A5033227425- Plant Molecular Biology Research
- Genomics and Phylogenetic Studies
- Genetic diversity and population structure
- Scientific Computing and Data Management
- Plant Reproductive Biology
- Light effects on plants
- Genetics, Bioinformatics, and Biomedical Research
- Distributed and Parallel Computing Systems
- Cloud Computing and Resource Management
- Cancer-related molecular mechanisms research
- Plant and Fungal Interactions Research
- Greenhouse Technology and Climate Control
- Insect and Pesticide Research
- Chromosomal and Genetic Variations
- Bioinformatics and Genomic Networks
- Insect Resistance and Genetics
- Genetic Mapping and Diversity in Plants and Animals
- Plant and animal studies
- Wheat and Barley Genetics and Pathology
- Forest Insect Ecology and Management
- Plant Disease Resistance and Genetics
- Species Distribution and Climate Change
- Photosynthetic Processes and Mechanisms
- Research Data Management Practices
- Plant responses to water stress
GreenLight Biosciences (United States)
2023-2025
Université Bourgogne Franche-Comté
2025
Triangle
2025
University of Arizona
2016-2024
University of California, Davis
2013-2020
University of Freiburg
2020
Oregon State University
2013-2016
University of Nottingham
2010
Significance One of the most important technological advances by humans is domestication plant species for production food. We have used high-throughput sequencing to identify changes in DNA sequence and gene expression that differentiate cultivated tomato its wild relatives. also hundreds candidate genes evolved new protein sequences or changed levels response natural selection Taken together, our analyses provide a snapshot genome evolution under artificial conditions.
Transcriptional feedback loops are key to circadian clock function in many organisms. Current models of the Arabidopsis network consist several coupled composed almost exclusively transcriptional repressors. Indeed, a central regulatory mechanism is repression evening-phased genes via binding morning-phased Myb-like repressors evening element (EE) promoter motifs. We now demonstrate that related protein, REVEILLE8 (RVE8), direct activator EE-containing and output genes. Loss RVE8 its close...
CyVerse, the largest publicly-funded open-source research cyberinfrastructure for life sciences, has played a crucial role in advancing data-driven since 2010s. As technology landscape evolved with emergence of cloud computing platforms, machine learning and artificial intelligence (AI) applications, CyVerse enabled access by providing interfaces, Software as Service (SaaS), cloud-native Infrastructure Code (IaC) to leverage new technologies. services enable researchers integrate...
Shade from neighboring plants limits light for photosynthesis; as a consequence, have variety of strategies to avoid canopy shade and compete with their neighbors light. Collectively the response foliar is called avoidance syndrome (SAS). The SAS includes elongation organs, acceleration flowering time, additional physiological responses, which are seen throughout plant life cycle. However, current mechanistic knowledge mainly limited shade-induced seedlings. Here we use phenotypic profiling...
Summary Improved predictions of fitness and yield may be obtained by characterizing the genetic controls environmental dependencies organismal ontogeny. Elucidating shape growth curves reveal novel that single‐time‐point ( STP ) analyses do not because, in theory, infinite numbers can result same final measurement. We measured leaf lengths widths Brassica rapa recombinant inbred lines RIL s) throughout modeled allometry as function valued traits FVT ), examined correlations between these...
FLOWERING LOCUS T (FT) and TERMINAL FLOWER1 (TFL1) proteins share highly conserved amino acid residues but they play opposite regulatory roles in promoting repressing the flowering response, respectively. Previous substitution models functional analysis have identified several key which are critical for promotion of flowering. However, precise relationship between naturally occurring FT/TFL1 homologs mechanism their role is still unclear. In this study, from eight Rosaceae species, namely,...
<ns4:p>Docker has become a very popular container-based virtualization platform for software distribution that revolutionized the way in which scientific and dependencies (software stacks) can be packaged, distributed, deployed. Docker makes complex time-consuming installation procedures needed one-time process. Because it enables platform-independent installation, versioning of environments, easy redeployment reproducibility, is an ideal candidate deployment identical stacks on different...
Long intergenic non-coding RNAs (lincRNAs) are an abundant and functionally diverse class of eukaryotic transcripts. Reported lincRNA repertoires in mammals vary, but commonly the thousands to tens transcripts, covering ~90% genome. In addition elucidating function, there is particular interest understanding origin evolution lincRNAs. Aside from mammals, populations have been sparsely sampled, precluding evolutionary analyses focused on their emergence persistence. Here we present Evolinc, a...
A network of environmental inputs and internal signaling controls plant growth, development organ elongation. In particular, the growth-promoting hormone gibberellin (GA) has been shown to play a significant role in The use tomato as model organism study elongation presents an opportunity genetic control internode-specific eudicot species with sympodial growth habit substantial internodes that can do respond external stimuli. To investigate internode elongation, mutant elongated hypocotyl...
Exquisitely regulated plastid-to-nucleus communication by retrograde signaling pathways is essential for fine-tuning of responses to the prevailing environmental conditions. The plastidial metabolite methylerythritol cyclodiphosphate (MEcPP) has emerged as a stress signal transduced into diverse ensemble response outputs. Here, we demonstrate enhanced phytochrome B protein abundance in red light-grown MEcPP-accumulating ceh1 mutant Arabidopsis (Arabidopsis thaliana) plants relative wild-type...
Double-stranded RNA (dsRNA) biopesticides offer the potential for highly targeted pest control with minimal off-target impacts. Varroa mites (Varroa destructor) are an important of honey bees (Apis mellifera) that primarily managed by synthetic pesticides. A next-generation treatment using a varroa-active dsRNA, vadescana, has been developed to target calmodulin expression in varroa. We evaluated exposure non-target species vadescana. First, we assessed gene silencing effects on 39...
Abstract The mapping and functional analysis of quantitative traits in Brassica rapa can be greatly improved with the availability physically positioned, gene-based genetic markers accurate genome annotation. In this study, deep transcriptome RNA sequencing (RNA-Seq) was undertaken two objectives: SNP detection We performed on varieties that are parents a population to aid development marker system for subsequent high-resolution map. An constructed detect novel transcripts improve current...
Abstract Transcriptomic analyses from across eukaryotes indicate that most of the genome is transcribed at some point in developmental trajectory an organism. One class these transcripts termed long intergenic noncoding RNAs (lincRNAs). Recently, attention has focused on understanding evolutionary dynamics lincRNAs, particularly their conservation within genomes. Here, we take a comparative genomic and phylogenetic approach to uncover factors influencing lincRNA emergence persistence plant...
Plants have sophisticated mechanisms for sensing neighbor shade. To maximize their ability to compete light, plants respond shade through enhanced elongation and physiological changes. The avoidance response affects many different organs growth stages, yet the signaling pathways underlying this mostly been studied in seedlings. We assayed transcriptome changes across a 2-d time course wild type 12 Arabidopsis (Arabidopsis thaliana) mutants. resulting temporal map of transcriptional responses...
Next-generation RNA-sequencing is an incredibly powerful means of generating a snapshot the transcriptomic state within cell, tissue, or whole organism. As questions addressed by RNA-seq become both more complex and greater in number, there need to simplify processing workflows, make them efficient interoperable, capable handling large small datasets. This especially important for researchers who process hundreds tens thousands To address these needs, we have developed scalable,...
Floral attraction traits can significantly affect pollinator visitation patterns, but adaptive evolution of these may be constrained by correlations with other traits. In some cases, molecular pathways contributing to floral are well characterized, offering the opportunity explore loci potentially underlying variation among individuals. Here, we quantify range in UV patterning (i.e. 'bulls-eye nectar guides) crop and wild accessions Brassica rapa. We then use experimental crosses examine...
is the widest-ranging tree species in North America and an ecologically important component of mesic forest ecosystems displaced by Pleistocene glaciations. Using phylogeographic analyses genome-wide SNPs (34,796 SNPs, 183 individuals) ecological niche modeling, we inferred population structure, ploidy levels, admixture, range dynamics
Abstract CyVerse, the largest publicly-funded open-source research cyberinfrastructure for life sciences, has played a crucial role in advancing data-driven since 2010s. As technology landscape evolved with emergence of cloud computing platforms, machine learning and artificial intelligence (AI) applications, CyVerse enabled access by providing interfaces, Software as Service (SaaS), cloud-native Infrastructure Code (IaC) to leverage new technologies. services enable researchers integrate...
Meiotic recombination in eukaryotes requires two homologues of the E. coli RecA proteins: Rad51 and Dmc1. Both proteins play important roles binding single stranded DNA, homology search, strand invasion exchange. has been well studied Arabidopsis, rice, maize orthologues RAD51 DMC1 have characterized. However genetic analysis genes bread wheat hampered due to absence complete sequence information because existence multiple copies each gene hexaploid genome. In this study we identified that...
Abstract Brassica rapa is a model species for agronomic, ecological, evolutionary, and translational studies. Here, we describe high-density SNP discovery genetic map construction B. recombinant inbred line (RIL) population derived from field collected RNA sequencing (RNA-Seq) data. This genotype data enables the detection correction of putative genome misassemblies accurate assignment scaffold sequences to their likely genomic locations. These assembly improvements represent 7.1–8.0%...
<ns4:p>Docker has become a very popular container-based virtualization platform for software distribution that revolutionized the way in which scientific and dependencies (software stacks) can be packaged, distributed, deployed. Docker makes complex time-consuming installation procedures needed one-time process. Because it enables platform-independent installation, versioning of environments, easy redeployment reproducibility, is an ideal candidate deployment identical stacks on different...
This workflow allows novice researchers to leverage advanced computational resources such as cloud computing carry out pairwise comparative transcriptomics. It also serves a primer for biologists develop data scientist skills, e.g. executing bash commands, visualization and management of large sets. All command line code further explanations each or step can be found on the wiki (https://wiki.cyverse.org/wiki/x/dgGtAQ). The Discovery Environment Atmosphere platforms are connected together...
Juncus effusus L. (family: Juncaceae; order: Poales) is a helophytic rush growing in temperate damp or wet terrestrial habitats and of almost cosmopolitan distribution. The species has been studied intensively with respect to its interaction co-occurring plants as well microbes being involved major biogeochemical cycles. J. biotechnological value component Constructed Wetlands where the plant employed phytoremediation contaminated water. Its genome not sequenced.In this study we carried out...
Abstract RNA‐seq is a vital method for understanding gene structure and expression patterns. Typical analysis protocols use sequencing reads of length 50 to 150 nucleotides alignment the reference genome assembly transcripts. The resultant transcripts are quantified used differential visualization. Existing tools vast diverse; given their differences in performance, it critical select an protocol that scalable, accurate, easy use. Tuxedo, popular alignment‐based analysis, has been updated...