A5018498646- Phytoplasmas and Hemiptera pathogens
- Genomics and Phylogenetic Studies
- Insect symbiosis and bacterial influences
- Plant Virus Research Studies
- Plant Pathogens and Resistance
- Plant Pathogens and Fungal Diseases
- Chromosomal and Genetic Variations
- Banana Cultivation and Research
- Insect Resistance and Genetics
- Genetic Mapping and Diversity in Plants and Animals
- Studies on Chitinases and Chitosanases
- Plant Gene Expression Analysis
- Microbial Metabolic Engineering and Bioproduction
- Plant Reproductive Biology
- Cocoa and Sweet Potato Agronomy
- Plant-Microbe Interactions and Immunity
- Cassava research and cyanide
- Insect-Plant Interactions and Control
- Plant Pathogenic Bacteria Studies
- Genetic diversity and population structure
- Entomopathogenic Microorganisms in Pest Control
- Plant Molecular Biology Research
- Coffee research and impacts
- Plant biochemistry and biosynthesis
- Photosynthetic Processes and Mechanisms
Ithaca College
2016-2025
Cornell University
2016-2025
University Medical Center of the Johannes Gutenberg University Mainz
2025
Johannes Gutenberg University Mainz
2025
Robert W. Holley Center for Agriculture & Health
2021
Agricultural Research Service
2021
Kansas State University
2021
U.S. Horticultural Research Laboratory
2021
University of Cincinnati
2021
University of Arizona
2021
The MetaCyc database (MetaCyc.org) is a freely accessible comprehensive describing metabolic pathways and enzymes from all domains of life. majority are small-molecule that have been experimentally determined. contains more than 2400 derived >46 000 publications, the largest curated collection pathways. BioCyc (BioCyc.org) 5700 organism-specific Pathway/Genome Databases (PGDBs), each containing full genome predicted network one organism, including metabolites, enzymes, reactions, pathways,...
This paper reports the genome sequence of domesticated tomato, a major crop plant, and draft for its closest wild relative; comparative genomics reveal very little divergence between two genomes but some important differences with potato genome, another food in genus Solanum. Tomato (Solanum lycopersicum) is plant model system fruit development. Solanum one largest angiosperm genera1 includes annual perennial plants from diverse habitats. Here we present high-quality relative,...
The MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible describing metabolic pathways enzymes from all domains of life. are experimentally determined, mostly small-molecule curated the primary scientific literature. contains >2100 derived >37 000 publications, largest collection currently available. BioCyc (BioCyc.org) >3000 organism-specific Pathway/Genome Databases (PGDBs), each containing full genome predicted network one organism, including metabolites, enzymes,...
Zhangjun Fei and colleagues report the draft genome of a Chinese elite watermelon inbred line 97103 resequencing 20 diverse accessions that represent three subspecies Citrullus lunatus. Comparative genome-wide analyses identify extent genetic diversity population structure germplasm. Watermelon, lanatus, is an important cucurbit crop grown throughout world. Here we high-quality sequence east Asia cultivar (2n = 2× 22) containing 23,440 predicted protein-coding genes. genomics analysis...
The Sol Genomics Network (SGN, http://solgenomics.net) is a web portal with genomic and phenotypic data, analysis tools for the Solanaceae family close relatives. SGN hosts whole genome data an increasing number of members including tomato, potato, pepper, eggplant, tobacco Nicotiana benthamiana. database also stores loci phenotype which researchers can upload edit user-friendly interfaces. Tools such as BLAST, GBrowse JBrowse browsing genomes, expression map viewers, locus community...
The MetaCyc database (http://metacyc.org/) provides a comprehensive and freely accessible resource for metabolic pathways enzymes from all domains of life. in are experimentally determined, small-molecule curated the primary scientific literature. contains more than 1800 derived 30 000 publications, is largest collection currently available. Most reactions linked to one or well-characterized enzymes, both annotated with reviews, evidence codes literature citations. BioCyc...
The MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible resource for metabolic pathways enzymes from all domains of life. in are experimentally determined, small-molecule curated the primary scientific literature. With more than 1400 pathways, largest collection currently available. Pathways reactions linked to one or well-characterized enzymes, both annotated with reviews, evidence codes, literature citations. BioCyc (BioCyc.org) 500 organism-specific Pathway/Genome...
Abstract The SOL Genomics Network (SGN; http://sgn.cornell.edu) is a rapidly evolving comparative resource for the plants of Solanaceae family, which includes important crop and model such as potato (Solanum tuberosum), eggplant melongena), pepper (Capsicum annuum), tomato lycopersicum). aim SGN to relate these species one another using genomics approach tie them other dicots through fully sequenced genome Arabidopsis (Arabidopsis thaliana). currently houses map marker data species, large...
Abstract Controlled vocabularies are increasingly used by databases to describe genes and gene products because they facilitate identification of similar within an organism or among different organisms. One The Arabidopsis Information Resource's goals is associate all with terms developed the Gene Ontology Consortium that molecular function, biological process, subcellular location a product. We have also describing anatomy developmental stages use these annotate published expression data....
Nicotiana benthamiana is a widely used model plant species for the study of fundamental questions in molecular plant-microbe interactions and other areas biology. This popularity derives from its well-characterized susceptibility to diverse pathogens and, especially, amenability virus-induced gene silencing transient protein expression methods. Here, we report generation 63-fold coverage draft genome sequence N. availability on Sol Genomics Network both BLAST searches downloading local...
Abstract AraCyc is a database containing biochemical pathways of Arabidopsis, developed at The Arabidopsis Information Resource (http://www.arabidopsis.org). aim to represent metabolism as completely possible with user-friendly Web-based interface. It presently features more than 170 that include information on compounds, intermediates, cofactors, reactions, genes, proteins, and protein subcellular locations. uses Pathway Tools software, which allows the users visualize bird's eye view all...
Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they generally colossal. Here, we report on of Azolla filiculoides and Salvinia cucullata (Salviniales) present evidence for episodic whole-genome duplication in ferns-one at base 'core leptosporangiates' one specific Azolla. One fern-specific gene identified, recently shown confer high insect resistance, seems have been derived from bacteria through horizontal transfer. coexists a...
Petunia hybrida is a popular bedding plant that has long history as genetic model system. We report the whole-genome sequencing and assembly of inbred derivatives its two wild parents, P. axillaris N inflata S6. The assemblies include 91.3% 90.2% coverage their diploid genomes (1.4 Gb; 2n = 14) containing 32,928 36,697 protein-coding genes, respectively. reveal lineage experienced at least rounds hexaploidization: older gamma event, which shared with most Eudicots, more recent Solanaceae...
Tobacco (Nicotiana tabacum) is an important plant model system that has played a key role in the early development of molecular biology. The tobacco genome large and its characterisation challenging because it allotetraploid, likely arising from hybridisation between diploid N. sylvestris tomentosiformis ancestors. A draft assembly was recently published for tabacum, but aforementioned complexities limited utility due to high level fragmentation. Here we report improved assembly, which,...
Tomato (Solanum lycopersicum) is an established model for studying fruit biology; however, most studies of tomato growth and ripening are based on homogenized pericarp, do not consider the internal tissues, or expression signatures individual cell tissue types. We present a spatiotemporally resolved transcriptome analysis ontogeny, using laser microdissection (LM) hand dissection coupled with RNA-Seq analysis. Regulatory structural gene networks, including families transcription factors...
Missing heritability in genome-wide association studies defines a major problem genetic analyses of complex biological traits1,2. The solution to this is identify all causal variants and measure their individual contributions3,4. Here we report graph pangenome tomato constructed by precisely cataloguing more than 19 million from 838 genomes, including 32 new reference-level genome assemblies. This was used for study estimation 20,323 gene-expression metabolite traits. average estimated trait...
The Sol Genomics Network (SGN; http://solgenomics.net/) is a clade-oriented database (COD) containing biological data for species in the Solanaceae and their close relatives, with types ranging from chromosomes genes to phenotypes accessions. SGN hosts several genome maps sequences, including pre-release of tomato (Solanum lycopersicum cv Heinz 1706) reference genome. A new transcriptome component has been added store RNA-seq microarray data. also an open source software project,...
Abstract The original Heinz 1706 reference genome was produced by a large team of scientists from across the globe variety input sources that included 454 sequences in addition to full-length BACs, BAC and fosmid ends sequenced with Sanger technology. We present here latest tomato (SL4.0) assembled de novo PacBio long reads scaffolded using Hi-C contact maps. assembly validated Bionano optical maps 10X linked-read sequences. This is highly contiguous fewer gaps compared previous builds...
The Cucurbita genus (squashes, pumpkins and gourds) includes important domesticated species such as C. pepo, maxima moschata. In this study, we present a high-quality draft of the zucchini (C. pepo) genome. assembly has size 263 Mb, scaffold N50 1.8 Mb 34 240 gene models. It 92% conserved BUSCO core set, it is estimated to cover 93.0% genome organized in 20 pseudomolecules that represent 81.4% assembly, integrated with genetic map 7718 SNPs. Despite small size, three independent lines...
Abstract Coffea arabica , an allotetraploid hybrid of eugenioides and canephora is the source approximately 60% coffee products worldwide, its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies a di-haploid C. accession modern representatives diploid progenitors, . The three species exhibit largely conserved genome structures between parents descendant subgenomes, with no obvious global subgenome dominance. find evidence for founding...
Abstract AN9 is a glutathione S-transferase from petunia (Petunia hybrida) required for efficient anthocyanin export the site of synthesis in cytoplasm into permanent storage vacuole. For many xenobiotics it well established that covalent (GSH) tag mediates recognition molecules destined vacuolar sequestration by tonoplast-localized ATP-binding cassette pump. Here we inquired whether catalyzes formation GSH conjugates with flavonoid substrates. Using high-performance liquid chromatography...
Abstract We report herein the application of a set algorithms to identify large number (2869) single-copy orthologs (COSII), which are shared by most, if not all, euasterid plant species as well model Arabidopsis. Alignments orthologous sequences across multiple enabled design “universal PCR primers,” can be used amplify corresponding from broad range taxa, including those lacking any sequence databases. Functional annotation revealed that these conserved, encode higher-than-expected...
Abstract MetaCyc (http://metacyc.org) contains experimentally determined biochemical pathways to be used as a reference database for metabolism. In conjunction with the Pathway Tools software, can computationally predict metabolic pathway complement of an annotated genome. To increase breadth and enzymes, more than 60 plant-specific have been added or updated in recently. contrast MetaCyc, which data wide range organisms, AraCyc is species-specific containing only enzymes found model plant...