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Axel Visel - One of the best experts on this subject based on the ideXlab platform.
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de novo transcriptome assembly of drought tolerant cam plants Agave deserti and Agave tequilana
BMC Genomics, 2013Co-Authors: Stephen Gross, Jeffrey Martin, June Simpson, Maria Jazmin Abrahamjuarez, Zhong Wang, Axel ViselAbstract:Background Agaves are succulent monocotyledonous plants native to xeric environments of North America. Because of their adaptations to their environment, including crassulacean acid metabolism (CAM, a water-efficient form of photosynthesis), and existing technologies for ethanol production, Agaves have gained attention both as potential lignocellulosic bioenergy feedstocks and models for exploring plant responses to abiotic stress. However, the lack of comprehensive Agave sequence datasets limits the scope of investigations into the molecular-genetic basis of Agave traits.
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De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana.
BMC Genomics, 2013Co-Authors: Stephen Gross, Jeffrey Martin, June Simpson, Zhong Wang, María Jazmín Abraham-juárez, Axel ViselAbstract:Background: Agaves are succulent monocotyledonous plants native to xeric environments of North America. Because of their adaptations to their environment, including crassulacean acid metabolism (CAM, a water-efficient form of photosynthesis), and existing technologies for ethanol production, Agaves have gained attention both as potential lignocellulosic bioenergy feedstocks and models for exploring plant responses to abiotic stress. However, the lack of comprehensive Agave sequence datasets limits the scope of investigations into the molecular-genetic basis of Agave traits. Results: Here, we present comprehensive, high quality de novo transcriptome assemblies of two Agave species, A. tequilana and A. deserti, built from short-read RNA-seq data. Our analyses support completeness and accuracy of the de novo transcriptome assemblies, with each species having a minimum of approximately 35,000 protein-coding genes. Comparison of Agave proteomes to those of additional plant species identifies biological functions of gene families displaying sequence divergence in Agave species. Additionally, a focus on the transcriptomics of the A. deserti juvenile leaf confirms evolutionary conservation of monocotyledonous leaf physiology and development along the proximal-distal axis. Conclusions: Our work presents a comprehensive transcriptome resource for two Agave species and provides insight into their biology and physiology. These resources are a foundation for further investigation of Agave biology and their improvement for bioenergy development.
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Transcriptome Analysis of Drought-Tolerant CAM plants Agave deserti and Agave tequilana
2013Co-Authors: Stephen Gross, Jeffrey Martin, June Simpson, Zhong Wang, Axel ViselAbstract:Agaves are succulent monocotyledonous plants native to hot and arid environments of North America. Because of their adaptations to their environment, including crassulacean acid metabolism (CAM, a water-efficient form of photosynthesis) and existing technologies for ethanol production, Agaves have gained attention both as potential lignocellulosic bioenergy feedstocks and models for exploring plant responses to abiotic stress. However, the lack of comprehensive Agave sequence datasets limits the scope of investigations into the molecular-genetic basis of Agave traits. Here, we present comprehensive, high quality de novo transcriptome assemblies of two Agave species, A. tequilana and A. deserti, from short-read RNA-seq data. Our analyses support completeness and accuracy of the de novo transcriptome assemblies, with each species having approximately 35,000 protein-coding genes. Comparison of Agave proteomes to those of additional plant species identifies biological functions of gene families displaying sequence divergence in Agave species. Additionally, we use RNA-seq data to gain insights into biological functions along the A. deserti juvenile leaf proximal-distal axis. Our work presents a foundation for further investigation of Agave biology and their improvement for bioenergy development.
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Mining the Agave Microbiome for adaptions to arid environments
2013Co-Authors: Devin Coleman-derr, Stephen Gross, Tanja Wojke, Gretchen B. North, Laila P. Partida-martinez, Kristen Deangeli, Scott Clingenpeel, Susannah G. Tringe, Axel ViselAbstract:A major challenge facing the biofuels industry is the identification of high-yield plant feedstocks that can be cultivated with minimal resource inputs without competing for land and water supplies with existing food crops. Recent research has demonstrated that the Agave plant, cultivated in Mexico and Southwestern United States for the production of fiber and alcohol, meets these criteria1. Agaves grow on non-arable rocky soils in regions characterized by prolonged drought and extreme temperatures, due in part to physiological adaptions that prevent excess water-loss in arid environments2. Plant-microbial symbioses can play a role in helping plants adapt to heat and drought stress, increasing the accessibility of soil nutrients, or compete with plant pathogens3. Whether Agaves have similar beneficial microbe interactions in their native environment is unknown. We aim to provide a comprehensive characterization of the Agave microbiome, with the goal of identifying specific community members that may contribute to Agave biotic and abiotic stress tolerance
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Agave: a biofuel feedstock for arid and semi-arid environments
2011Co-Authors: Stephen Gross, Jeffrey Martin, June Simpson, Zhong Wang, Axel ViselAbstract:Efficient production of plant-based, lignocellulosic biofuels relies upon continued improvement of existing biofuel feedstock species, as well as the introduction of newfeedstocks capable of growing on marginal lands to avoid conflicts with existing food production and minimize use of water and nitrogen resources. To this end, specieswithin the plant genus Agave have recently been proposed as new biofuel feedstocks. Many Agave species are adapted to hot and arid environments generally unsuitable forfood production, yet have biomass productivity rates comparable to other second-generation biofuel feedstocks such as switchgrass and Miscanthus. Agavesachieve remarkable heat tolerance and water use efficiency in part through a Crassulacean Acid Metabolism (CAM) mode of photosynthesis, but the genes andregulatory pathways enabling CAM and thermotolerance in Agaves remain poorly understood. We seek to accelerate the development of Agave as a new biofuelfeedstock through genomic approaches using massively-parallel sequencing technologies. First, we plan to sequence the transcriptome of A. tequilana to provide adatabase of protein-coding genes to the Agave research community. Second, we will compare transcriptome-wide gene expression of Agaves under different environmentalconditions in order to understand genetic pathways controlling CAM, water use efficiency, and thermotolerance. Finally, we aim to compare the transcriptome of A.tequilana with that of other more » Agave species to gain further insight into molecular mechanisms underlying traits desirable for biofuel feedstocks. These genomicapproaches will provide sequence and gene expression information critical to the breeding and domestication of Agave species suitable for biofuel production. « less
Stephen Gross - One of the best experts on this subject based on the ideXlab platform.
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plant compartment and biogeography affect microbiome composition in cultivated and native Agave species
New Phytologist, 2016Co-Authors: Stephen Gross, Scott Clingenpeel, Devin Colemanderr, Damaris Desgarennes, Citlali Fonsecagarcia, Tanja WoykeAbstract:Desert plants are hypothesized to survive the environmental stress inherent to these regions in part thanks to symbioses with microorganisms, and yet these microbial species, the communities they form, and the forces that influence them are poorly understood. Here we report the first comprehensive investigation of the microbial communities associated with species of Agave, which are native to semiarid and arid regions of Central and North America and are emerging as biofuel feedstocks. We examined prokaryotic and fungal communities in the rhizosphere, phyllosphere, leaf and root endosphere, as well as proximal and distal soil samples from cultivated and native Agaves, through Illumina amplicon sequencing. Phylogenetic profiling revealed that the composition of prokaryotic communities was primarily determined by the plant compartment, whereas the composition of fungal communities was mainly influenced by the biogeography of the host species. Cultivated A. tequilana exhibited lower levels of prokaryotic diversity compared with native Agaves, although no differences in microbial diversity were found in the endosphere. Agaves shared core prokaryotic and fungal taxa known to promote plant growth and confer tolerance to abiotic stress, which suggests common principles underpinning Agave-microbe interactions.
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de novo transcriptome assembly of drought tolerant cam plants Agave deserti and Agave tequilana
BMC Genomics, 2013Co-Authors: Stephen Gross, Jeffrey Martin, June Simpson, Maria Jazmin Abrahamjuarez, Zhong Wang, Axel ViselAbstract:Background Agaves are succulent monocotyledonous plants native to xeric environments of North America. Because of their adaptations to their environment, including crassulacean acid metabolism (CAM, a water-efficient form of photosynthesis), and existing technologies for ethanol production, Agaves have gained attention both as potential lignocellulosic bioenergy feedstocks and models for exploring plant responses to abiotic stress. However, the lack of comprehensive Agave sequence datasets limits the scope of investigations into the molecular-genetic basis of Agave traits.
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De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana.
BMC Genomics, 2013Co-Authors: Stephen Gross, Jeffrey Martin, June Simpson, Zhong Wang, María Jazmín Abraham-juárez, Axel ViselAbstract:Background: Agaves are succulent monocotyledonous plants native to xeric environments of North America. Because of their adaptations to their environment, including crassulacean acid metabolism (CAM, a water-efficient form of photosynthesis), and existing technologies for ethanol production, Agaves have gained attention both as potential lignocellulosic bioenergy feedstocks and models for exploring plant responses to abiotic stress. However, the lack of comprehensive Agave sequence datasets limits the scope of investigations into the molecular-genetic basis of Agave traits. Results: Here, we present comprehensive, high quality de novo transcriptome assemblies of two Agave species, A. tequilana and A. deserti, built from short-read RNA-seq data. Our analyses support completeness and accuracy of the de novo transcriptome assemblies, with each species having a minimum of approximately 35,000 protein-coding genes. Comparison of Agave proteomes to those of additional plant species identifies biological functions of gene families displaying sequence divergence in Agave species. Additionally, a focus on the transcriptomics of the A. deserti juvenile leaf confirms evolutionary conservation of monocotyledonous leaf physiology and development along the proximal-distal axis. Conclusions: Our work presents a comprehensive transcriptome resource for two Agave species and provides insight into their biology and physiology. These resources are a foundation for further investigation of Agave biology and their improvement for bioenergy development.
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Transcriptome Analysis of Drought-Tolerant CAM plants Agave deserti and Agave tequilana
2013Co-Authors: Stephen Gross, Jeffrey Martin, June Simpson, Zhong Wang, Axel ViselAbstract:Agaves are succulent monocotyledonous plants native to hot and arid environments of North America. Because of their adaptations to their environment, including crassulacean acid metabolism (CAM, a water-efficient form of photosynthesis) and existing technologies for ethanol production, Agaves have gained attention both as potential lignocellulosic bioenergy feedstocks and models for exploring plant responses to abiotic stress. However, the lack of comprehensive Agave sequence datasets limits the scope of investigations into the molecular-genetic basis of Agave traits. Here, we present comprehensive, high quality de novo transcriptome assemblies of two Agave species, A. tequilana and A. deserti, from short-read RNA-seq data. Our analyses support completeness and accuracy of the de novo transcriptome assemblies, with each species having approximately 35,000 protein-coding genes. Comparison of Agave proteomes to those of additional plant species identifies biological functions of gene families displaying sequence divergence in Agave species. Additionally, we use RNA-seq data to gain insights into biological functions along the A. deserti juvenile leaf proximal-distal axis. Our work presents a foundation for further investigation of Agave biology and their improvement for bioenergy development.
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Mining the Agave Microbiome for adaptions to arid environments
2013Co-Authors: Devin Coleman-derr, Stephen Gross, Tanja Wojke, Gretchen B. North, Laila P. Partida-martinez, Kristen Deangeli, Scott Clingenpeel, Susannah G. Tringe, Axel ViselAbstract:A major challenge facing the biofuels industry is the identification of high-yield plant feedstocks that can be cultivated with minimal resource inputs without competing for land and water supplies with existing food crops. Recent research has demonstrated that the Agave plant, cultivated in Mexico and Southwestern United States for the production of fiber and alcohol, meets these criteria1. Agaves grow on non-arable rocky soils in regions characterized by prolonged drought and extreme temperatures, due in part to physiological adaptions that prevent excess water-loss in arid environments2. Plant-microbial symbioses can play a role in helping plants adapt to heat and drought stress, increasing the accessibility of soil nutrients, or compete with plant pathogens3. Whether Agaves have similar beneficial microbe interactions in their native environment is unknown. We aim to provide a comprehensive characterization of the Agave microbiome, with the goal of identifying specific community members that may contribute to Agave biotic and abiotic stress tolerance
Judith Esmeralda Uriassilvas - One of the best experts on this subject based on the ideXlab platform.
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thermal properties of Agave fructans Agave tequilana weber var azul
Carbohydrate Polymers, 2012Co-Authors: Hugo Espinosaandrews, Judith Esmeralda UriassilvasAbstract:Abstract Thermal properties of Agave ( A. tequilana Weber var. Azul) at different water contents were investigated. HP-TLC results showed a complex mixture of mono-, di-, oligo, and polysaccharides in Agave fructans samples. The thermal decomposition temperatures were observed below to 200 °C. Modulated-differential scanning calorimetry studies showed a glass transition and a relaxation enthalpy processes in Agave fructans. Samples with the highest moieties of monosaccharides showed the lower glass transition temperatures ( Tg ). The moisture sorption isotherm of Agave fructans was determined at 20 °C and fitted to the GAB model. Gordon–Taylor equation was used to fit the Tg experimental data as a function of water content. Agave fructans was found to be an amorphous material. At low water activity ( a w ) values ( a w (0.4–0.75) collapsed and caked; and at high a w (>0.75) changed in a highly viscous liquid-like solution.
Hugo Espinosaandrews - One of the best experts on this subject based on the ideXlab platform.
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thermal properties of Agave fructans Agave tequilana weber var azul
Carbohydrate Polymers, 2012Co-Authors: Hugo Espinosaandrews, Judith Esmeralda UriassilvasAbstract:Abstract Thermal properties of Agave ( A. tequilana Weber var. Azul) at different water contents were investigated. HP-TLC results showed a complex mixture of mono-, di-, oligo, and polysaccharides in Agave fructans samples. The thermal decomposition temperatures were observed below to 200 °C. Modulated-differential scanning calorimetry studies showed a glass transition and a relaxation enthalpy processes in Agave fructans. Samples with the highest moieties of monosaccharides showed the lower glass transition temperatures ( Tg ). The moisture sorption isotherm of Agave fructans was determined at 20 °C and fitted to the GAB model. Gordon–Taylor equation was used to fit the Tg experimental data as a function of water content. Agave fructans was found to be an amorphous material. At low water activity ( a w ) values ( a w (0.4–0.75) collapsed and caked; and at high a w (>0.75) changed in a highly viscous liquid-like solution.
Jeffrey Martin - One of the best experts on this subject based on the ideXlab platform.
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de novo transcriptome assembly of drought tolerant cam plants Agave deserti and Agave tequilana
BMC Genomics, 2013Co-Authors: Stephen Gross, Jeffrey Martin, June Simpson, Maria Jazmin Abrahamjuarez, Zhong Wang, Axel ViselAbstract:Background Agaves are succulent monocotyledonous plants native to xeric environments of North America. Because of their adaptations to their environment, including crassulacean acid metabolism (CAM, a water-efficient form of photosynthesis), and existing technologies for ethanol production, Agaves have gained attention both as potential lignocellulosic bioenergy feedstocks and models for exploring plant responses to abiotic stress. However, the lack of comprehensive Agave sequence datasets limits the scope of investigations into the molecular-genetic basis of Agave traits.
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De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana.
BMC Genomics, 2013Co-Authors: Stephen Gross, Jeffrey Martin, June Simpson, Zhong Wang, María Jazmín Abraham-juárez, Axel ViselAbstract:Background: Agaves are succulent monocotyledonous plants native to xeric environments of North America. Because of their adaptations to their environment, including crassulacean acid metabolism (CAM, a water-efficient form of photosynthesis), and existing technologies for ethanol production, Agaves have gained attention both as potential lignocellulosic bioenergy feedstocks and models for exploring plant responses to abiotic stress. However, the lack of comprehensive Agave sequence datasets limits the scope of investigations into the molecular-genetic basis of Agave traits. Results: Here, we present comprehensive, high quality de novo transcriptome assemblies of two Agave species, A. tequilana and A. deserti, built from short-read RNA-seq data. Our analyses support completeness and accuracy of the de novo transcriptome assemblies, with each species having a minimum of approximately 35,000 protein-coding genes. Comparison of Agave proteomes to those of additional plant species identifies biological functions of gene families displaying sequence divergence in Agave species. Additionally, a focus on the transcriptomics of the A. deserti juvenile leaf confirms evolutionary conservation of monocotyledonous leaf physiology and development along the proximal-distal axis. Conclusions: Our work presents a comprehensive transcriptome resource for two Agave species and provides insight into their biology and physiology. These resources are a foundation for further investigation of Agave biology and their improvement for bioenergy development.
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Transcriptome Analysis of Drought-Tolerant CAM plants Agave deserti and Agave tequilana
2013Co-Authors: Stephen Gross, Jeffrey Martin, June Simpson, Zhong Wang, Axel ViselAbstract:Agaves are succulent monocotyledonous plants native to hot and arid environments of North America. Because of their adaptations to their environment, including crassulacean acid metabolism (CAM, a water-efficient form of photosynthesis) and existing technologies for ethanol production, Agaves have gained attention both as potential lignocellulosic bioenergy feedstocks and models for exploring plant responses to abiotic stress. However, the lack of comprehensive Agave sequence datasets limits the scope of investigations into the molecular-genetic basis of Agave traits. Here, we present comprehensive, high quality de novo transcriptome assemblies of two Agave species, A. tequilana and A. deserti, from short-read RNA-seq data. Our analyses support completeness and accuracy of the de novo transcriptome assemblies, with each species having approximately 35,000 protein-coding genes. Comparison of Agave proteomes to those of additional plant species identifies biological functions of gene families displaying sequence divergence in Agave species. Additionally, we use RNA-seq data to gain insights into biological functions along the A. deserti juvenile leaf proximal-distal axis. Our work presents a foundation for further investigation of Agave biology and their improvement for bioenergy development.
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Agave: a biofuel feedstock for arid and semi-arid environments
2011Co-Authors: Stephen Gross, Jeffrey Martin, June Simpson, Zhong Wang, Axel ViselAbstract:Efficient production of plant-based, lignocellulosic biofuels relies upon continued improvement of existing biofuel feedstock species, as well as the introduction of newfeedstocks capable of growing on marginal lands to avoid conflicts with existing food production and minimize use of water and nitrogen resources. To this end, specieswithin the plant genus Agave have recently been proposed as new biofuel feedstocks. Many Agave species are adapted to hot and arid environments generally unsuitable forfood production, yet have biomass productivity rates comparable to other second-generation biofuel feedstocks such as switchgrass and Miscanthus. Agavesachieve remarkable heat tolerance and water use efficiency in part through a Crassulacean Acid Metabolism (CAM) mode of photosynthesis, but the genes andregulatory pathways enabling CAM and thermotolerance in Agaves remain poorly understood. We seek to accelerate the development of Agave as a new biofuelfeedstock through genomic approaches using massively-parallel sequencing technologies. First, we plan to sequence the transcriptome of A. tequilana to provide adatabase of protein-coding genes to the Agave research community. Second, we will compare transcriptome-wide gene expression of Agaves under different environmentalconditions in order to understand genetic pathways controlling CAM, water use efficiency, and thermotolerance. Finally, we aim to compare the transcriptome of A.tequilana with that of other more » Agave species to gain further insight into molecular mechanisms underlying traits desirable for biofuel feedstocks. These genomicapproaches will provide sequence and gene expression information critical to the breeding and domestication of Agave species suitable for biofuel production. « less
