A5051220614- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Genetic Mapping and Diversity in Plants and Animals
- Agricultural pest management studies
- Peanut Plant Research Studies
- Coconut Research and Applications
- CRISPR and Genetic Engineering
- Gene expression and cancer classification
- Biomedical Text Mining and Ontologies
- Research Data Management Practices
- Bioinformatics and Genomic Networks
- Plant Virus Research Studies
- Genetic and Environmental Crop Studies
- Plant Disease Resistance and Genetics
- Wheat and Barley Genetics and Pathology
- RNA and protein synthesis mechanisms
- Genetics and Plant Breeding
- Legume Nitrogen Fixing Symbiosis
- Maritime Ports and Logistics
- Microbial Metabolic Engineering and Bioproduction
- Scientific Computing and Data Management
- GNSS positioning and interference
- Plant-Microbe Interactions and Immunity
- Soybean genetics and cultivation
- Plant nutrient uptake and metabolism
Agricultural Research Service
2008-2025
United States Department of Agriculture
2008-2024
Ames National Laboratory
2023
Iowa State University
2011-2021
Plant Gene Expression Center
2009-2011
University of Missouri
2008-2011
University of Arizona
2011
Université Paris-Sud
2008
Centre National de la Recherche Scientifique
2008
Commonwealth Scientific and Industrial Research Organisation
2008
David Bertioli and colleagues report the genomes of Arachis duranensis ipaensis, diploid ancestors cultivated peanut, hypogaea. Their analyses are a first step in understanding evolution peanut's tetraploid genome. Cultivated peanut (Arachis hypogaea) is an allotetraploid with closely related subgenomes total size ∼2.7 Gb. This makes assembly chromosomal pseudomolecules very challenging. As foundation to genome we sequences its ipaensis). We show that these similar A B use them identify...
Like many other crops, the cultivated peanut (Arachis hypogaea L.) is of hybrid origin and has a polyploid genome that contains essentially complete sets chromosomes from two ancestral species. Here we report sequence show after its origin, evolved through mobile-element activity, deletions by flow genetic information between corresponding (that is, homeologous recombination). Uniformity patterns recombination at ends favors single for wild counterpart A. monticola. However, much genome,...
We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as founders maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. results demonstrate ancient tetraploid character continues to degrade by fractionation present day. Excellent contiguity over repeat arrays complete annotation centromeres revealed additional variation major...
Since its 2015 update, MaizeGDB, the Maize Genetics and Genomics database, has expanded to support sequenced genomes of many maize inbred lines in addition B73 reference genome assembly. Curation development efforts have targeted high quality datasets tools trait analysis, germplasm genetic studies, breeding. MaizeGDB hosts a wide range data including recent new types metadata, RNA-seq, proteomics, synteny, large-scale diversity. To improve access visualization several been implemented to:...
The maize W22 inbred has served as a platform for genetics since the mid twentieth century. To streamline genome analyses, we have sequenced and de novo assembled reference using short-read sequencing technologies. We show that significant structural heterogeneity exists in comparison to B73 at multiple scales, from transposon composition copy number variation single-nucleotide polymorphisms. generation of this enables accurate placement thousands Mutator (Mu) Dissociation (Ds) transposable...
MaizeGDB is a highly curated, community-oriented database and informatics service to researchers focused on the crop plant model organism Zea mays ssp. mays. Although some form of maize community has existed over last 25 years, there have only been two major releases. In 1991, original genetics MaizeDB was created. 2003, combined contents sequence data from ZmDB were made accessible as single resource named MaizeGDB. Over next decade, became more driven while still maintaining traditional...
Abstract Research in the past decade has demonstrated that a single reference genome is not representative of species’ diversity. MaizeGDB introduces pan-genomic approach to hosting genomic data, leveraging large number diverse maize genomes and their associated datasets quickly efficiently connect genomes, gene models, expression, epigenome, sequence variation, structural transposable elements, diversity data across so researchers can easily track functional differences locus its orthologs...
Legume Information System (LIS), at http://legumeinfo.org, is a genomic data portal (GDP) for the legume family. LIS provides access to genetic and information major crop model legumes. With more than two-dozen domesticated species, there are numerous specialists working on particular also GDPs these species. has been redesigned in last three years both better integrate sets across legumes, accommodate specialized that serve To sets, genome map viewers, holds synteny mappings among all...
Abstract The genomes of most, if not all, flowering plants have undergone whole genome duplication events during their evolution. impact such polyploidy is poorly understood, as the fate most duplicated genes. We sequenced an approximately 1 million-bp region in soybean (Glycine max) centered on Rpg1-b disease resistance gene and compared this with a 10 to 14 million years ago. These two regions were also homologous several related legume species (a second genotype, Glycine tomentella,...
Abstract Over the last 20 million years, Andropogoneae tribe of grasses has evolved to dominate 17% global land area. Domestication these in 10,000 years yielded our most productive crops, including maize, sugarcane, and sorghum. The majority species, show a history polyploidy – condition that, while offering evolutionary advantage multiple gene copies, poses challenges basic cellular processes, expression, epigenetic regulation. Genomic studies have been limited by sparse sampling taxa...
A framework for understanding the synthesis and catalysis of metabolites other biochemicals by proteins is crucial unraveling physiology cells. To create such a Zea mays L. subsp. (maize), we developed MaizeCyc, metabolic network enzyme catalysts, proteins, carbohydrates, lipids, amino acids, secondary plant products, annotating genes identified in maize reference genome sequenced from B73 variety. MaizeCyc version 2.0.2 collection 391 pathways involving 8889 mapped to 2110 reactions 1468...
The future of agricultural research depends on data. sheer volume biological data being produced today makes excellent management essential. Governmental agencies, publishers and science funders require plans for publicly funded research. Furthermore, the value increases exponentially when they are properly stored, described, integrated shared, so that can be easily utilized in analyses. AgBioData (https://www.agbiodata.org) is a consortium people working at databases, archives knowledgbases...
Plant phenotype datasets include many different types of data, formats, and terms from specialized vocabularies. Because these were designed for audiences, they frequently contain language details tailored to investigators with research objectives backgrounds. Although comparisons across have long been possible on a small scale, comprehensive queries analyses that span broad set reference species, disciplines, knowledge domains continue be severely limited by the absence common semantic...
Due to the recent domestication of peanut from a single tetraploidization event, relatively little genetic diversity underlies extensive morphological and agronomic in cultivars today. To broaden variation future breeding programs, it is necessary characterize germplasm accessions for new sources leverage power genome-wide association studies (GWAS) discover markers associated with traits interest. We report an analysis linkage disequilibrium (LD), population structure, diversity, examine...
First released in 1991 with the name MaizeDB, Maize Genetics and Genomics Database, now MaizeGDB, celebrates its 20th anniversary this year. MaizeGDB has transitioned from a focus on comprehensive curation of literature, genetic maps stocks to paradigm that accommodates recent release reference maize genome sequence, multiple diverse genomes sequence-based gene expression data sets. The Team is relatively small, relies heavily research community provide data, nomenclature standards most...
MaizeGDB is the maize research community's central repository for genetic and genomic information about crop plant model Zea mays ssp. mays. The team endeavors to meet needs as they evolve based on researcher feedback guidance. Recent work has focused better integrating existing data with sequence it becomes available B73, Mo17 Palomero Toluqueño genomes. Major along these lines include implementation of a genome browser graphically represent sequences; POPcorn, portal ancillary that offers...
Abstract Legumes, comprising one of the largest, most diverse, and economically important plant families, are subject vibrant research development worldwide. Continued improvement legume crops will benefit from recent proliferation genetic (including genomic) resources; but diversity, scale, complexity these resources presents challenges to those managing using them. A workshop held in March 2019 addressed questions data priorities for legumes. The identified various needs recommendations:...
Abstract An international consortium is sequencing the euchromatic genespace of Medicago truncatula. Extensive bioinformatic and database resources support marker-anchored bacterial artificial chromosome (BAC) strategy. Existing physical genetic maps deep BAC-end help to guide effort, while EST databases provide essential for genome annotation as well transcriptome characterization microarray design. Finished BAC sequences are joined into overlapping sequence assemblies undergo an automated...
Knobs are conspicuous heterochromatic regions found on the chromosomes of maize and its relatives. The number, locations, sizes knobs vary dramatically, with most lines containing between four eight in mid-arm positions. Prior data suggest that some may reduce recombination. However, comprehensive tests have not been carried out, primarily because placed genetic map. We used fluorescent situ hybridization two recombinant inbred populations to map seven accurately place three from B73 genomic...
Abstract We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as founders maize nested association mapping population. The data indicate number of pan-genes exceeds 103,000 ancient tetraploid character continues to degrade by fractionation present day. Excellent contiguity over repeat arrays complete annotation centromeres further reveal locations internal structures major cytological landmarks. show combining structural variation...
Abstract The rapid increase in the number of reference-quality genome assemblies presents significant new opportunities for genomic research. However, absence standardized naming conventions and annotations across datasets creates substantial challenges. Inconsistent hinders identification correct assemblies, complicates integration bioinformatics pipelines, makes it difficult to link multiple resources. To address this, we developed a specification standardizing reference improve...
SummaryBarleyBase (http://barleybase.org/) and its successor, PLEXdb (http://plexdb.org/), are public resources for large-scale gene expression analysis plants plant pathogens. BarleyBase/PLEXdb provides a unified web interface to support the functional interpretation of highly parallel microarray experiments integrated with traditional structural genomics phenotypic data. Users can perform hypothesis building queries from multiple interlinked resources, e.g., particular gene, protein class,...