A5020640250- Plant Molecular Biology Research
- Plant Disease Resistance and Genetics
- Plant-Microbe Interactions and Immunity
- Chromosomal and Genetic Variations
- Wheat and Barley Genetics and Pathology
- Plant tissue culture and regeneration
- Powdery Mildew Fungal Diseases
- Plant Pathogens and Fungal Diseases
- RNA modifications and cancer
- Plant Virus Research Studies
- Weed Control and Herbicide Applications
- Plant Reproductive Biology
- Plant and Fungal Interactions Research
- Genomics and Phylogenetic Studies
- Photosynthetic Processes and Mechanisms
- Plant Pathogens and Resistance
- Pesticide and Herbicide Environmental Studies
- Plant Disease Management Techniques
- Yeasts and Rust Fungi Studies
- Mycorrhizal Fungi and Plant Interactions
- GABA and Rice Research
- Genetically Modified Organisms Research
- Plant Gene Expression Analysis
- Fungal Plant Pathogen Control
- RNA Research and Splicing
Donald Danforth Plant Science Center
2017-2024
Universidade Federal de Lavras
2014-2022
Syngenta (Switzerland)
2021
University of Missouri
2020
Australian Research Council
2020
Australian National University
2020
University of Delaware
2011-2018
Biotechnology Institute
2016-2018
Universidade Federal de Santa Catarina
2011
Universidade de São Paulo
2006
Sex chromosomes evolved from autosomes many times across the eukaryote phylogeny. Several models have been proposed to explain this transition, some involving male and female sterility mutations linked in a region of suppressed recombination between X Y (or Z/W, U/V) chromosomes. Comparative experimental analysis reference genome assembly for double haploid YY garden asparagus (Asparagus officinalis L.) individual implicates separate but genes as responsible sex determination. Dioecy has...
Significance New discoveries have been continuously made in recent years on the roles of noncoding RNAs regulating biological processes. Phased small-interfering (phasiRNAs) may be newest member discovered years. The photoperiod-sensitive male sterility (PSMS) rice is a very valuable germplasm that started era two-line hybrid rice. Here we show phasiRNAs generated by long-noncoding RNA PMS1T encoded Pms1 locus regulates PSMS This work provides case associating with trait, especially an...
The molecular mechanisms of plant recognition, colonization, and nutrient exchange between diazotrophic endophytes plants are scarcely known. Herbaspirillum seropedicae is an endophytic bacterium capable colonizing intercellular spaces grasses such as rice sugar cane. genome H. strain SmR1 was sequenced annotated by Paraná State Genome Programme—GENOPAR. composed a circular chromosome 5,513,887 bp contains total 4,804 genes. sequence revealed that highly versatile microorganism with capacity...
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 Background Rice blast is the most threatening disease to cultivated rice. Magnaporthe oryzae , its causal agent, likely encounter environmental challenges during invasive growth in host plants that require shifts gene expression establish a compatible interaction. Here, we tested hypothesis patterns planta are similar vitro stress conditions, such as nutrient limitation, temperature up shift and oxidative stress, determined which condition closely mimicked of growth. Gene data were...
The rice blast fungus, Magnaporthe oryzae is a destructive pathogen of and other related crops, causing significant yield losses worldwide. Endogenous small RNAs (sRNAs), including interfering (siRNAs) microRNAs (miRNAs) are critical components gene regulation in many eukaryotic organisms. Recently several new species sRNAs have been identified fungi. This fact along with the availability genome sequence makes M. compelling target for sRNA profiling. We examined their biosynthetic genes...
In grasses, two pathways that generate diverse and numerous 21-nt (premeiotic) 24-nt (meiotic) phased siRNAs are highly enriched in anthers, the male reproductive organs. These "phasiRNAs" analogous to mammalian piRNAs, yet their functions evolutionary origins remain largely unknown. The meiotic phasiRNAs have only been described wherein biogenesis is dependent on a specialized Dicer (DCL5). To assess how evolution gave rise this pathway, we examined phasiRNA nongrass monocots: garden...
Plants encounter pathogenic and non-pathogenic microorganisms on a nearly constant basis. Small RNAs such as siRNAs miRNAs/milRNAs influence pathogen virulence host defense responses. We exploited the biotrophic interaction between powdery mildew fungus, Blumeria graminis f. sp. hordei (Bgh), its diploid plant, barley (Hordeum vulgare) to explore fungal plant sRNAs expressed during Bgh infection of leaf epidermal cells.RNA was isolated from four fast-neutron immune-signaling mutants their...
Summary Post‐transcriptional gene silencing in plants results from independent activities of diverse small RNA types. In anthers grasses, hundreds loci yield noncoding s that are processed into 21‐ and 24‐nucleotide (nt) phased interfering (phasi s); these triggered by miR2118 miR2275. We characterized ‘reproductive phasi s’ rice ( Oryza sativa ) panicles across seven developmental stages. Our computational analysis identified characteristics the 21‐nt reproductive impact their biogenesis,...
Coffee leaf rust caused by the fungus Hemileia vastatrix is one of most important diseases coffee plantations worldwide. Current knowledge H. genome limited and only a small fraction total fungal secretome has been identified. In order to obtain more comprehensive understanding its secretome, we aimed sequence assemble entire using two next-generation sequencing platforms hybrid assembly strategy. This resulted in 547 Mb race XXXIII (Hv33), with 13,364 predicted genes that encode 13,034...
Abstract Recently, the siRNAs pathways, and especially reproductive phasiRNAs, have attracted attention in eudicots since their biological roles are still unknown biogenesis took different evolutionary pathways compared to monocots. In this work, we used Coffea arabica L., a recent allotetraploid formed from hybridization of canephora C. eugenioides unreduced gametes, explore microsporogenesis small RNAs‐related eudicot crop. First, identified stages during anther development revealing that...
Abstract Plant small RNAs are ∼20 to 24 nucleotide noncoding that typically have repressive regulatory roles in gene expression, functioning at the transcriptional or post‐transcriptional level. This influence on regulation of developmental and physiological processes has direct effects phenotype. High‐throughput sequencing technologies enabled millions RNAs. Along with decreased costs, recent improvements RNA library construction facilitated ability use minimal amounts input for analysis....
Abstract In monocots other than maize (Zea mays) and rice (Oryza sativa), the repertoire diversity of microRNAs (miRNAs) populations phased, secondary, small interfering RNAs (phasiRNAs) are poorly characterized. To remedy this, we sequenced (sRNA) from vegetative dissected inflorescence tissue in 28 phylogenetically diverse several early-diverging angiosperm lineages, as well publicly available data 10 additional monocot species. We annotated miRNAs, (siRNAs) phasiRNAs across phylogeny,...
Species of Diaporthe cause major diseases in soybean (Glycine max (L.) Merr.), including (Phomopsis) seed decay, pod and stem blight, canker. This diagnostic guide offers an overview the symptoms caused by species, as well a summary methods for culture isolation, identification, long-term storage, pathogenicity tests.
Plants and animals have evolved a first line of defense response to pathogens called innate or basal immunity. While defenses in these organisms are well studied, there is almost complete lack understanding such systems fungal species, more specifically, how they able detect mount upon pathogen attack. Hence, the goal present study was understand fungi respond biotic stress by assessing transcriptional profile rice blast pathogen, Magnaporthe oryzae, when challenged with bacterial antagonist...
Abstract Phased, secondary siRNAs (phasiRNAs) are found widely in plants, from protein-coding transcripts and long, non-coding RNAs; animal piRNAs also phased. Integrated methods characterizing “PHAS” loci unavailable, existing quite limited inefficient handling large volumes of sequencing data. The PHASIS suite described here provides complete tools for the computational characterization PHAS loci, with an emphasis on which these numerous. Benchmarked comparisons demonstrate that is...
Signals originating within plastids modulate organelle differentiation by transcriptionally regulating nuclear-encoded genes. These retrograde signals are also integral regulators of plant development, including leaf morphology. The clb5 mutant displays severe morphology defects due to Apocarotenoid Signal 1 (ACS1) accumulation in the developmentally arrested plastid. Transcriptomic analysis validates that ACS1 deregulates hundreds nuclear genes, suppression most genes encoding plastid...
SUMMARY Noncoding and coding RNAs are key regulators of plant growth, development, stress responses. To investigate the types transcripts accumulated during vegetative to reproductive transition floral development in Coffea arabica L., we sequenced small RNA libraries from eight developmental stages, up anthesis. We combined these data with messenger PARE sequencing two important stages that marks an apparent latent a rapid growth stage. In addition, took advantage multiple silico tools...
Summary Little is known about the characteristics and function of reproductive phased, secondary, small interfering RNA s (phasi s) in Poaceae, despite availability significant genomic resources, experimental data, a growing number computational tools. We utilized machine‐learning methods to identify sequence‐based positional features that distinguish phasi rice maize from other ( sRNA s). developed Random Forest classifiers can complex sets sequencing utilizing (k‐mers) describing...
Small nonprotein-coding microRNAs (miRNAs) are present in most eukaryotes and central effectors of RNA silencing-mediated mechanisms for gene expression regulation. In plants, DICER-LIKE1 (DCL1) is the founding member a highly conserved family RNase III-like endonucleases that function as core machinery proteins to process hairpin-like precursor transcripts into mature miRNAs, small regulatory RNAs, 21-22 nucleotides length. Zinc finger nucleases (ZFNs) were used generate single...
Fungicides of the succinate dehydrogenase inhibitors (SDHIs) group have been used in soybean to control Asian rust (ASR) caused by Phakopsora pachyrhizi. Fungal populations with less sensitivity SDHI fungicides reported since 2015.In this study, fungal benzovindiflupyr (BZV) and fluxapyroxad (FXD) was assessed using a total 770 P. pachyrhizi sampled over four growing seasons. Cross-resistance, intrinsic activity, frequency SDHC-I86F mutation were also analyzed. The average effective...
Abstract The rust and brown eye spot, caused by H emileia vastatrix C ercospora coffeicola , respectively, are the most important fungal diseases on coffee in South America. Their management is mainly chemical treatment, there no genetic resistance to spot known so far. Considering need for developing alternative products their control, goal of this work was evaluate effects phosphites by‐products citrus industries spot. Formulations industry by‐products, combination with fungicide were...