Current position (Example: PhD student, PhD candidate, Postdoc, Research Associate, Assistant professor etc.)
Current Affiliation (e.g., Department and University)
Year of PhD graduation if already obtained, or write PhD student, PhD candidate, etc
List 5 keywords describing your expertise. Separate them by commas.
Link to your Google scholar or Pubmed (a list of papers you have authored)
Provide a short abstract of a talk you might give. This is to get a sense of your research, it is not a commitment.
Please indicate what group(s) you identify yourself with. Some examples may include female, LGBTQ+, person with disability, under-represented minority in STEM etc. If you belong to several groups, mention all of them and put comma in between.
|Twitter handle (optional)|
Ecology, Evolution, Environmental Bio; Columbia University
phylogenetic methods, hybridization, Amaranthus, herbicide resistance,
Amaranthus is a genus of 60 species, including grain and leafy vegetable crops, herbicide resistant agricultural weeds, and rare endemics. Hybridization within this group has the potential to spread traits between crops and wild relatives and spread herbicide resistance between crops. Being able to estimate an age calibrated species tree for this genus would allow us to understand to what extent hybridization is a driver in adaptive evolution in Amaranthus. There are no known fossils in Amaranthaceae, but the genus likely originated and radiated out of the Americas. Previous estimations of the time diversification relied on 85 million year old fossils in the Chenopodioideae and the substitution rate in a single chloroplast gene to estimate a divergence time of 16-11 MYA (Waselkov et al. 2018). We developed superBPP, a new tool to estimate species divergence times, that is based on genome wide loci and the multispecies coalescent. Our method allows analysis of much larger trees than previously possible and is quicker than other methods by distributing divergence time estimates on subtrees of larger phylogenies, replicated over distributions of sampled loci in parallel, to infer a distribution of node age estimates for every node in a large species tree. We found a divergence time of 6 MYA, younger than was previously reported, with higher confidence in our results. An accurate estimate of the time of diversification of Amaranthus is fundamental to our understanding of evolutionary history of this group.
|8/12/2021 11:33:firstname.lastname@example.org||Dorota Kawa||Postdoc|
Plant Biology and Genome Center, University of California, Davis
root development, parasitic plants, beneficial microbes, sorghum, Striga
Mechanisms of microbe-induced sorghum resistance to Striga
Sorghum bicolor is one of the most important cereal crops in the world, predominantly grown in sub-Saharan Africa by smallholder farmers. Despite its outstanding resilience to the abiotic stresses, around 20% of sorghum yield is annually lost on the African continent due to the infestation with the parasitic weed Striga. Existing Striga management strategies often show low efficiency and are not easily integrated into current agricultural practices. Microbial-based solutions may prove an effective, low-cost mode for reducing Striga parasitism in sub-Saharan Africa.
We identified a field soil whose microbiome component suppressed Striga infection. Potential mechanisms underlying the soil microbiome’s influence on the host plant have been characterized and are predicted to result in resistance to Striga.
We found that the soil microbiome promotes endodermal suberization which coincides with fewer Striga attachments to sorghum root. Moreover, in a presence of microbes, we observed a depletion of haustorium inducing factors (compounds essential for Striga to establish the host-parasite association) and an increased level of the products of their degradation. Integration of root transcription, metabolite and exudation profiles were used to identify specific genes and pathways that may underlie these traits.
We identified two mechanisms by which microbes suppress Striga infection: first, where microbes induce suberized barrier for Striga parasitism in sorghum roots, and second, where microbes degrade compounds crucial for Striga to attach to the host root. Our results provide a framework for high-throughput screening of individual microbial isolates that can potentially elicit Striga resistance.
|8/12/2021 12:13:email@example.com||Maria Maldonado||Postdoc|
Molecular and Cellular Biology Department, University of California-Davis
2012 (took 6-year break in industry before postdoc)
respiratory complexes/supercomplexes, cryoEM, biochemistry, mitochondria
Mitochondrial complex III (CIII2) and complex IV (CIV), which can associate into a higher-order supercomplex (SC III2+IV), play key roles in respiration. However, structures of these plant complexes remain unknown. We present atomic models of CIII2, CIV, and SC III2+IV from Vigna radiata determined by single-particle cryoEM. The structures reveal plant-specific differences in the MPP domain of CIII2 and define the subunit composition of CIV. Conformational heterogeneity analysis of CIII2 revealed long-range, coordinated movements across the complex, as well as the motion of CIII2’s iron-sulfur head domain. The CIV structure suggests that, in plants, proton translocation does not occur via the H channel. The supercomplex interface differs significantly from that in yeast and bacteria in its interacting subunits, angle of approach and limited interactions in the mitochondrial matrix. These structures challenge long-standing assumptions about the plant complexes and generate new mechanistic hypotheses.
|female, Latin American||@mm5200|
|8/12/2021 12:25:firstname.lastname@example.org||Simon Snoeck||Postdoc|
University of Washington, department of Biology
plant immunity, plant-herbivore interaction, transmembrane receptor evolution, host plant adaptation, pesticide resistance in arthropods
Plants use germline-encoded receptors to recognize pathogen/pest-associated molecular patterns (PAMPs). The origin and evolution of specific leucine-rich repeat (LRR) receptors, which go beyond a single species, have remained understudied due to underdeveloped resources in closely related plant species. Last year, the inceptin receptor (INR) was identified, a LRR receptor triggered by inceptin (In11), a PAMP present in the oral secretion of caterpillars (Lepidoptera). INR is restricted to certain legume species, and its receptor functions (binding, signaling, and defense outputs) can be rapidly assessed through expression in the non-legume species of N. benthamiana. INR thus provides an excellent functional and comparative genomic model for the evolution of novel receptor functions in plants.
First, to pinpoint emergence of INR function within legumes, we measured immune responses triggered by In11 across twenty-two legume species of the NPAAA papillionoids. Combined with the species phylogeny, this revealed that In11 recognition is a novel trait within a relatively small subclade of the NPAAA papillionoids.
Second, we cloned a sample of the copy number and sequence variable INR homologs and tested for functionality by expressing each homolog in N. benthamiana, revealing functional and non-functional receptor homologs. The functionally validated INR-homologs are members of the same clade in a phylogenetic analysis of all mined INR homologs.
Third, we used parts of the functional and the non-functional cowpea (V. unguiculata) INR to create nine chimeric receptors. This revealed that multiple parts of the LRR-domain are crucial for maintaining the ability to respond to In11.
Given this evidence we used ancestral reconstruction to resurrect the predicted LRR-domain sequence ancestral to all functional INR-homologs and the closest related non-functional ancestral sequence.
In summary, we conducted a comprehensive evolutionary study of an LRR receptor which uncovered the origin, as well as the specific amino acid changes resulting in the gain of a novel receptor function.
|8/12/2021 13:46:email@example.com||Prem Prasad Kandel||Postdoc|
Department of Plant Pathology and Environmental Microbiology, Penn State University
Xylella, natural competence, genomics, tailocins, toxin-antitoxin systems
Talk on stress survival responses in plant pathogenic bacteria. Roles of bacteriocins and toxin-antitoxin systems in stress survival, competition, and niche adaptation
|8/12/2021 14:01:firstname.lastname@example.org||Weston Testo||Postdoc|
Department of Biological Sciences, Gothenburg University
Macroevolution, biogeography, tropics, ferns, phylogenomics
Mountains, especially in the tropics, harbor a disproportionately high percentage of Earth’s biodiversity and a remarkable number of small-ranged and rare species. This exceptional diversity is the product of varied evolutionary mechanisms, including rapid speciation in young mountain systems, biotic interchange along montane corridors, and niche segregation along steep environmental gradients. In many cases, these same processes that enable the generation of this remarkable biodiversity also result in many montane lineages being rare and threatened with extinction, highlighting the importance of mountains as areas of conservation priority. To explore why tropical mountains are so biodiverse, I’ll focus on the evolution of ferns and lycophytes, two plant lineages that are conspicuously overrepresented in mountains. I’ll discuss some of my recent and ongoing research on this topic, which includes specimen-based research, phylogenomics, integration of environmental and phylogenetic data, and the application of machine learning approaches to conservation biology.
|First-gen, Middle Eastern||westo_fernnerd|
|Mehran Dastmalchi||Assistant Professor|
McGill University, Department of Plant Science
Plant metabolism, Legumes, Natural products, Synthetic Biology, Biochemistry
Plants produce a diverse array of medicinal compounds, contributing to or inspiring over 75% of approved antibiotics and anticancer drugs in use today. The study of plant metabolism has revealed the secrets of plants such as opium poppy and Madagascar periwinkle. Knowledge of the genes and enzymes required to convert simple compounds to complex drugs is the first step in leveraging plant chemistry. Transfer of the plant metabolic machinery to engineered microorganisms (e.g., yeast) can facilitate the bio-production of the opioid antidote naloxone, and anticancer drugs vinblastine and vincristine. Along the way, we have identified bottlenecks to heterologous production in yeast, found new catalysts, and improved metabolic flux into the desired pathways. Engineered microorganisms can relieve dependence on plant cultivation and provide a dynamic, scalable, global supply of plant-derived drugs.
|8/12/2021 14:57:email@example.com||Jithesh Vijayan||Postdoc|
University of Nebraska-Lincoln
ROS, TOR-kinase, metabolism, algae, physiology
Many microbes accumulate energy storage molecules such as triglycerides and starch during nutrient limitation. In eukaryotic green algae grown under nitrogen limiting conditions, triglyceride accumulation is coupled with chlorosis and growth arrest. In this study we show that accumulation of reactive oxygen species (ROS) under nitrogen limitation in the microalga Chlorella sorokiniana is involved in thylakoid membrane remodeling, leading to chlorosis. We show that ROS accumulation under nitrogen limitation is an active process involving downregulation of expression of ROS-quenching enzymes, such as superoxide dismutases, catalase, peroxiredoxin, and glutathione peroxidase-like, and upregulation of enzymes involved in generating ROS, such as NADPH oxidase, xanthine oxidase and amine oxidases. Expression of enzymes involved in ascorbate and glutathione metabolism are also affected under these conditions. We also show that calcium influx plays a putative role in activation of NADPH oxidases, leading to ROS generation and membrane remodeling. Quenching ROS under nitrogen limitation reduces TAG accumulation, adding additional evidence for the role of ROS signaling in the process.
|8/13/2021 9:56:firstname.lastname@example.org||Vinay Shukla||Postdoc|
Department of Plant Biology and Botany, University of Geneva
Root development, Suberin, Oxygen-sensing, stress physiology, Cell-biology
Suberin is a hydrophobic biopolymer that can be deposited at the periphery of cells, forming protective barriers against biotic and abiotic stress. In roots, suberin forms lamellae at the periphery of endodermal cells where it plays crucial roles in the control of water and mineral transport. Suberin formation is highly regulated by developmental and environmental cues. However, the mechanisms controlling its spatiotemporal regulation are poorly understood. Here, we show that endodermal suberin is regulated independently by developmental and exogenous signals to fine tune suberin deposition in roots. We found a set of four MYB transcription factors (MYB41, MYB53, MYB92 and MYB93), that are regulated by these two signals, and are sufficient to promote endodermal suberin. Mutation of these four transcription factors simultaneously through genome editing, lead to a dramatic reduction of suberin formation in response to both developmental and environmental signals. Most suberin mutants analyzed at physiological levels are also affected in another endodermal barrier made of lignin (Casparian strips), through a compensatory mechanism. Through the functional analysis of these four MYBs we generated plants allowing unbiased investigations of endodermal suberin function without accounting for confounding effects due to Casparian strip defects, and could unravel specific roles of suberin in nutrient homeostasis.
|8/14/2021 0:48:email@example.com||Shiqi Zhang||Postdoc|
Boyce Thompson Institute
Ion homeostasis, Ion transport, AM symbiosis, FRET imaging, Biosensor,
In many soils, plant-available phosphate (Pi) levels are limiting for plant growth. Many plants can form symbiotic associations with arbuscular mycorrhizal (AM) fungi and acquire Pi from the fungal symbiont. Pi is transferred through arbuscules which are branched hyphae structures in cortical cells. To date, real-time mapping of the intracellular Pi content of host roots has not been reported. Here, we used a genetically-encoded Pi sensor to quantitatively image the relative Pi content of the cytosol and plastids during AM symbiosis. We found that Brachypodium distachyon root cells colonized with AM fungus Diversispora epigaea have a higher cytosolic Pi content relative to non-colonized cells. External application of Pi to the symbiotic root system induced a transient increase in cytosolic Pi in the cortical cells at 0.5h, which disappeared after 1h indicating that the sensor can detect dynamic changes in Pi content. To follow Pi transfer through the fungus, we used an experimental system that allows local 32Pi feeding to AM fungal hyphae. This revealed an increase in radioactivity in colonized root regions 18h after feeding the hyphae. The Pi sensors indicated that cortical cell cytosolic Pi levels also increased at the 18-hour timepoint, indicating that Pi uptake and transfer to the root cells occurs in this timeframe. Using a plastid-targeted sensor, we imaged the Pi content of plastids within colonized cells of an infected root region. This revealed that plastid Pi levels were the highest at the growing front and lower in cells distal from the growing front. This gradient correlates with the predicted metabolic activity of the cells. The results begin to reveal how AM fungal colonization influences intracellular Pi homeostasis of host root cells.
|8/16/2021 8:39:firstname.lastname@example.org||Yosef Fichman||Postdoc|
Division of Plant Science & Technology, Bond Life Science Center, University of Missouri
Reactive oxygen species, systemic signaling, abiotic stress, Imaging, acclimation
Systemic signaling and systemic acquired acclimation (SAA) are key to the survival of plants during episodes of abiotic stress. These processes depend on a continuous chain of cell-to-cell signaling events that extends from the initial tissue that senses the stress (local tissue) to the entire plant (systemic tissues). Among the different systemic signaling molecules and processes thought to be involved in this cell-to-cell signaling mechanism are reactive oxygen species (ROS), calcium, electric and hydraulic signals. How these different signals and processes are interlinked, and how they transmit the systemic signal all the way from the local tissue to the entire plant, remain however largely unknown. Using a newly-developed whole-plant ROS imaging method, we studied the systemic response of different Arabidopsis thaliana mutants to a local treatment of excess light stress. We report that respiratory burst oxidase homolog D (RBOHD)-generated ROS enhances cell-to-cell transport and plasmodesmata (PD) pore size in a process that depends on the function of PD-localized proteins (PDLPs) 1 and 5, promoting the cell-to-cell transport of systemic signals during responses to light stress. We further identify the aquaporin plasma intrinsic protein (PIP2;1), and several different calcium-permeable channels, belonging to the glutamate receptor-like (GLR3.3;GLR3.6), mechanosensitive small conductance-like (MSL2), and cyclic nucleotide-gated families (CNGC2), as involved in this process, but determine that their function is primarily required for the maintenance of the signal in each cell along the path of the systemic signal, as well as for the establishment of acclimation at the local and systemic tissues. PD and RBOHD-generated ROS orchestrate therefore light stress-induced rapid cell-to-cell spread of systemic signals in Arabidopsis.
|8/16/2021 10:54:email@example.com||Guangchao Sun||Postdoc|
University of Nebraska Lincoln
Plant genomics, Transcriptomics, Bioinformatics, Plant-microbe interaction, Fungal genetics,
In many cases wild species exhibit stress tolerance superior to that of domesticated crops, yet it remains unclear whether or how these properties can be transferred to crop species. Paspalum (Paspalum vaginatum) is a stress-tolerant relative of maize and sorghum that requires less nitrogen. Here we describe the assembly and annotation of the paspalum genome. Comparative genomic analysis revealed that genes involved in trehalose metabolism exhibit accelerated rates of protein sequence evolution in paspalum. Comparative metabolomics identified paspalum-specific accumulation of trehalose in
response to nutrient-deficit. Artificially induced trehalose accumulation in maize was associated with evidence of increased autophagy and greater biomass accumulation, earlier flowering and larger reproductive structures. Our findings suggest that increased turnover of cellular components via the autophagy pathway may be responsible for the decreased plasticity observed in paspalum in response to nutrient limitation. This study also provides evidence for the possibility of translating this mechanism for nutrient-deficit tolerance from wild relatives to major crops.
|8/16/2021 13:39:firstname.lastname@example.org||Keely Brown||Postdoc|
Botany and Plant Sciences, UC Riverside
Plant genetics, transcriptomics, evolution, balancing selection, genomics
We measured the floral bud transcriptome of 151 fully sequenced lines of Mimulus guttatus from one natural population. Thousands of single nucleotide polymorphisms (SNPs) are implicated as transcription regulators, but there is a striking difference in the Allele Frequency Spectrum (AFS) of cis-acting and trans-acting mutations. Cis-SNPs have intermediate frequencies (consistent with balancing selection) while trans-SNPs exhibit a rare-alleles model (consistent with purifying selection). This pattern only becomes clear when transcript variation is normalized on a gene-to-gene basis. Without this, asymmetric transcript distributions combined with “rarity disequilibrium” produce a super-abundance of false positives for trans-acting SNPs. To explore the cause of purifying selection on trans-acting mutations, we identified gene “expression modules” as sets of co-expressed genes. The extent to which trans-acting mutations influence modules is a strong predictor of allele frequency. Mutations altering expression of genes with high “connectedness” (those that are highly predictive of the representative module expression value) have the lowest allele frequency. The expression modules can also predict whole-plant traits such as flower size. We find that a substantial portion of the genetic (co)variance among traits can be described as an emergent property of genetic effects on expression modules.
|8/27/2021 9:42:email@example.com||Samar Sheat||Psotdoc|
Leibniz institute -DSMZ, Plant virus Department
PhD obatained November 2020
Cassava, viruses, screening, resistant, hybridization
Sheat, S.; Margaria, P.,Winter, S. 2021.Differential Tropism in Roots and Shoots of Resistant and Susceptible Cassava (Manihot esculenta Crantz) Infected by Cassava Brown Streak Viruses. Cells 2021, 10, (5)
Sheat, S., Winter, S. Margaria, P. 2020. Duplex In Situ Hybridization of Virus Nucleic Acids in Plant Tissues Using RNAscope®. Methods in Molecular Biology, Vol. 2148, 203-2015.
Sheat, S., Fuerholzner, B., Stein, B., Winter, S., 2019. Resistance Against Cassava Brown Streak Viruses From Africa in Cassava Germplasm From South America. Frontiers in plant science 10.
Munganyinka, E., Margaria, P., Sheat, S., Ateka, E.M., Tairo, F., Ndunguru, J., Winter, S., 2018. Localization of cassava brown streak virus in Nicotiana rustica and cassava Manihot esculenta (Crantz) using RNAscope® in situ hybridization. Virol J 15.
Mbewe, W., Tairo, F., Sseruwagi, P., Ndunguru, J., Duffy, S., Mukasa, S., Benesi, I., Sheat, S., Koerbler, M., Winter, S., 2017. Variability in P1 gene redefines phylogenetic relationships among cassava brown streak viruses. Virol J 14, 118.
Cassava brown streak and cassava mosaic viruses are severe viruses affecting the cassava crops causing severe losses.Our work focuses on identifying and understanding the mechanism of the resistance in CBSD and CMD.
We have identified resistance in cassava against Cassava brown streak virus (CBSV, Mo) and Ugandan cassava brown streak virus (UCBSV, Ke). The viruses cause a systemic infection in their host which leads to the destruction of the edible tuberous roots. The resistance we have identified in several germplasm lines is associated with a restriction of virus replication and, a restriction of virus movement from the phloem companion cells to the neighboring parenchyma cells and, is acting globally, on both virus species or, differentially, targeting only one of the species.
Since cellular processes are involved in virus movement and include plasmodesmata, we are investigating the role of virus genes (Ham 1, CP, VPg and P1) in opening the gate for cell to cell movement. We have generated cDNA clones of the viruses (ICs) that are infectious in cassava and in the model plant Nicotiana benthamiana. Using GFP labeled viruses and recombinant CBSV and UCBSV constructs carrying respective genes of the opposite species, we follow the infection process to gain insight into viral and host genes associated with the resistance response. A unique Maf/ham1-like pyrophosphatase (Ham1) present only in cassava brown streak species was our first candidate. GFP labeled clones for both CBSV and UCBSV showed different patterns in unloading in the systemically infected leaf in N.benthamiana. CBSV unloaded from the lateral veins while UCBSV used the main veins, deletion of the Ham1 didn't have any effect on the virus infection in N. benthamiana and tracing both the CBSV and UCBSV clones and the clones that were lacking the Ham1 didn't show any difference in the cellular level. While in early infections the viruses are absent in mesophyll cells, virus accumulation in the perinucleolar compartment (PNC) and virus aggregates in plasmodesmata and in plasma membranes during later stages provide evidence for extensive trafficking through those channels.
However Ham1 is indispensable for infections in cassava. Exchanging the Ham1 of CBSV with Ham1 of UCBSV (CBSVΔHamKe) caused an attenuation of the systemic infection and reduction of virus titer. In contrast, replacing Ham1 of UCBSV with the respective gene of CBSV enhanced symptom expression and dramatically enhanced virus replication and plant invasion. The symptoms caused in cassava with Ham1 recombinant viruses were similar to the Ham1 wild type origin. When plants of the cassava line DSC167 with resistance against CBSV but not UCBSV were infected, resistance in DSC167 against UCBSVΔHam1Mo mutant viruses was achieved the virus remained restricted to phloem companion cells only. Further studies about specific virus proteins interacting with particular PD proteins to understand trafficking through PD may then contribute towards an explanation why in virus resistant cassava plants this trafficking does not takes place.
ore over in case of CMD, using the resistant identified plant we were able to prove that resistant is based on restriction of virus replication and delay in virus movement(long distant).
Crossing between CBSV resistant plants and CMB resistant plants had provided dual resistance for CBSV and CBSD with the hope to tackle those diseases
|9/21/2021 0:10:firstname.lastname@example.org||Bulbul Ahmed||Postdoc|
Plant science, McGill university
Functional genomics, microbiome, plant-microbe interaction
|Visible minority (Asian)|
University of Massachusetts, Boston; Department of Biology
plant genetics; plant breeding; genomics; phenomics; gene mapping
Genomic solutions for plant breeding: towards a sustainable agriculture
While doing your groceries or selecting which plants to grow in your garden, you might notice the variety of colors, shapes, smells, and flavors of crop plants. This extraordinary phenotypic variability results from years of traditional and advanced plant breeding, which is the process of creating improved plant individuals with desirable characteristics. Generally, an improved crop variety derives from the selection and crossing of parents with outstanding profiles for traits of interest, a practice old as much as agriculture that has evolved in final goals and procedures across human history. Today advances in genetics and genomics are revolutionizing and accelerating plant breeding, by providing instruments to (i) access genetic diversity in a multitude of wild and cultivated accessions; (ii) understand the evolutionary history of crop species; and (iii) identify genomic regions involved in the control of traits crucial for commercial use and adaptation to changing environments. During my research, I have used approaches of quantitative and population genetics to provide fundamental insights on trait variation in different crop species, including grapevine (Vitis vinifera L.), walnut (Juglans regia L.), and rice (Oryza sativa L.). In this talk, I will illustrate the development and application of advanced genomic tools in these crops, and their precious impact on addressing present and future needs in agriculture. With modern technologies in constant evolution, plant breeding represents an opportunity for agriculture to keep sustaining a growing global population while reducing land and resource exploitation.
|ISHAN AJMERA||Research Scholar||Penn State University||2016|
Mathematical and Computational Modeling, Systems Biology, Plant Phenotying, Root Biology,
University of Nebraska-Lincoln
Heat stress, Endosperm cellularization, Rice, Cell cycle, Endosplasmic reticulum
Rice seed is comprised of embryo, endosperm and maternal tissues, where endosperm occupies ~88% of seed volume. After fertilization, endosperm development proceeds rapidly with repeated acytokinetic mitotic divisions resulting in a nuclear/coenocytic endosperm, followed by a transition to the cellularized state. The duration and rate of nuclear divisions during the coenocytic stage are key determinants of yield since the number of coenocytic nuclei typically correlates with mature seed size. Further, endosperm cellularization exhibits high heat sensitivity.
Here we used the developing seed transcriptome to develop a differential co-expression network that identified OsMYB3R-3 and several other regulators of early seed development. Characterization of OsMYB3R-3, a three MYB repeat protein, showed that it is implicated in cytokinin-mediated regulation of early seed growth under heat stress. OsMYB3R-3 deficiency increased seed size and weight under control conditions but reduced heat resilience of seeds. Collectively, this study enhances our understanding of the molecular mechanisms controlling the interactions between temperature and developmental dynamics in developing seeds.
Female, International scholar
Sunil K. Kenchanmane Raju
Plant Biology, Michigan State University
Epigenetics, comparative epigenomics, regulatory genomics, abiotic stress
Epigenome divergence drives expression specificity and mutation rate changes in A. thaliana paralogs.
The complex interactions of genome and epigenome on duplicate gene evolution across a broad phylogenetic scale remains elusive. We identified pervasive trends in the association of DNA methylation with gene duplication, age of duplication, and sequence evolution by comparing genomes and methylomes of 43 plant species. DNA methylation was associated with duplicate age, sequence divergence, and expression specificity. Younger WGDs tend to show CG methylation (gene body methylation; gbM), while younger SGDs showed enrichment for both CG and non-CG methylation (transposon-like methylation; teM). Across the sampled plant species, we see that DNA methylation is a strong marker of duplicate gene age, sequence evolution, and expression specificity. At a population scale, across 928 A. thaliana ecotypes, more recent duplicates show increased frequency of teM. TeM genes show higher single-nucleotide polymorphisms in natural population. This higher polymorphism and increased de novo mutations from mutation accumulation lines combined with a more negative population genetic test statistic, Tajima’s D, suggests that the increased rate of polymorphisms in teM genes is more likely due to higher mutation rates. Furthermore, duplicate pairs where one of the paralogs is teM shows higher absolute difference in mutation rate, independent of C-to-T transitions, suggesting that epigenome divergence drives mutation rate differences between A. thaliana paralogs.
|Kaushal Kumar Bhati||Postdoc|
University of Louvain, Belgium
Crop improvement, microProteins, abiotic stress
Under represented minority in STEM, First Generation
Batthula Vijaya Lakshmi Vadde
Plant developmental biology, cell biology, genetics, transcriptomics
|Female, First generation|
|6/24/2022 13:46:email@example.com||Dustin Ray|
Postdoctoral Research Associate
University of Minnesota Duluth
structure, function, phloem, petiole, leaf
Plants must transport water to the leaves and sugar to the plant body for survival, but are there constraints on how water and sugar can be moved? My work will address this general question from two perspectives: that of the organ (the leaf and specifically the petiole), and that of a specific tissue (the sugar conducting tissue).
|Felix Juan Martinez Rivas||Postdoc|
Max Planck institute for molecular plant physiology
Ripening, metabolomics, transcription factor, gene regulation, stress response
|6/25/2022 2:09:firstname.lastname@example.org||Mayuri Sadoine||Postdoc||Heinrich-Heine University||2018|
Biosensors, Biophysics, plant-pathogens, plant-microbes, plant-pathogen interactions
“If you want to go fast, go alone. If you want to go far, go together” – African proverb
Being mutualistic or egoistic that is the question.
Female, under-represented minority in STEM
Max Planck institute for Biology Tuebingen
Epigenetic memory, rna-silencing, paramutation, tomato, DNA methylation
Defying Mendel’s laws: CMT3/KYP maintain paramutation in tomato plants.
Paramutation represents a clear exception to the principles of inheritance established by Gregor Mendel in the 19th century. It involves the transfer of repressive epigenetic marks from a silent to an active allele and thereby violates Mendel’s first law of independent allele segregation. By violating Mendel’s first law of independent allele segregation, Paramutation results from the transfer of repressive epigenetic marks from silent to active homologous alleles. It is best known from conspicuous pigmentation phenotypes in maize but the Paramutation phenomena was also reported across diverse plant and animal species. Paramutation-like events are common in tomato hybrids suggesting that paramutation may be less exceptional and rather a frequently co-occurring process during cross-hybridisation.
Here we use the classic example of paramutation in tomato – sulfurea (sulf), an understudied chlorosis phenotype associated with transgenerationally dependent allele segregation patterns – to dissect the epigenetic- and transgenerational mechanisms underlying paramutation in tomato plants. Our results show that the DNA- and histone-methyl transferases CMT3 and KYP are required for the maintenance of paramutation and that there is a change in chromatin architecture associated with the silent epiallele. We further demonstrate that in tomato the developmental and transgenerational maintenance of paramutation is independent of sRNAs, a mechanism previously suggested to explain the trans-communication between homologues as well as the maintenance of silent paramutated states across mitotic and meiotic divisions in maize. Together, our data significantly extends the current understanding of the paramutation model in plants by integrating existing concepts into a revised framework of non-Mendelian heredity.
Female, First gen, Immigrant
|8/4/2022 12:50:email@example.com||Caroline Dong||Postdoc|
Tulane University, Department of Ecology and Evolutionary Biology
speciation, hybridization, coloration, phenotype, evolutionary genetics
Divergence and speciation can occur across as spectrum of geographic context. In sympatry with gene flow, the forces of selection and gene flow oppose each other. While gene flow acts as a homogenizing force, strong selection drives divergence of alleles between lineages. Theory predicts that in this scenario, the genomic signature of speciation is that of islands of divergence. During gene flow, recombination breaks up linkage between alleles making it difficult to evolve and maintain traits contributing to assortative mating. However, traits which contribute to both local adaptation and reproductive isolation are very effective at driving the process of speciation (‘magic traits’). An emerging potential ‘magic trait’ is ultraviolet (UV) floral coloration. I examine two monkeyflower (Mimulus) species that are locally adapted to contrasting microhabitats and display variation in UV morphs. My research examines the underlying genetic architecture of UV coloration in allopatric and sympatric populations using QTL mapping, and its role in local adaptation and reproductive isolation using field experiments.
Biology department, University of Massachusetts Amherst
Cell biology, nuclear movement, cell polarity, asymmetric cell division
An outer nuclear membrane protein dictates the nuclear positioning and future division site
First-gen, Immigrant, Muslim, People of color