A5039340001- Chromosomal and Genetic Variations
- Plant Molecular Biology Research
- Genomics and Chromatin Dynamics
- Genomics and Phylogenetic Studies
- Single-cell and spatial transcriptomics
- Genetic Mapping and Diversity in Plants and Animals
- Plant Pathogens and Resistance
- Machine Learning in Bioinformatics
- Plant Disease Resistance and Genetics
- Plant Virus Research Studies
- Photosynthetic Processes and Mechanisms
- Cancer Genomics and Diagnostics
- Plant Reproductive Biology
- Plant Genetic and Mutation Studies
- CRISPR and Genetic Engineering
- Wheat and Barley Genetics and Pathology
- Trypanosoma species research and implications
- Signaling Pathways in Disease
- Plant Gene Expression Analysis
- Epigenetics and DNA Methylation
- Soybean genetics and cultivation
- Cell Image Analysis Techniques
- Plant Pathogens and Fungal Diseases
- Bioenergy crop production and management
- Potato Plant Research
University of Michigan–Ann Arbor
2023-2024
University of Georgia
2019-2024
Michigan State University
2022
University of Wisconsin–Madison
2015-2019
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...
Cold stress can greatly affect plant growth and development. Plants have developed special systems to respond tolerate cold stress. While scientists discovered numerous genes involved in responses stress, few studies been dedicated investigation of genome-wide chromatin dynamics induced by or other abiotic stresses.Genomic regions containing active cis-regulatory DNA elements be identified as DNase I hypersensitive sites (DHSs). We develop high-resolution DHS maps potato (Solanum tuberosum)...
Summary Cultivated potato ( Solanum tuberosum L.) is a highly heterozygous autotetraploid that presents challenges in genome analyses and breeding. Wild species serve as resource for the introgression of important agronomic traits into cultivated potato. One key chacoense diploid, inbred clone M6, which self‐compatible has desirable tuber market quality disease resistance traits. Sequencing assembly M6 S. generated an 825 767 562 bp 8260 scaffolds with N50 scaffold size 713 602 bp....
Genomic regions free of nucleosomes, which are hypersensitive to DNase I digestion, known as sites (DHSs) and frequently contain cis-regulatory DNA elements. To investigate their prevalence characteristics in maize (Zea mays), we developed high-resolution genome-wide DHS maps using a modified DNase-seq technique. Maize DHSs exhibit depletion nucleosomes low levels methylation enriched with conserved noncoding sequences (CNSs). We protoplast-based transient transformation assay assess the...
Significance Crop genomes can be very large, with many repetitive elements and pseudogenes. Distilling a genome down to the relatively small fraction of regions that are functionally valuable for trait variation like looking needles in haystack. The location these is often not obvious, current detection technologies impractically expensive intensive research projects. unmethylated highly stable during vegetative development reveal locations potentially expressed genes or cis-regulatory...
With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, stewardship, energy, technology healthcare. This effort requires conceptual technological framework identify map all cell types, comprehensively annotate localization organization molecules at cellular tissue levels. framework, called Plant Cell Atlas (PCA), for understanding...
Abstract Single-cell ATAC-seq has emerged as a powerful approach for revealing candidate cis-regulatory elements genome-wide at cell-type resolution. However, current single-cell methods suffer from limited throughput and high costs. Here, we present novel technique called scifi-ATAC-seq, combinatorial fluidic indexing ATAC-sequencing, which combines barcoded Tn5 pre-indexing step with droplet-based using the 10X Genomics platform. With up to 200,000 nuclei across multiple samples can be...
Meiotic recombination is the foundation for genetic variation in natural and artificial populations of eukaryotes. Although maps have been developed numerous plant species since late 1980s, few these provided necessary resolution needed to investigate genomic epigenomic features underlying meiotic crossovers. Using a whole genome sequencing-based approach, we two high-density reference-based haplotype using diploid potato clones as parents. The vast majority (81%) crossovers were mapped less...
Gene expression is regulated by orchestrated binding of regulatory proteins to promoters and other cis-regulatory DNA elements (CREs). Several plant databases have been developed for mapping or motifs associated with promoters. However, there a lack that allow investigation all CREs. Here we present PlantDHS (http://plantdhs.org), DNase I hypersensitive site (DHS) database integrates histone modification, RNA sequencing, nucleosome positioning/occupancy, transcription factor sites, genomic...
Abstract Cis -regulatory elements (CREs) are critical in regulating gene expression, and yet understanding of CRE evolution remains challenging. Here, we constructed a comprehensive single-cell atlas chromatin accessibility Oryza sativa , integrating data from 103,911 nuclei representing 126 discrete cell states across nine distinct organs. We used comparative genomics to compare cell-type resolved between O. 57,552 four additional grass species ( Zea mays, Sorghum bicolor, Panicum miliaceum...
Summary Cis -regulatory elements (CREs) precisely control spatiotemporal gene expression in cells. Using a spatially resolved single-cell atlas of with chromatin accessibility across ten soybean tissues, we identified 103 distinct cell types and 303,199 accessible regions (ACRs). Nearly 40% the ACRs showed cell-type-specific patterns were enriched for transcription factor (TF) motifs defining diverse identities. We de novo TF explored conservation regulatory networks underpinning legume...
Recombination plays an integral role in the creation of novel genetic variation sexually reproducing species. Despite this important role, determinants and evolution crossover hotspots have remained poorly understood plants. Here, we present a comparative analysis two rice (Oryza sativa) historical recombination maps from subspecies (indica japonica) using 150 resequenced genomes. Fine-scale rates were validated by comparison with consensus map empirically derived crossovers, respectively....
Base J, β-D-glucosyl-hydroxymethyluracil, is a modification of thymine DNA base involved in RNA Polymerase (Pol) II transcription termination kinetoplastid protozoa. Little understood regarding how specific residues are targeted for J-modification or the mechanism J regulated termination. To identify proteins J-synthesis, we expressed tagged version J-glucosyltransferase (JGT) Leishmania tarentolae, and identified four co-purified by mass spectrometry: protein phosphatase (PP1), homolog...
Abstract While considerable knowledge exists about the enzymes pivotal for C 4 photosynthesis, much less is known cis- regulation important specifying their expression in distinct cell types. Here, we use single-cell-indexed ATAC-seq to identify cell-type-specific accessible chromatin regions (ACRs) associated with five different grass species. This study spans four species, covering three photosynthetic subtypes: Zea mays and Sorghum bicolor (NADP-ME), Panicum miliaceum (NAD-ME), Urochloa...
While considerable knowledge exists about the enzymes pivotal for C
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...
Understanding how cis-regulatory elements facilitate gene expression is a key question in biology. Recent advances single-cell genomics have led to the discovery of cell-specific chromatin landscapes that underlie transcription programs animal models. However, high equipment and reagent costs commercial systems limit their applications for many laboratories. In this study, we developed combinatorial index dual PCR barcode strategy profile Arabidopsis thaliana root epigenome without any...