A5023870690- Plant Molecular Biology Research
- Chromosomal and Genetic Variations
- Horticultural and Viticultural Research
- Genetic Mapping and Diversity in Plants and Animals
- Plant Reproductive Biology
- Dark Matter and Cosmic Phenomena
- Phytoplasmas and Hemiptera pathogens
- Legume Nitrogen Fixing Symbiosis
- Genomics and Phylogenetic Studies
- Plant nutrient uptake and metabolism
- Plant Virus Research Studies
- Fermentation and Sensory Analysis
- Plant Pathogenic Bacteria Studies
- Plant and animal studies
- Wine Industry and Tourism
- Plant tissue culture and regeneration
- Particle physics theoretical and experimental studies
- Genetic diversity and population structure
- Particle Detector Development and Performance
- Nematode management and characterization studies
- CRISPR and Genetic Engineering
- Plant-Microbe Interactions and Immunity
- Cocoa and Sweet Potato Agronomy
- Tree Root and Stability Studies
- Soybean genetics and cultivation
University of California, Riverside
2019-2025
Brown University
2020-2023
University of California System
2022-2023
Max Planck Institute for Biology
2022
University of California, Irvine
2017-2020
Lawrence Berkeley National Laboratory
2020
University of California, Berkeley
2020
University of Liverpool
2019
Imperial College London
2019
University of Maryland, College Park
2018
DNA methylation is an ancient molecular modification found in most eukaryotes. In plants, not only critical for transcriptionally silencing transposons, but can also affect phenotype by altering expression of protein coding genes. The extent its contribution to phenotypic diversity over evolutionary time is, however, unclear, because limited stability epialleles that are linked mutations. To dissect the relative transposon surveillance and host gene regulation, we leveraged information from...
Light signaling pathways and the circadian clock interact to help organisms synchronize physiological developmental processes with periodic environmental cycles. The plant photoreceptors responsible for resetting have been characterized, but components that link remain be identified. Here we describe a family of night light–inducible clock-regulated genes ( LNK ) play key role linking light regulation gene expression control daily seasonal rhythms in Arabidopsis thaliana . A genomewide...
Abstract Background Vegetatively propagated clones accumulate somatic mutations. The purpose of this study was to better appreciate clone diversity and involved defining the nature mutations throughout genome. Fifteen Zinfandel winegrape genomes were sequenced compared one another using a highly contiguous genome reference produced from clones, 03. Results Though most heterozygous variants shared, accumulated in individual subsets clones. Overall, frequent intergenic space more introns than...
Abstract
 Plant uptake and assimilation of essential nitrogen compounds from the soil are mainly in form nitrate ammonium ions. transporters (NRTs) play a crucial role into roots. NRT structural analysis reveals mechanisms by which these function. Similarly, plant (AMTs) mediate ions, their has provided valuable information on mechanisms. After roots, metabolism pathway involves incorporation organic compounds. Glutamine synthetase (GS) glutamate synthase (GoGAT) master players this...
Citrus nematode (Tylenchulus semipenetrans) is one of the dominant plant-parasitic nematodes in citrus-growing regions, resulting an average yield loss between 10 and 30%. Tylenchulus semipenetrans a sedentary semi-endoparasitic that infects roots citrus trees, causing stunted growth, reduced fruit yield, poor quality; collectively this pathology thus disease caused referred to as slow decline citrus. Despite its huge importance, regarded neglected parasite, most research focuses on...
Gene model annotations are important community resources that ensure comparability and reproducibility of analyses typically the first step for functional annotation genomic regions. Without up-to-date genome annotations, sequences cannot be used to maximum advantage. It is therefore essential regularly update gene by integrating latest information guarantee reference can remain a common basis various types analyses. Here, we report an improvement Arabidopsis lyrata using extensive RNA-seq...
Quantitative trait loci (QTL) mapping is a powerful tool for investigating the genetic basis of natural variation. QTL can be mapped using number different population designs, but recombinant inbred lines (RILs) are among most effective. Unfortunately, homozygous RIL populations time consuming to construct, typically requiring at least six generations selfing starting from heterozygous F(1). Haploid plants produced an F(1) combine two parental genomes and have only one allele every locus....
Significance Micro RNAs (miRNAs) are small RNA molecules that regulate gene expression posttranscriptionally in a process known as silencing. Fine-tuning the production of miRNAs is essential for correct silencing their targets, which turn important homeostasis and development. To fine-tune miRNAs, plants deploy combination proteins act cofactors miRNA-processing machinery. Here, we describe REGULATOR OF CBF GENE EXPRESSION 3 (RCF3) tissue-specific regulator miRNA biogenesis plants. RCF3...
The ubiquity of nonparental hybrid phenotypes, such as vigor and inferiority, has interested biologists for over a century is considerable agricultural importance. Although examples both phenomena have been subject to intense investigation, no general model the molecular basis nonadditive genetic variance emerged, prediction phenotypes from parental information continues be challenge. Here we explore genetics phenotype in 435 Arabidopsis thaliana individuals derived intercrosses 30 parents...
Citrus HLB caused by Candidatus Liberibacter asiaticus is a pathogen-triggered immune disease. Here, we identified putative genetic determinants of pathogenicity integrating citrus genomic resources to characterize the pan-genome accessions that differ in their response HLB. Genome-wide association mapping and analysis allele-specific expression between susceptible, tolerant, resistant further refined candidates underlying We first developed phased diploid assembly sinensis 'Newhall' genome...
Abstract A subset of genes in plant genomes are labeled with DNA methylation specifically at CG residues. These genes, known as gene-body methylated (gbM), have a number associated characteristics. They tend to longer sequences, be enriched for intermediate expression levels, and slower rates molecular evolution. Most importantly, gbM maintain their level between species, suggesting that this trait is under evolutionary constraint. Given the degree conservation gbM, we still know...
Methylated CHH (mCHH) islands are peaks of methylation that occur primarily upstream to genes. These regions actively targeted by the machinery, at boundaries between heterochromatin and euchromatin, tend be near highly expressed Here we took an evolutionary perspective studying mCHH across a sample eight grass species. Using statistical approach define as differ from genome-wide background levels, demonstrated common associate with 39% genes, on average. We hypothesized should more frequent...
DNA methylation labels a specific subset of genes in plant genomes. Recent work has shown that this gene-body (gbM) is conserved feature orthologs, because highly methylated one species tend to be another. In study, we examined the exceptions rule by identifying differ gbM status between two species—Arabidopsis thaliana and Arabidopsis lyrata. Using Capsella grandiflora as an outgroup, polarized loss gain for orthologs lineage. Our survey identified few hundred differed ingroup species, out...
ABSTRACT Bacterial diseases like huanglongbing (HLB) and citrus canker severely impact production. HLB, caused by “ Candidatus Liberibacter asiaticus” ( C Las), leads to tree decline, while canker, Xanthomonas citri pv. (Xcc) causes necrotic lesions on leaves fruit. Many bacterial pathogens secrete effector proteins that suppress host plant immunity promote pathogenesis through the upregulation of host‐encoded susceptibility genes. Xcc uses type III secretion system introduce such as...
Abstract In plants, mammals and insects, some genes are methylated in the CG dinucleotide context, a phenomenon called gene body methylation (gbM). It has been controversial whether this any functional role. Here, we took advantage of availability 876 leaf methylomes Arabidopsis thaliana to characterize population frequency at level estimate site-frequency spectrum allelic states. Using genetics model specifically designed for epigenetic data, found that with ancestral gbM under significant...
Although much is known about the responses of model plants to microbial features, we still lack an understanding extent variation in immune perception across members a plant family. In this work, analyzed Citrus and wild relatives, surveying 86 Rutaceae genotypes with differing leaf morphologies disease resistances. We found that features vary both within between members. Species 2 subtribes, Balsamocitrinae Clauseninae, can recognize flagellin (flg22), cold shock protein (csp22), chitin,...