A5031536173- Plant Molecular Biology Research
- Soybean genetics and cultivation
- Chromosomal and Genetic Variations
- Plant Reproductive Biology
- Legume Nitrogen Fixing Symbiosis
- Plant nutrient uptake and metabolism
- Horticultural and Viticultural Research
- Plant Stress Responses and Tolerance
- Plant responses to water stress
- Plant tissue culture and regeneration
- Genomics and Phylogenetic Studies
- Epigenetics and DNA Methylation
- Fermentation and Sensory Analysis
- Plant Water Relations and Carbon Dynamics
- Plant Gene Expression Analysis
- Insect-Plant Interactions and Control
- Plant Virus Research Studies
- Plant biochemistry and biosynthesis
- Biocrusts and Microbial Ecology
- Plant and animal studies
- RNA modifications and cancer
- Photosynthetic Processes and Mechanisms
- Evolution and Genetic Dynamics
- Plant Pathogens and Resistance
- Neuroendocrine regulation and behavior
Michigan State University
2018-2025
University of Missouri
2011-2022
University of Georgia
2013-2017
David Bertioli and colleagues report the genomes of Arachis duranensis ipaensis, diploid ancestors cultivated peanut, hypogaea. Their analyses are a first step in understanding evolution peanut's tetraploid genome. Cultivated peanut (Arachis hypogaea) is an allotetraploid with closely related subgenomes total size ∼2.7 Gb. This makes assembly chromosomal pseudomolecules very challenging. As foundation to genome we sequences its ipaensis). We show that these similar A B use them identify...
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,...
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...
Although draft genomes are available for most agronomically important plant species, the majority incomplete, highly fragmented, and often riddled with assembly scaffolding errors. These issues hinder advances in tool development functional genomics systems biology.Here we utilized a robust, cost-effective approach to produce high-quality reference genomes. We report near-complete genome of diploid woodland strawberry (Fragaria vesca) using single-molecule real-time sequencing from Pacific...
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,...
The nonmethylable cytosine analogs, 5-azacytidine and zebularine, are widely used to inhibit DNA methyltransferase activity reduce genomic methylation. In this study, whole-genome bisulfite sequencing is construct maps of methylation with single base pair resolution in Arabidopsis thaliana seedlings treated each demethylating agent. We find that both inhibitor treatments result nearly indistinguishable patterns genome-wide had a slightly greater effect at higher concentrations across the...
Allopolyploidisation merges evolutionarily distinct parental genomes (subgenomes) into a single nucleus. A frequent observation is that one subgenome 'dominant' over the other subgenome, often being more highly expressed. Here, we 'replayed evolutionary tape' with six isogenic resynthesised Brassica napus allopolyploid lines and investigated dominance patterns first 10 generations postpolyploidisation. We found same was consistently dominantly expressed in all >70% of biased gene pairs...
Abstract Background Abscission is a mechanism by which plants shed entire organs in response to both developmental and environmental signals. Arabidopsis thaliana , only the floral abscise, has been used extensively study genetic, molecular cellular processes controlling abscission. requires two genes that encode functionally redundant receptor-like protein kinases, HAESA ( HAE ) HAESA-LIKE 2 HSL2 ). Double hae hsl2 mutant fail abscise their at any stage of development maturation. Results...
Abstract Subgenome dominance has been reported in diverse allopolyploid species, where genes from one subgenome are preferentially retained and more highly expressed than those other subgenome(s). However, the molecular mechanisms responsible for remain poorly understood. Here, we develop genome-wide map of accessible chromatin regions (ACRs) cultivated strawberry (2 n = 8 x 56, with A, B, C, D subgenomes). Each ACR is identified as an MNase hypersensitive site (MHS). We discover that...
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...
Abstract Background Bud sports occur spontaneously in plants when new growth exhibits a distinct phenotype from the rest of parent plant. The Witch’s Broom bud sport occurs occasionally various grapevine ( Vitis vinifera ) varieties and displays suite developmental defects, including dwarf features reduced fertility. While it is highly detrimental for growers, also serves as useful tool studying development. We used to understand trajectories sports, well potential genetic basis. analyzed...
A critical aspect of mammalian gametogenesis is the reprogramming genomic DNA methylation. The catalytically inactive adaptor Dnmt3L essential to ensuring this occurs correctly, but mechanism by which it functions unclear. Using gene targeting engineer a single-amino-acid mutation, we show that histone H3 binding domain (ADD) necessary for spermatogenesis. Genome-wide single-base-resolution methylome analysis mutant germ cells revealed overall reductions in CG methylation at repetitive...
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...
Teinturier grapevines, known for their pigmented flesh berries due to anthocyanin production, are valuable enhancing the pigmentation of wine, potential health benefits, and investigating production in plants. Here, we assembled annotated Dakapo Rubired genomes, two teinturier varieties. For Dakapo, combined Nanopore sequencing, Illumina scaffolding existing grapevine assembly generate a final 508.5 Mbp. Combining de novo annotation lifting over annotations from reference produced 36,940...
Chromosomal inversion polymorphisms are ubiquitous across the diversity of diploid organisms and play a significant role in evolution adaptations those species. Inversions thought to operate as supergenes by trapping adaptive alleles at multiple linked loci through suppression recombination. While there is now considerable support for supergene mechanism evolution, extent which inversions trap pre-existing genetic variation versus accumulate new variants over time remains unclear. In this...
Abstract Chromosomal inversion polymorphisms are ubiquitous across the diversity of diploid organisms and play a significant role in evolution adaptations those species. Inversions thought to operate as supergenes by trapping adaptive alleles at multiple linked loci through suppression recombination. While there is now considerable support for supergene mechanism evolution, extent which inversions trap pre-existing genetic variation versus accumulate new variants over time remains unclear....
Summary Processes affecting rates of sequence polymorphism are fundamental to the evolution gene duplicates. The relationship between activity and can influence likelihood that functionally redundant copies co‐maintained in stable evolutionary equilibria vs other outcomes such as neofunctionalization. Here, we investigate genic variation epigenome‐associated Arabidopsis thaliana consider whether these affect We compared frequency patterns genetic differentiation genes classified by exon...
Specialized plant cells arise from undifferentiated through a series of developmental steps. The decision to enter into certain differentiation pathway depends in many cases on signals neighbouring cells. ability engage short-range intercellular communication permits the coordination cell actions necessary processes. Overexpression genes DEVIL/ROTUNDIFOLIA (DVL/ROT) family results severe alterations, but very little is known about their mechanism action. This work presents evidence that...