A5023701026- Plant Molecular Biology Research
- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Telomeres, Telomerase, and Senescence
- Cancer-related molecular mechanisms research
- RNA Research and Splicing
- RNA modifications and cancer
- Plant and Fungal Interactions Research
- Plant biochemistry and biosynthesis
- Plant Stress Responses and Tolerance
- Plant Gene Expression Analysis
- CRISPR and Genetic Engineering
- Photosynthetic Processes and Mechanisms
- RNA and protein synthesis mechanisms
- Silicon Effects in Agriculture
- Genetic diversity and population structure
- Microbial Metabolic Engineering and Bioproduction
- Plant Reproductive Biology
- Plant Physiology and Cultivation Studies
- Genetics, Bioinformatics, and Biomedical Research
- Greenhouse Technology and Climate Control
- DNA Repair Mechanisms
- Plant nutrient uptake and metabolism
- Plant Genetic and Mutation Studies
- Protist diversity and phylogeny
Cornell University
2019-2025
Ithaca College
2020-2024
Wageningen University & Research
2024
King Abdullah University of Science and Technology
2024
University of California, Davis
2024
Lanzhou University
2024
Smith Institute
2024
Tohoku University
2022
University of Arizona
2013-2019
Western Regional Research Center
2019
Cultivated strawberry emerged from the hybridization of two wild octoploid species, both descendants merger four diploid progenitor species into a single nucleus more than 1 million years ago. Here we report near-complete chromosome-scale assembly for cultivated (Fragaria × ananassa) and uncovered origin evolutionary processes that shaped this complex allopolyploid. We identified extant relatives each provide support North American strawberry. examined dynamics among subgenomes in presence...
N6-methyladenosine (m6A) is a dynamic, reversible, covalently modified ribonucleotide that occurs predominantly toward 3′ ends of eukaryotic mRNAs and essential for their proper function regulation. In Arabidopsis thaliana, many RNAs contain at least one m6A site, yet the transcriptome-wide remains mostly unknown. Here, we show m6A-modified in have reduced abundance absence this mark. The decrease due to transcript destabilization caused by cleavage occurring 4 or 5 nt directly upstream...
Soil salinity is one of the major threats to agricultural productivity worldwide. Salt stress exposure alters root and shoot growth rates, thereby affecting overall plant performance. While past studies have extensively documented effect salt on elongation development separately, here we take an innovative approach by examining coordination under conditions. Utilizing a newly developed tool for quantifying root:shoot ratio in agar-grown Arabidopsis seedlings, found that results loss between...
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...
Summary Water scarcity, resulting from climate change, poses a significant threat to ecosystems. Syntrichia ruralis , dryland desiccation‐tolerant moss, provides valuable insights into survival of water‐limited conditions. We sequenced the genome S. conducted transcriptomic analyses, and performed comparative genomic analyses with existing genomes transcriptomes, including close relative caninervis . took genetic approach characterize role an transcription factor, identified in Arabidopsis...
Abstract Long intergenic noncoding RNAs (lincRNAs) are a large yet enigmatic class of eukaryotic transcripts that can have critical biological functions. The wealth RNA-sequencing (RNA-seq) data available for plants provides the opportunity to implement harmonized identification and annotation effort lincRNAs enables cross-species functional genomic comparisons as well prioritization candidates. In this study, we processed >24 Tera base pairs RNA-seq from >16,000 experiments...
Dyskerin binds the H/ACA box of human telomerase RNA and is a core subunit required for RNP biogenesis enzyme function in vivo. Missense mutations dyskerin result dyskeratosis congenita, complex syndrome characterized by bone marrow failure, deficiency, progressive telomere shortening. Here we demonstrate that also contributes to maintenance Arabidopsis thaliana. We report both AtNAP57, homolog, AtTERT, catalytic subunit, accumulate plant nucleolus, AtNAP57 associates with active particles...
Abstract Plants, and the biological systems around them, are key to future health of planet its inhabitants. The Plant Science Decadal Vision 2020–2030 frames our ability perform vital far‐reaching research in plant sciences, essential how we value participants apply emerging technologies. We outline a comprehensive vision for addressing some most pressing global problems through discovery, practical applications, education. was developed by at Summit 2019, community event organized Research...
Abstract Phylogenomic analyses are recovering previously hidden histories of hybridization, revealing the genomic consequences these events on architecture extant genomes. We applied phylogenomic techniques and several complementary statistical tests to show that introgressive hybridization appears have occurred between close relatives Arabidopsis, resulting in cytonuclear discordance impacting our understanding species relationships group. The composition introgressed retained genes...
The enormous sequence heterogeneity of telomerase RNA (TR) subunits has thus far complicated their characterization in a wider phylogenetic range. Our recent finding that land plant TRs are, similarly to known ciliate TRs, transcribed by polymerase III and under the control type-3 promoter, allowed us design novel strategy characterize early diverging Viridiplantae taxa, as well ciliates other Diaphoretickes lineages. Starting with upstream element type 3 promoter is conserved number small...
Abstract The role of the RNA degradation product 2′,3′-cyclic adenosine monophosphate (2′,3′-cAMP) is poorly understood. Recent studies have identified 2′,3′-cAMP in plant material and determined its stress signaling. level increases upon wounding, dark, under heat, binding to an RNA-binding protein, Rbp47b, promotes granule (SG) assembly. To gain further mechanistic insights into function 2′,3′-cAMP, we used a multi-omics approach by combining transcriptomics, metabolomics, proteomics...
Abstract How the noncoding genome affects cellular functions is a key biological question. A particular challenge to distinguish effects of DNA elements from long RNAs (lncRNAs) that coincide at same loci. Here, we identified flowering‐associated intergenic lncRNA ( FLAIL ) in Arabidopsis through early flowering flail mutants. Expression RNA different chromosomal location combination with strand‐specific knockdown characterized as trans‐acting molecule. directly binds differentially...
Teleost fishes, which are the largest and most diverse group of living vertebrates, have a rich history ancient recent polyploidy. Previous studies allotetraploid common carp goldfish (cyprinids) reported dominant subgenome, is more expressed exhibits biased gene retention. However, underlying mechanisms contributing to observed 'subgenome dominance' remains poorly understood. Here we report high-quality genomes twenty-one cyprinids investigate origin subsequent subgenome evolution patterns...
Covalent RNA modifications (RCMs) are post-transcriptional changes to the chemical composition of RNA. RCMs influence mRNA stability, regulate transcription and translation efficiency, play critical roles in growth development eukaryotes. However, their role plants remains poorly understood, particularly as they relate performance field under stress conditions. In this study, we grew a panel six diverse sorghum (S. bicolor) accessions during summer central Arizona examined physiological...
Soil salinity is one of the major threats to agricultural productivity worldwide. Salt stress exposure alters root and shoots growth rates, thereby affecting overall plant performance. While past studies have extensively documented effect salt on elongation shoot development separately, here we take an innovative approach by examining coordination under conditions. Utilizing a newly developed tool for quantifying root:shoot ratio in agar-grown Arabidopsis seedlings, found that results loss...
Abstract Conversion of a double-strand break into telomere is dangerous, potentially lethal event. However, little known about the mechanism and control de novo formation (DNTF). DNTF can be instigated by insertion repeat array (TRA) host genome, which seeds new telomere, resulting in chromosome truncation. Such events are rare concentrated at ends. Here, we introduce tetraploid Arabidopsis thaliana as robust genetic model for DNTF. Transformation 2.6-kb TRA plants resulted efficiency 56%,...
The EPIC-CoGe browser is a web-based genome visualization utility that integrates the GMOD JBrowse with extensive CoGe database (currently containing over 30 000 genomes). In addition, boasts many additional features basic JBrowse, including enhanced search capability and on-the-fly analyses for comparisons between all types of functional diversity genomics data. There no installation required data (genome, annotation, genomic data) can be loaded by following simple point click wizard, or...
Plants exhibit different physiological and molecular responses to adverse changes in their environment. One such response is the sequestration of proteins, RNAs, metabolites into cytoplasmic bodies called stress granules (cSGs). Here we report that, addition cSGs, heat also induces formation SG-like foci (cGs) chloroplasts model plant Arabidopsis thaliana. Similarly (i) cpSG assemble rapidly disappear when ceases, (ii) inhibited by treatment with a translation inhibitor (lincomycin), (iii)...