A5066299455- Soybean genetics and cultivation
- Plant Molecular Biology Research
- Plant Reproductive Biology
- Plant nutrient uptake and metabolism
- Legume Nitrogen Fixing Symbiosis
- Chromosomal and Genetic Variations
- Insect and Arachnid Ecology and Behavior
- Genetic diversity and population structure
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Plant Gene Expression Analysis
- bioluminescence and chemiluminescence research
- Epigenetics and DNA Methylation
- Insect symbiosis and bacterial influences
- Genomics and Phylogenetic Studies
- Hemiptera Insect Studies
- Plant and animal studies
- RNA modifications and cancer
- Amphibian and Reptile Biology
- Plant Virus Research Studies
- Plant-Microbe Interactions and Immunity
- Genomics and Chromatin Dynamics
- Genetic Mapping and Diversity in Plants and Animals
- Neurobiology and Insect Physiology Research
- Plant tissue culture and regeneration
- Advanced biosensing and bioanalysis techniques
University of Georgia
2015-2024
Bayer (United States)
2021
McMaster University
2010-2015
Stony Brook University
2010
Sudbury Regional Hospital
2009
Laurentian University
2009
DNA methylation is an important feature of plant epigenomes, involved in the formation heterochromatin and affecting gene expression. Extensive variation patterns within a species has been uncovered from studies natural variation. However, extent to which varies between flowering still unclear. To understand genomic patterning across species, we compared single base resolution methylomes 34 diverse angiosperm species.By analyzing whole-genome bisulfite sequencing data phylogenetic context,...
DNA methylation contributes to gene and transcriptional regulation in eukaryotes, therefore has been hypothesized facilitate the evolution of plastic traits such as sociality insects. However, is sparsely studied Therefore, we documented patterns across a wide diversity We predicted that underlying enzymatic machinery concordant with methylation. Finally, given suggestion facilitated social Hymenoptera, tested hypothesis system will be associated presence/absence among other insect orders....
Significance DNA methylation in plants is found at CG, CHG, and CHH sequence contexts. In plants, CG enriched the transcribed regions of many constitutively expressed genes (gene body methylation; gbM) shows correlations with several chromatin modifications. Contrary to other types methylation, evolution function gbM are largely unknown. Here we show two independent concomitant losses methyltransferase CHROMOMETHYLASE 3 (CMT3) without predicted disruption transcription modifications...
Recent studies have shown that one of the parental subgenomes in ancient polyploids is generally more dominant, having retained genes and being highly expressed, a phenomenon termed subgenome dominance. The genomic features determine how quickly which dominates within newly formed polyploid remain poorly understood. To investigate rate emergence dominance, we examined gene expression, methylation, transposable element (TE) methylation natural, <140-year-old allopolyploid (Mimulus...
The evolution of gene body methylation (gbM), its origins, and functional consequences are poorly understood. By pairing the largest collection transcriptomes (>1000) methylomes (77) across Viridiplantae, we provide novel insights into gbM relationship to CHROMOMETHYLASE (CMT) proteins.CMTs evolutionary conserved DNA methyltransferases in Viridiplantae. Duplication events gave rise what now referred as CMT1, 2 3. Independent losses 2, 3 eudicots, CMT2 ZMET monocots monocots/commelinids,...
Fireflies and their luminous courtships have inspired centuries of scientific study. Today firefly luciferase is widely used in biotechnology, but the evolutionary origin bioluminescence within beetles remains unclear. To shed light on this long-standing question, we sequenced genomes two species that diverged over 100 million-years-ago: North American Photinus pyralis Japanese Aquatica lateralis. compare bioluminescent origins, also genome a related click beetle, Caribbean Ignelater...
The function of cytosine (DNA) methylation in insects remains inconclusive due to a lack mutant and/or genetic studies.Here, we provide evidence for the functional role maintenance DNA methyltransferase 1 (Dnmt1) an insect using experimental manipulation. Through RNA interference (RNAi), successfully posttranscriptionally knocked down Dnmt1 ovarian tissue hemipteran Oncopeltus fasciatus (the large milkweed bug). Individuals depleted Dnmt1, and subsequently methylation, failed reproduce. Eggs...
DM-W is a dominant, female-specific, regulator of sex determination in the African clawed frog Xenopus laevis. This gene derived from partial duplication DMRT1, male-related autosomal gene. We set out to better understand by studying this pair genes. found that evolved after divergence sister genus Silurana but before X. laevis and clivii, arose DMRT1β, which one two DMRT1 paralogs tetraploid ancestor Xenopus. Using rate ratio nonsynonymous synonymous substitutions per site multilocus...
Somatic embryogenesis is an important tissue culture technique that sometimes leads to phenotypic variation via genetic and/or epigenetic changes. To understand the genomic and epigenomic impacts of somatic embryogenesis, we characterized soybean (Glycine max) epigenomes sampled from embryos at 10 different stages ranging 6 weeks 13 years continuous culture. We identified genome-wide increases in DNA methylation cultured samples, especially CHH sites. The hypermethylation almost exclusively...
Abstract The African clawed frog Xenopus laevis has a large native distribution over much of sub‐Saharan Africa and is model organism for research, proposed disease vector, an invasive species. Despite its prominent role in research abundance nature, surprisingly little known about the phylogeography evolutionary history this group. Here, we report analysis molecular variation clade based on 17 loci (one mitochondrial, 16 nuclear) up to 159 individuals sampled throughout distribution....
Abstract Duckweeds are among the fastest reproducing plants, able to clonally divide at exponential rates. However, genetic and epigenetic impact of clonality on plant genomes is poorly understood. 5-methylcytosine (5mC) a modified base often described as necessary for proper regulation certain genes transposons maintenance genome integrity in plants. extent this dogma limited by current phylogenetic sampling land species diversity. Here we analyzed DNA methylomes, small RNAs, mRNA-seq,...
In flowering plants, gene body methylation (gbM) is associated with a subset of constitutively expressed genes. It has been proposed that gbM modulates expression. Here, we show there are no consistent and direct differences to expression following the loss gbM. By comparing genes in Arabidopsis thaliana accessions orthologous two Eutrema salsugineum genotypes, identified both positive negative loss. However, largely unaffected by E. Expression between species were within variation observed...
The estimation of phylogenetic relationships is an essential component understanding evolution. Accurate difficult, however, when internodes are short and old, genealogical discordance common due to large ancestral effective population sizes or structure, homoplasy prevalent. Inference divergence times also hampered by unknown uneven rates evolution, the incomplete fossil record, uncertainty in between extant lineages, age fossils. Ideally, these challenges can be overcome developing...
Gene coexpression networks are a useful tool for summarizing transcriptomic data and providing insight into patterns of gene regulation in variety species. Though there has been considerable interest studying the evolution network topology across species, less attention paid to relationship between position molecular evolution. Here, we generated from publicly available expression seven flowering plant taxa (Arabidopsis thaliana, Glycine max, Oryza sativa, Populus spp., Solanum lycopersicum,...
Abstract To understand the variation in genomic patterning of DNA methylation we compared methylomes 34 diverse angiosperm species. By analyzing whole-genome bisulfite sequencing data a phylogenetic context it becomes clear that there is extensive throughout angiosperms gene body methylation, euchromatic silencing transposons and repeats, as well heterochromatic transposons. The Brassicaceae have reduced CHG levels also or loss CG methylation. Poaceae are characterized by lack reduction CHH...
Recent studies suggest that tumor cells overexpressing aldoketoreductases (AKRs) exhibit increased resistance to DNA damaging agents such as anthracyclines. AKRs may induce the anthracycline doxorubicin by catalyzing its conversion less toxic 13-hydroxy metabolite doxorubicinol. However, it has not been established whether during selection for resistance, AKR overexpression in can be correlated with onset or magnitude of drug and appreciable anthracyclines metabolites.Through microarray...
Sex chromosome divergence has been documented across phylogenetically diverse species, with amphibians typically having cytologically nondiverged ("homomorphic") sex chromosomes. With an aim of further characterizing amphibian, we used "RAD-tags" and Sanger sequencing to examine specificity heterozygosity in the Western clawed frog Silurana tropicalis (also known as Xenopus tropicalis). Our findings based on approximately 20 million genotype calls 200 polymerase chain reaction-amplified...
Summary The genetic basis and evolution of sex determination in dioecious plants is emerging as an active area research with exciting advances genome sequencing analysis technologies. As the sole species within sister lineage to all other extant flowering plants, Amborella trichopoda important model for understanding development flowers. Plants typically produce only male or female flowers, but mechanisms are unknown species. Sequence data derived from natural origin F1 mapping population...
Abstract We describe a suite of predictive models, coined FASTmC, for nonreference, cost-effective exploration and comparative analysis context-specific DNA methylation levels. Accurate estimations true levels can be obtained from as few several thousand short-reads generated whole-genome bisulfite sequencing. These models make high-resolution time course or developmental large diversity studies practical regardless species, genome size, availability reference genome.
Transposable elements (TEs) are repetitive DNA sequences that can make new copies of themselves inserted elsewhere in a host genome. The abundance and distributions TEs vary considerably among phylogenetically diverse hosts. With the aim exploring basis this variation, we evaluated correlations between several genomic variables presence non-TE repeats complete genome sequence Western clawed frog (Silurana tropicalis). This analysis reveals patterns TE insertion consistent with gene...