defenses using virulence factors that modulate endogenous host defenses. The Pseudomonas syringae phytotoxin coronatine (COR) is believed to promote by acting as a jasmonate analog, because COR-insensitive 1 (coi1) Arabidopsis thaliana and tomato mutants are impaired in signaling exhibit reduced susceptibility P. syringae. To further investigate the role of disease development, we analyzed several jasmonate-insensitive A. for pv. strain DC3000...
Phytopathogenic bacteria possess a large number of genes that allow them to grow and cause disease on plants. Many these should be induced when the come in contact with plant tissue. We used modified vivo expression technology (IVET) approach identify from pathogen Pseudomonas syringae pv. tomato are upon infection Arabidopsis thaliana isolated over 500 planta-expressed (ipx) promoter fusions. Sequence analysis 79 fusions revealed several known potential virulence genes, including hrp/hrc,...
We present the draft genome for Rickettsia endosymbiont of Ixodes scapularis (REIS), a symbiont deer tick vector Lyme disease in North America. Among species (Alphaproteobacteria: Rickettsiales), REIS has largest sequenced to date (>2 Mb) and contains 2,309 genes across chromosome four plasmids (pREIS1 pREIS4). The most remarkable finding within is extraordinary proliferation mobile genetic elements (MGEs), which contributes limited synteny with other genomes. In particular, an integrative...
Abstract Background Ichthyophthirius multifiliis , commonly known as Ich, is a highly pathogenic ciliate responsible for 'white spot', disease causing significant economic losses to the global aquaculture industry. Options control are extremely limited, and Ich's obligate parasitic lifestyle makes experimental studies challenging. Unlike most well-studied protozoan parasites, Ich belongs phylum composed primarily of free-living members. Indeed, it closely related model organism Tetrahymena...
The genera Aspergillus and Penicillium include some of the most beneficial as well harmful fungal species such penicillin-producer chrysogenum human pathogen fumigatus, respectively. Their mitochondrial genomic sequences may hold vital clues into mechanisms their evolution, population genetics, biology, yet only a handful these genomes have been fully sequenced annotated. Here we report complete sequence annotation six three species: A. clavatus, oryzae, flavus, Neosartorya fischeri (A....
The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in annotations produced independently by NCBI Ensembl group at EMBL-EBI. This is product an international collaboration includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics University California, Santa Cruz. Identically coding regions, which generated using automated pipeline pass multiple...
Reference sequences and annotations serve as the foundation for many lines of research today, from organism sequence identification to providing a core description genes, transcripts proteins found in an organism's genome. Interpretation data including transcriptomics, proteomics, variation comparative analyses based on reference gene informs our understanding function possible disease mechanisms, leading new biomedical discoveries. The Sequence (RefSeq) resource created at National Center...
Summary Pseudomonas syringae pv. tomato ( Pst ) strain DC3000 infects the model plants Arabidopsis thaliana and tomato, causing disease symptoms characterized by necrotic lesions surrounded chlorosis. One mechanism used to infect host is type III protein secretion system, which thought deliver multiple effector proteins plant cell. The exact number of effectors in or any other pathogenic bacterium not known. All known genes P. are regulated HrpS, an NtrC family protein, HrpL alternative...
Understanding the nature of species" boundaries is a fundamental question in evolutionary biology. The availability genomes from several species genus Aspergillus allows us for first time to examine demarcation fungal at whole-genome level. Here, we four case studies, two which involve intraspecific comparisons, whereas other deal with interspecific genomic comparisons between closely related species. These reveal significant variation across Aspergillus. For example, A. fumigatus and...
The ability of Pseudomonas syringae pv. phaseolicola to cause halo blight bean is dependent on its translocate effector proteins into host cells via the hypersensitive response and pathogenicity (Hrp) type III secretion system (T3SS). To identify genes encoding effectors other potential virulence factors that are regulated by HrpL alternative sigma factor, we used a hidden Markov model, weight matrix targeting-associated patterns search genome P. 1448A, which recently was sequenced...
The soil fungus Rhizoctonia solani is a pathogen of agricultural crops. Here, we report on the 51,705,945 bp draft consensus genome sequence R. strain Rhs1AP. A comprehensive understanding heterokaryotic complexity and organization may provide insight into plant disease ecology adaptive behavior fungus.
Invasive aspergillosis (IA) due to Aspergillus fumigatus is a major cause of mortality in immunocompromised patients. The discovery highly fertile strains A. opened the possibility merge classical and contemporary genetics address key questions about this pathogen. merger involves sexual recombination, selection desired traits, genomics identify any associated loci. We constructed isogenic pair with opposite mating types used them investigate whether type virulence find genetic loci involved...