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David P Horvath - One of the best experts on this subject based on the ideXlab platform.
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gene space and transcriptome assemblies of leafy spurge Euphorbia Esula identify promoter sequences repetitive elements high quality markers and a full length chloroplast genome
Weed Science, 2018Co-Authors: David P Horvath, Michael E Foley, James V Anderson, Wun S Chao, Munevver Dogramaci, Sagar Patel, Brian E Scheffler, Gerard R Lazo, Kevin M Dorn, Changhui YanAbstract:Leafy spurge (Euphorbia Esula L.) is an invasive perennial weed infesting range and recreational lands of North America. Previous research and omics projects with E. Esula have helped develop it as a model for studying many aspects of perennial plant development and response to abiotic stress. However, the lack of an assembled genome for E. Esula has limited the power of previous transcriptomics studies to identify functional promoter elements and transcription factor binding sites. An assembled genome for E. Esula would enhance our understanding of signaling processes controlling plant development and responses to environmental stress and provide a better understanding of genetic factors impacting weediness traits, evolution, and herbicide resistance. A comprehensive transcriptome database would also assist in analyzing future RNA-seq studies and is needed to annotate and assess genomic sequence assemblies. Here, we assembled and annotated 56,234 unigenes from an assembly of 589,235 RNA-seq-derived contigs and a previously published Sanger-sequenced expressed sequence tag collection. The resulting data indicate that we now have sequence for >90% of the expressed E. Esula proteincoding genes. We also assembled the gene space of E. Esula by using a limited coverage (18X) genomic sequence database. In this study, the programs Velvet and Trinity produced the best gene-space assemblies based on representation of expressed and conserved eukaryotic genes. The results indicate that E. Esula contains as much as 23% repetitive sequences, of which 11% are unique. Our sequence data were also sufficient for assembling a full chloroplast and partial mitochondrial genome. Further, marker analysis identified more than 150,000 high-quality variants in our E. Esula L-RNA–scaffolded, whole-genome, Trinity-assembled genome. Based on these results, E. Esula appears to have limited heterozygosity. This study provides a blueprint for low-cost genomic assemblies in weed species and new resources for identifying conserved and novel promoter regions among coordinately expressed genes of E. Esula.
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the resemblance and disparity of gene expression in dormant and non dormant seeds and crown buds of leafy spurge Euphorbia Esula
BMC Plant Biology, 2014Co-Authors: Wun S Chao, Michael E Foley, James V Anderson, Munevver Dogramaci, David P HorvathAbstract:Background: Leafy spurge (Euphorbia Esula L.) is a herbaceous perennial weed and dormancy in both buds and seeds is an important survival mechanism. Bud dormancy in leafy spurge exhibits three well-defined phases of para-, endo- and ecodormancy; however, seed dormancy for leafy spurge is classified as physiological dormancy that requires after-ripening and alternating temperature for maximal germination. Overlaps in transcriptome profiles between different phases of bud and seed dormancy have not been determined. Thus, we compared various phases of dormancy between seeds and buds to identify common genes and molecular processes, which should provide new insights about common regulators of dormancy. Results: Cluster analysis of expression profiles for 201 selected genes indicated bud and seed samples clustered separately. Direct comparisons between buds and seeds are additionally complicated since seeds incubated at a constant temperature of 20°C for 21 days (21d C) could be considered paradormant (Para) because seeds may be inhibited by endosperm-generated signals, or ecodormant (Eco) because seeds germinate after being subjected to alternating temperature of 20:30°C. Since direct comparisons in gene expression between buds and seeds were problematic, we instead examined commonalities in differentially-expressed genes associated with different phases of dormancy. Comparison between buds and seeds (‘Para to Endo buds’ and ‘21d C to 1d C seeds’), using endodormant buds (Endo) and dormant seeds (1d C) as common baselines, identified transcripts associated with cell cycle (HisH4), stress response/transcription factors (ICE2, ERFB4/ABR1), ABA and auxin response (ABA1, ARF1, IAA7, TFL1), carbohydrate/protein degradation (GAPDH_1), and transport (ABCB2). Comparison of transcript abundance for the ‘Eco to Endo buds’ and ‘21d C to 1d C seeds’ identified transcripts associated with ABA response (ATEM6), auxin response (ARF1), and cell cycle (HisH4). These results indicate that the physiological state of 21d C seeds is more analogous to paradormant buds than that of ecodormant buds. Conclusion: Combined results indicate that common molecular mechanisms associated with dormancy transitions of buds and seeds involve processes associated with ABA and auxin signaling and transport, cell cycle, and AP2/ERF transcription factors or their up-stream regulators.
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initial changes in the transcriptome of Euphorbia Esula seeds induced to germinate with a combination of constant and diurnal alternating temperatures
Plant Molecular Biology, 2010Co-Authors: Michael E Foley, James V Anderson, Wun S Chao, Munevver Dogramaci, David P HorvathAbstract:We investigated transcriptome changes in Euphorbia Esula (leafy spurge) seeds with a focus on the effect of constant and diurnal fluctuating temperature on dormancy and germination. Leafy spurge seeds do not germinate when incubated for 21 days at 20°C constant temperatures, but nearly 30% germinate after 21 days under fluctuating temperatures 20:30°C (16:8 h). Incubation at 20°C for 21 days followed by 20:30°C resulted in approximately 63% germination in about 10 days. A cDNA microarray representing approximately 22,000 unique sequences was used to profile transcriptome changes in the first day after transfer of seeds from constant to alternating temperature conditions. Functional classification based on MIPS and gene ontology revealed active metabolism including up-regulation of energy, protein synthesis, and signal transduction processes. Down-regulated processes included translation elongation, translation, and some biosynthetic processes. Subnetwork analysis identified genes involved in abscisic acid, sugar, and circadian clock signaling as key regulators of physiological activity in seeds soon after the transfer to alternating conditions.
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the effects of temperature photoperiod and vernalization on regrowth and flowering competence in Euphorbia Esula Euphorbiaceae crown buds
Botany, 2009Co-Authors: Michael E Foley, James V Anderson, David P HorvathAbstract:The herbaceous perennial weed Euphorbia Esula L. (Euphorbiaceae) reproduces by vegetative and sexual means, characteristics that are key to its persistence and survival. In this study, we examined ...
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transcriptome analysis of leafy spurge Euphorbia Esula crown buds during shifts in well defined phases of dormancy
Weed Science, 2006Co-Authors: David P Horvath, James V Anderson, Mauricio Sotosuarez, Wun S ChaoAbstract:Abstract Microarray analysis was used to follow changes in gene expression coinciding with seasonal changes in the dormancy status of crown buds of field-grown leafy spurge. Known cold-regulated genes were induced, and numerous gibberellic acid–responsive genes were down-regulated during the transition from paradormancy to endodormancy. Genes involved in photomorphogenesis were induced during endodormancy. Also, ethylene signaling responses were observed during ecodormancy rather than endodormancy. These results provide additional insights into the signals regulating expression of several genes previously associated with transition from paradormancy to growth in root buds. Nomenclature: Leafy spurge, Euphorbia Esula L. EPHES.
Auge Matthew - One of the best experts on this subject based on the ideXlab platform.
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Genetic characterization of a red color morph of Euphorbia Esula subsp. Esula (Euphorbiaceae) in the floodplains of Saône (Eastern France)
NRC Research Press (a division of Canadian Science Publishing), 2016Co-Authors: Auge Matthew, Bon Marie-claude, Hardion Laurent, Le Bourgeois Thomas, René Fh SforzaAbstract:A new morph of Leafy spurge, Euphorbia Esula L., was discovered in the floodplains of the Val de Saône (VDS) France. In this region, the plant, an emerging weed, is showing two different morph colors: the common “green” variant, and a "red" variant, observed at a low proportion. We compared the sequence data for the plastid trnT trnF region among individuals of both morphs from the VDS, as well other populations from Europe, and North America, where this plant is invasive. In addition, we analysed the ploidy found among VDS individuals for both colors. Results showed that both morphs share two of the three cpDNA haplotypes found in the VDS and are both hexaploids (2n=6x=60). These results suggest that the red morph is only an environmental variant of E. Esula subsp. Esula. Our results indicated that leafy spurge infestations in this region form a genetically diverse structuring composed of three cpDNA haplotypes, two of which are shared by the two morphs.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author
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Genetic characterization of a red color morph of Euphorbia Esula subsp. Esula (Euphorbiaceae) in the floodplains of Saône (Eastern France)
'Canadian Science Publishing', 2016Co-Authors: Auge Matthew, Bon Marie-claude, Hardion Laurent, Le Bourgeois Thomas, Sforza RenéAbstract:A new morph of leafy spurge, Euphorbia Esula L., was discovered in the floodplains of the Val de Saône (VDS), France. In this region, this emerging weed shows two different morph colours: the common “green” variant and a rarer “red” variant. We compared the sequence data for the plastid trnT–trnF region among individuals of both morphs from the VDS, as well as other populations from Europe and North America, where this plant is invasive. In addition, we analysed the ploidy found among VDS individuals for both colours. Results showed that both morphs share two of the three chloroplast DNA (cpDNA) haplotypes found in the VDS and are both hexaploids (2n=6x = 60). These results suggest that the red morph is only an environmental variant of E. Esula subsp. Esula. Our results indicate that leafy spurge infestations in this region form a genetically diverse structuring composed of three cpDNA haplotypes, two of which are shared by the two morphs. (Résumé d'auteur
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Genetic characterization of a red colour morph of Euphorbia Esula subsp. Esula (Euphorbiaceae) in the floodplains of the Saône (Eastern France)
'Canadian Science Publishing', 2016Co-Authors: Auge Matthew, Bon Marie-claude, Hardion Laurent, Le Bourgeois Thomas, Sforza, René F.h.Abstract:International audienceA new morph of Leafy spurge, Euphorbia Esula L., was discovered in the floodplains of the Val de Saône (VDS) France. In this region, the plant, an emerging weed, is showing two different morph colors: the common “green” variant, and a "red" variant, observed at a low proportion. We compared the sequence data for the plastid trnT trnF region among individuals of both morphs from the VDS, as well other populations from Europe, and North America, where this plant is invasive. In addition, we analysed the ploidy found among VDS individuals for both colors. Results showed that both morphs share two of the three cpDNA haplotypes found in the VDS and are both hexaploids (2n=6x=60). These results suggest that the red morph is only an environmental variant of E. Esula subsp. Esula. Our results indicated that leafy spurge infestations in this region form a genetically diverse structuring composed of three cpDNA haplotypes, two of which are shared by the two morph
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Compréhension des facteurs d'invasion de l'euphorbe ésule (Euphorbia Esula L.) : Interactions biotiques, abiotiques et anthropiques, dans un contexte de lutte intégrée
Montpellier SupAgro, 2014Co-Authors: Auge MatthewAbstract:Les prairies humides du Val de Saône forment l'une des dernières grandes entités prairiales inondables d'Europe. A ce titre, elle possède une diversité floristique et faunistique unique, conditionnée par divers facteurs agroenvironnementaux, fortement protégée par différents réseaux (Natura 2000, ZICO, ZNIEFF). Depuis les années 1990, les agriculteurs et les gestionnaires de ces prairies, annuellement fauchées puis pâturées, demandent des solutions à une problématique de plante envahissante : Euphorbia Esula L. (Euphorbiaceae). L'euphorbe ésule se développe en taches denses dans les prairies, et compte tenu de la présence d'un latex blanc, devient toxique pour le bétail quand elle est incorporée dans le foin après la fauche. A partir de 10% de recouvrement d'une parcelle par la plante, le foin devient ainsi impropre à la consommation. La perte économique induite entraine à son tour un risque écologique : l'abandon ou la reconversion des prairies. Dans le cadre d'un vaste programme de lutte initie en 1999, nous avons, dans un premier temps, caractérise la population envahissante du Val de Saône à l'aide de marqueurs ADN chloroplastiques et l'avons comparée a d'autres populations d'euphorbe ésule envahissantes ou non. 11 apparait que l'espèce est probablement native et que sa prolifération est due à une perturbation anthropique qu'il restait à déterminer. Nous avons ensuite étudiés les différents facteurs agro-environnementaux pouvant jouer un rôle dans l'expansion de l'euphorbe ésule. Des expérimentations ont été menées sur des taches d'euphorbe dans la partie nord des prairies du Val de Sa6ne, entre 2011 et 2013. Les résultats obtenus permettent de proposer un nouvel itinéraire cultural permettant de diminuer par 90% les densités de tiges d'euphorbe en 3 ans. Deux étapes sont nécessaires: 1) ne pas faucher les taches; 2) mettre en pâture les parcelles possédant des taches non fauchées. Nous avons également montre l'impact des pratiques agriculturales classiques sur les populations de régulateurs naturels. Dans le Val de Saône les deux principaux régulateurs sont Oberea erythrocephala (Col. Cerambycidae) et Spurgia Euphorbiae (Dipt. Cecidomyiidae). Le programme de lutte intégrée propose aux agriculteurs, notamment un nouvel itinéraire cultural, devrait permettre la régulation sur le long terme de la population envahissante d'euphorbe ésule tout en augmentant l'efficacité des insectes indigènes. (Résumé d'auteur
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How understanding ecological interactions provides tools for conservation biocontrol of the weedy leafy spurge (Euphorbia Esula)
EWRS, 2013Co-Authors: Auge Matthew, Bon Marie-claude, Le Bourgeois Thomas, Contet J.m., Sforza RenéAbstract:Leafy spurge (Euphorbia Esula L. subsp. Esula, Euphorbiaceae) is a well known invasive species, not only in North America but also in Europe, its native range. Since the 1990s, its invasiveness has been reported in the floodplains of Val de Saône in central-eastern France, which are considered the last and largest European flood-meadows. Growing in dense patches, this latex-rich plant is toxic to cattle when present in cut hay. Annually mowed grasslands are losing their profitability as soon as they are infested. This economic loss may lead to ecological issues such as the shifting of mowed pastures into intensive agriculture (corn) and forestry (poplar). Natural annual floods and various agricultural practices such as mowing and grazing promote a rich floral and faunal diversity, which is protected under the Natura 2000 network. Our project is an original multidisciplinary approach to the study of invasive plant/natural regulator/agricultural practice/biotic factor interactions in two ways: 1) we are determining the biological, genetic, ecological, and agricultural factors triggering leafy spurge invasiveness, and how these factors interact; and 2) we are proposing an integrated biocontrol program combining previously obtained data, by targeting invasive plant/natural regulators interactions, connected with agricultural practices, based upon field and laboratory tests. Preliminary field results show that, as suspected, all factors tested are influencing the plant/insect complex. Mowing has a major impact on shoot density (shoots/m2), increasing it by two times on average. Mowing also negatively impacts the population size of the insect Oberea erythrocephala (Cerambycidae) by suppressing older shoots. This beetle is one of the natural phytophagous regulators of leafy spurge, and aged shoots are its major oviposition substrate. Grazing, including trampling caused by this practice, has an opposite effect, mainly on non-mowed patches that appear to attract cows. Shoot density decreased by 50 to 95% in August. This practice occurs only after O. erythrocephala population and oviposition peaks, reducing the potential impact on the density of its population. The flood factor does not seem to impair plant health. Further studies may show a positive impact on the spread of the seeds
Rodney G Lym - One of the best experts on this subject based on the ideXlab platform.
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discrimination of leafy spurge Euphorbia Esula and purple loosestrife lythrum salicaria based on field spectral data
Weed Technology, 2020Co-Authors: Kathryn Hooge M Hom, Sreekala G Bajwa, Rodney G Lym, John NowatzkiAbstract:Leafy spurge (Euphorbia Esula L.) and purple loosestrife (Lythrum salicaria L.) are invasive weeds that displace native vegetation. Herbicides are often applied to these weeds during flowering, so it would be ideal to identify them early in the season, possibly by the leaves. This paper evaluates the spectral separability of the inflorescences and leaves of these plants from surrounding vegetation. Leafy spurge, purple loosestrife, and surrounding vegetation were collected from sites in southeastern North Dakota and subjected to spectral analysis. Partial least-squares discriminant analysis (PLS-DA) was used to separate the spectral signatures of these weeds in the visible and near-infrared wavelengths. Using PLS-DA, the weeds were discriminated from their surroundings with R² values of 0.86 to 0.92. Analysis of the data indicated that the bands contributing the most to each model were in the red and red-edge spectral regions. Identifying these weeds by the leaves allows them to be mapped earlier in the season, providing more time for herbicide application planning. The spectral signatures identified in this proof of concept study are the first step before using ultra–high resolution aerial imagery to classify and identify leafy spurge and purple loosestrife. Nomenclature: Leafy spurge, Euphorbia Esula L.; purple loosestrife, Lythrum salicaria L.
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leafy spurge Euphorbia Esula control and soil seedbank composition fifteen years after release of aphthona biological control agents
Invasive Plant Science and Management, 2017Co-Authors: Blake M Thilmony, Rodney G LymAbstract:Aphthona spp. flea beetles were released in two ecological sites of the Little Missouri National Grasslands in southwestern North Dakota in 1999 to control leafy spurge. The change in leafy spurge density and soil seedbank composition was monitored to evaluate the effectiveness of the biological weed control agent and the associated change in plant communities 5, 10, and 15 yr after release in loamy overflow (valleys) and loamy sites (ridges). In 2014, 15 yr after release, leafy spurge stem density had decreased 94% from 110 to 7 stems m−2 in the loamy overflow sites and 88% from 78 to 9 stems m−2 in the loamy sites. Leafy spurge represented only 2% and 6% of the loamy overflow and loamy seedbanks in 2004, respectively, compared with nearly 67% and 70%, respectively, in 1999. There was a slow shift to reintroduction of native species into the seedbank over the last 15 yr. The number of desirable species increased to 21 by 2014 (more than three times the number of species in 1999) in the loamy overflow sites, and doubled to 14 species in the loamy sites, while less desirable forb species doubled in both sites. Desirable grass species doubled in the loamy overflow sites by 2014 but remained unchanged in loamy sites. Aphthona spp. successfully controlled leafy spurge for more than 15 yr without any additional control methods or costs to land managers and resulted in the slow return of a subset of native species.Nomenclature: Leafy spurge, Euphorbia Esula L.
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integration of biological control agents with other weed management technologies successes from the leafy spurge Euphorbia Esula ipm program
Biological Control, 2005Co-Authors: Rodney G LymAbstract:Abstract An invasive weed can occupy a variety of environments and ecological niches and generally no single control method can be used across all areas the weed is found. Biological control agents integrated with other methods can increase and/or improve site-specific weed control, but such combinatorial approaches have not been widely utilized. The successful leafy spurge ( Euphorbia Esula L.) control program provides examples for future integrated weed programs that utilize biological control agents with traditional methods. Weed control methods can be used separately, such as when the leafy spurge gall midge ( Spurgia Esulae Gagne) reduced seed production in wooded areas while herbicides prevented further spread outside the tree line. Traditional methods also can be used directly with biological control agents. Incorporation of Aphthona spp. with herbicides has resulted in more rapid and complete leafy spurge control than either method used alone. Also, the insect population often increased rapidly following herbicide treatment, especially in areas where Aphthona spp. were established for several years but had been ineffective. Incorporation of Aphthona spp. with sheep or goat grazing has resulted in a larger decline in leafy spurge production than insects alone and in weed density than grazing alone. Controlled burns can aid establishment of biological control agents in marginally suitable environments, but timing of the fire must be coordinated to the insect’s life-cycle to ensure survival. Integration of biological control agents with revegetation programs required the agent to be the last method introduced because the cultivation and herbicide treatments necessary to establish desirable grasses and forbs were destructive to the insect. In a practical application, herbicides were combined with Aphthona spp. to help the insect establish and control leafy spurge in the habitat of the western prairie fringed orchid ( Platanthera praeclara Sheviak and Bowles), an endangered species. Several experimental designs can be used to evaluate biological control agents with cultural, mechanical, and chemical control methods or with additional biological agents.
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effect of leafy spurge Euphorbia Esula genotype on feeding damage and reproduction of aphthona spp implications for biological weed control
Biological Control, 2002Co-Authors: Rodney G Lym, Robert B CarlsonAbstract:Abstract North American leafy spurge (Euphorbia Esula L.) is genetically diverse and composed of multiple genotypes introduced from several areas of Europe and Asia. Five species of leafy spurge flea beetle (Aphthona spp.) have been introduced as biological control agents for leafy spurge, but were collected in a relatively small region of Europe. Greenhouse and field experiments were conducted to determine if observed variation in feeding preference and reproduction of Aphthona spp. on North American leafy spurge may be due in part to leafy spurge genotype. Leafy spurge genotypes were collected from Austria; Manitoba in Canada; and the states of Montana, Nebraska, North Dakota, South Dakota, and Wyoming in the United States. Leafy spurge genotype affected feeding but not egg laying by Aphthona spp. adults. Aphthona czwalinae/lacertosa fed slightly less in a free-choice test on a genotype from Manitoba (7%) compared to genotypes from Nebraska and North Dakota (14%). Aphthona flava tended to feed less on the Nebraska genotype than any other genotype evaluated. Reproduction of Aphthona spp. was greatly affected by leafy spurge genotype. For instance, A. czwalinae/lacertosa produced 72 adults per plant from a Nebraska genotype compared to 11 to 32 adults per plant from all other genotypes evaluated. Thus, some observed variation in establishment and reproduction of Aphthona spp. can be attributed to leafy spurge genotype.
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leafy spurge Euphorbia Esula control and herbage production with imazapic1
Weed Technology, 2001Co-Authors: Denise M Markle, Rodney G LymAbstract:Abstract: Greenhouse and field experiments were conducted in North Dakota to determine the effect of adjuvants applied with imazapic on the control of leafy spurge and production of various grass species and to determine the most effective fall-application timing of imazapic for optimum leafy spurge control with minimal effect on herbage. Imazapic applied with a methylated seed oil (MSO) adjuvant tended to provide greater leafy spurge control than when applied with other types of adjuvants. Imazapic applied alone or with adjuvants reduced production of some grass species in the greenhouse, but it did not decrease herbage production in the field. Imazapic at 140 g/ha applied with MSO or with 28% N plus MSO averaged 72% leafy spurge control 12 mo after treatment, compared to 33% control from imazapic alone and 40% control from picloram plus 2,4-D. Imazapic at 140 g/ha applied with MSO in mid-September provided greater leafy spurge control compared to August or October applications. Nomenclature: Imazapic; l...
Michael E Foley - One of the best experts on this subject based on the ideXlab platform.
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gene space and transcriptome assemblies of leafy spurge Euphorbia Esula identify promoter sequences repetitive elements high quality markers and a full length chloroplast genome
Weed Science, 2018Co-Authors: David P Horvath, Michael E Foley, James V Anderson, Wun S Chao, Munevver Dogramaci, Sagar Patel, Brian E Scheffler, Gerard R Lazo, Kevin M Dorn, Changhui YanAbstract:Leafy spurge (Euphorbia Esula L.) is an invasive perennial weed infesting range and recreational lands of North America. Previous research and omics projects with E. Esula have helped develop it as a model for studying many aspects of perennial plant development and response to abiotic stress. However, the lack of an assembled genome for E. Esula has limited the power of previous transcriptomics studies to identify functional promoter elements and transcription factor binding sites. An assembled genome for E. Esula would enhance our understanding of signaling processes controlling plant development and responses to environmental stress and provide a better understanding of genetic factors impacting weediness traits, evolution, and herbicide resistance. A comprehensive transcriptome database would also assist in analyzing future RNA-seq studies and is needed to annotate and assess genomic sequence assemblies. Here, we assembled and annotated 56,234 unigenes from an assembly of 589,235 RNA-seq-derived contigs and a previously published Sanger-sequenced expressed sequence tag collection. The resulting data indicate that we now have sequence for >90% of the expressed E. Esula proteincoding genes. We also assembled the gene space of E. Esula by using a limited coverage (18X) genomic sequence database. In this study, the programs Velvet and Trinity produced the best gene-space assemblies based on representation of expressed and conserved eukaryotic genes. The results indicate that E. Esula contains as much as 23% repetitive sequences, of which 11% are unique. Our sequence data were also sufficient for assembling a full chloroplast and partial mitochondrial genome. Further, marker analysis identified more than 150,000 high-quality variants in our E. Esula L-RNA–scaffolded, whole-genome, Trinity-assembled genome. Based on these results, E. Esula appears to have limited heterozygosity. This study provides a blueprint for low-cost genomic assemblies in weed species and new resources for identifying conserved and novel promoter regions among coordinately expressed genes of E. Esula.
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the resemblance and disparity of gene expression in dormant and non dormant seeds and crown buds of leafy spurge Euphorbia Esula
BMC Plant Biology, 2014Co-Authors: Wun S Chao, Michael E Foley, James V Anderson, Munevver Dogramaci, David P HorvathAbstract:Background: Leafy spurge (Euphorbia Esula L.) is a herbaceous perennial weed and dormancy in both buds and seeds is an important survival mechanism. Bud dormancy in leafy spurge exhibits three well-defined phases of para-, endo- and ecodormancy; however, seed dormancy for leafy spurge is classified as physiological dormancy that requires after-ripening and alternating temperature for maximal germination. Overlaps in transcriptome profiles between different phases of bud and seed dormancy have not been determined. Thus, we compared various phases of dormancy between seeds and buds to identify common genes and molecular processes, which should provide new insights about common regulators of dormancy. Results: Cluster analysis of expression profiles for 201 selected genes indicated bud and seed samples clustered separately. Direct comparisons between buds and seeds are additionally complicated since seeds incubated at a constant temperature of 20°C for 21 days (21d C) could be considered paradormant (Para) because seeds may be inhibited by endosperm-generated signals, or ecodormant (Eco) because seeds germinate after being subjected to alternating temperature of 20:30°C. Since direct comparisons in gene expression between buds and seeds were problematic, we instead examined commonalities in differentially-expressed genes associated with different phases of dormancy. Comparison between buds and seeds (‘Para to Endo buds’ and ‘21d C to 1d C seeds’), using endodormant buds (Endo) and dormant seeds (1d C) as common baselines, identified transcripts associated with cell cycle (HisH4), stress response/transcription factors (ICE2, ERFB4/ABR1), ABA and auxin response (ABA1, ARF1, IAA7, TFL1), carbohydrate/protein degradation (GAPDH_1), and transport (ABCB2). Comparison of transcript abundance for the ‘Eco to Endo buds’ and ‘21d C to 1d C seeds’ identified transcripts associated with ABA response (ATEM6), auxin response (ARF1), and cell cycle (HisH4). These results indicate that the physiological state of 21d C seeds is more analogous to paradormant buds than that of ecodormant buds. Conclusion: Combined results indicate that common molecular mechanisms associated with dormancy transitions of buds and seeds involve processes associated with ABA and auxin signaling and transport, cell cycle, and AP2/ERF transcription factors or their up-stream regulators.
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initial changes in the transcriptome of Euphorbia Esula seeds induced to germinate with a combination of constant and diurnal alternating temperatures
Plant Molecular Biology, 2010Co-Authors: Michael E Foley, James V Anderson, Wun S Chao, Munevver Dogramaci, David P HorvathAbstract:We investigated transcriptome changes in Euphorbia Esula (leafy spurge) seeds with a focus on the effect of constant and diurnal fluctuating temperature on dormancy and germination. Leafy spurge seeds do not germinate when incubated for 21 days at 20°C constant temperatures, but nearly 30% germinate after 21 days under fluctuating temperatures 20:30°C (16:8 h). Incubation at 20°C for 21 days followed by 20:30°C resulted in approximately 63% germination in about 10 days. A cDNA microarray representing approximately 22,000 unique sequences was used to profile transcriptome changes in the first day after transfer of seeds from constant to alternating temperature conditions. Functional classification based on MIPS and gene ontology revealed active metabolism including up-regulation of energy, protein synthesis, and signal transduction processes. Down-regulated processes included translation elongation, translation, and some biosynthetic processes. Subnetwork analysis identified genes involved in abscisic acid, sugar, and circadian clock signaling as key regulators of physiological activity in seeds soon after the transfer to alternating conditions.
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the effects of temperature photoperiod and vernalization on regrowth and flowering competence in Euphorbia Esula Euphorbiaceae crown buds
Botany, 2009Co-Authors: Michael E Foley, James V Anderson, David P HorvathAbstract:The herbaceous perennial weed Euphorbia Esula L. (Euphorbiaceae) reproduces by vegetative and sexual means, characteristics that are key to its persistence and survival. In this study, we examined ...
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growth regulators and chemicals stimulate germination of leafy spurge Euphorbia Esula seeds
Weed Science, 2008Co-Authors: Michael E Foley, Wun S ChaoAbstract:Baseline information on inducing germination of dormant leafy spurge seeds with growth regulators and chemicals is lacking. This study was conducted to survey the effect of various substances on germination of leafy spurge seeds. The nontreated control seeds in this population were nearly fully imbibed in 3 h and displayed approximately 35% germination in 21 d under the normal alternating temperature of 20/30 C (16/8 h). Gibberellic acid (GA3, 10 mM) induced 65% germination at constant temperatures of 20 and 30 C. The alternating temperature increased the effectiveness of 10 mM GA3 with 94% germination, a twofold increase over the control. Nontreated seeds did not germinate at the constant temperatures, suggesting that alternating temperature acts via a GA-independent pathway. Kinetin at 0.1 to 1 mM was no more effective than the control, but a saturated solution of kinetin induced 73% germination. Ethephon at 0.01 to 1 mM induced 58 to 66% germination, although there was little response to different concentrations. Ethylene gas at 1 ppm stimulated germination to 77%, a 1.8-fold increase over the control. Germination of seeds incubated continuously in 1 and 10 mM nitrate displayed 35 and 40% germination, respectively. Seeds pulsed for 24 h with 100 mM nitrate displayed 58% germination after 21 d. Potassium phosphate– citrate buffer (pH 3.4) and its individual components induced 60 to 70% germination. Fluridone (10 and 100 mM), 1-naphthaleneacetic acid (NAA, 0.1 to 10 mM), and ethanol (0.2 to 15%) had no effect on germination, but subsequent elongation in the presence of NAA was inhibited because of swelling of the radicle. This research reveals that GA3 is the most effective growth regulator for germination of dormant leafy spurge seeds, and its effect is independent of temperature. Nomenclature: Leafy spurge, Euphorbia Esula L. EPHES.
Wun S Chao - One of the best experts on this subject based on the ideXlab platform.
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gene space and transcriptome assemblies of leafy spurge Euphorbia Esula identify promoter sequences repetitive elements high quality markers and a full length chloroplast genome
Weed Science, 2018Co-Authors: David P Horvath, Michael E Foley, James V Anderson, Wun S Chao, Munevver Dogramaci, Sagar Patel, Brian E Scheffler, Gerard R Lazo, Kevin M Dorn, Changhui YanAbstract:Leafy spurge (Euphorbia Esula L.) is an invasive perennial weed infesting range and recreational lands of North America. Previous research and omics projects with E. Esula have helped develop it as a model for studying many aspects of perennial plant development and response to abiotic stress. However, the lack of an assembled genome for E. Esula has limited the power of previous transcriptomics studies to identify functional promoter elements and transcription factor binding sites. An assembled genome for E. Esula would enhance our understanding of signaling processes controlling plant development and responses to environmental stress and provide a better understanding of genetic factors impacting weediness traits, evolution, and herbicide resistance. A comprehensive transcriptome database would also assist in analyzing future RNA-seq studies and is needed to annotate and assess genomic sequence assemblies. Here, we assembled and annotated 56,234 unigenes from an assembly of 589,235 RNA-seq-derived contigs and a previously published Sanger-sequenced expressed sequence tag collection. The resulting data indicate that we now have sequence for >90% of the expressed E. Esula proteincoding genes. We also assembled the gene space of E. Esula by using a limited coverage (18X) genomic sequence database. In this study, the programs Velvet and Trinity produced the best gene-space assemblies based on representation of expressed and conserved eukaryotic genes. The results indicate that E. Esula contains as much as 23% repetitive sequences, of which 11% are unique. Our sequence data were also sufficient for assembling a full chloroplast and partial mitochondrial genome. Further, marker analysis identified more than 150,000 high-quality variants in our E. Esula L-RNA–scaffolded, whole-genome, Trinity-assembled genome. Based on these results, E. Esula appears to have limited heterozygosity. This study provides a blueprint for low-cost genomic assemblies in weed species and new resources for identifying conserved and novel promoter regions among coordinately expressed genes of E. Esula.
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the resemblance and disparity of gene expression in dormant and non dormant seeds and crown buds of leafy spurge Euphorbia Esula
BMC Plant Biology, 2014Co-Authors: Wun S Chao, Michael E Foley, James V Anderson, Munevver Dogramaci, David P HorvathAbstract:Background: Leafy spurge (Euphorbia Esula L.) is a herbaceous perennial weed and dormancy in both buds and seeds is an important survival mechanism. Bud dormancy in leafy spurge exhibits three well-defined phases of para-, endo- and ecodormancy; however, seed dormancy for leafy spurge is classified as physiological dormancy that requires after-ripening and alternating temperature for maximal germination. Overlaps in transcriptome profiles between different phases of bud and seed dormancy have not been determined. Thus, we compared various phases of dormancy between seeds and buds to identify common genes and molecular processes, which should provide new insights about common regulators of dormancy. Results: Cluster analysis of expression profiles for 201 selected genes indicated bud and seed samples clustered separately. Direct comparisons between buds and seeds are additionally complicated since seeds incubated at a constant temperature of 20°C for 21 days (21d C) could be considered paradormant (Para) because seeds may be inhibited by endosperm-generated signals, or ecodormant (Eco) because seeds germinate after being subjected to alternating temperature of 20:30°C. Since direct comparisons in gene expression between buds and seeds were problematic, we instead examined commonalities in differentially-expressed genes associated with different phases of dormancy. Comparison between buds and seeds (‘Para to Endo buds’ and ‘21d C to 1d C seeds’), using endodormant buds (Endo) and dormant seeds (1d C) as common baselines, identified transcripts associated with cell cycle (HisH4), stress response/transcription factors (ICE2, ERFB4/ABR1), ABA and auxin response (ABA1, ARF1, IAA7, TFL1), carbohydrate/protein degradation (GAPDH_1), and transport (ABCB2). Comparison of transcript abundance for the ‘Eco to Endo buds’ and ‘21d C to 1d C seeds’ identified transcripts associated with ABA response (ATEM6), auxin response (ARF1), and cell cycle (HisH4). These results indicate that the physiological state of 21d C seeds is more analogous to paradormant buds than that of ecodormant buds. Conclusion: Combined results indicate that common molecular mechanisms associated with dormancy transitions of buds and seeds involve processes associated with ABA and auxin signaling and transport, cell cycle, and AP2/ERF transcription factors or their up-stream regulators.
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increase in acc oxidase levels and activities during paradormancy release of leafy spurge Euphorbia Esula buds
Planta, 2013Co-Authors: Wun S Chao, Marcelo D Serpe, Jeffrey C Suttle, Ying JiaAbstract:The plant hormone ethylene is known to affect various developmental processes including dormancy and growth. Yet, little information is available about the role of ethylene during paradormancy release in underground adventitious buds of leafy spurge. In this study, we examined changes in ethylene evolution and the ethylene biosynthetic enzyme ACC oxidase following paradormancy release (growth induction). Our results did not show an obvious increase in ethylene during bud growth. However, when buds were incubated with 1 mM ACC, ethylene levels were higher in growing than non-growing buds, suggesting that the levels of ACC oxidase increased in growing buds. Real-time qPCR indicated that the transcript of a Euphorbia Esula ACC oxidase (Ee-ACO) increased up to threefold following growth induction. In addition, a 2.5- to 4-fold increase in ACO activity was observed 4 days after decapitation, and the Ee-ACO accounted for 40 % of the total ACO activity. Immunoblot analyses identified a 36-kD Ee-ACO protein that increased in expression during bud growth. This protein was highly expressed in leaves, moderately expressed in crown buds, stems and meristems, and weakly expressed in roots and flowers. Immunolocalization of Ee-ACO on growing bud sections revealed strong labeling of the nucleus and cytoplasm in cells at the shoot apical meristem and leaf primordia. An exception to this pattern occurred in cells undergoing mitosis, where labeling of Ee-ACO was negligible. Taken together, our results indicated an increase in the levels of Ee-ACO during paradormancy release of leafy spurge that was not correlated with an increase in ethylene synthesis.
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initial changes in the transcriptome of Euphorbia Esula seeds induced to germinate with a combination of constant and diurnal alternating temperatures
Plant Molecular Biology, 2010Co-Authors: Michael E Foley, James V Anderson, Wun S Chao, Munevver Dogramaci, David P HorvathAbstract:We investigated transcriptome changes in Euphorbia Esula (leafy spurge) seeds with a focus on the effect of constant and diurnal fluctuating temperature on dormancy and germination. Leafy spurge seeds do not germinate when incubated for 21 days at 20°C constant temperatures, but nearly 30% germinate after 21 days under fluctuating temperatures 20:30°C (16:8 h). Incubation at 20°C for 21 days followed by 20:30°C resulted in approximately 63% germination in about 10 days. A cDNA microarray representing approximately 22,000 unique sequences was used to profile transcriptome changes in the first day after transfer of seeds from constant to alternating temperature conditions. Functional classification based on MIPS and gene ontology revealed active metabolism including up-regulation of energy, protein synthesis, and signal transduction processes. Down-regulated processes included translation elongation, translation, and some biosynthetic processes. Subnetwork analysis identified genes involved in abscisic acid, sugar, and circadian clock signaling as key regulators of physiological activity in seeds soon after the transfer to alternating conditions.
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growth regulators and chemicals stimulate germination of leafy spurge Euphorbia Esula seeds
Weed Science, 2008Co-Authors: Michael E Foley, Wun S ChaoAbstract:Baseline information on inducing germination of dormant leafy spurge seeds with growth regulators and chemicals is lacking. This study was conducted to survey the effect of various substances on germination of leafy spurge seeds. The nontreated control seeds in this population were nearly fully imbibed in 3 h and displayed approximately 35% germination in 21 d under the normal alternating temperature of 20/30 C (16/8 h). Gibberellic acid (GA3, 10 mM) induced 65% germination at constant temperatures of 20 and 30 C. The alternating temperature increased the effectiveness of 10 mM GA3 with 94% germination, a twofold increase over the control. Nontreated seeds did not germinate at the constant temperatures, suggesting that alternating temperature acts via a GA-independent pathway. Kinetin at 0.1 to 1 mM was no more effective than the control, but a saturated solution of kinetin induced 73% germination. Ethephon at 0.01 to 1 mM induced 58 to 66% germination, although there was little response to different concentrations. Ethylene gas at 1 ppm stimulated germination to 77%, a 1.8-fold increase over the control. Germination of seeds incubated continuously in 1 and 10 mM nitrate displayed 35 and 40% germination, respectively. Seeds pulsed for 24 h with 100 mM nitrate displayed 58% germination after 21 d. Potassium phosphate– citrate buffer (pH 3.4) and its individual components induced 60 to 70% germination. Fluridone (10 and 100 mM), 1-naphthaleneacetic acid (NAA, 0.1 to 10 mM), and ethanol (0.2 to 15%) had no effect on germination, but subsequent elongation in the presence of NAA was inhibited because of swelling of the radicle. This research reveals that GA3 is the most effective growth regulator for germination of dormant leafy spurge seeds, and its effect is independent of temperature. Nomenclature: Leafy spurge, Euphorbia Esula L. EPHES.
