The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Jeffrey D. Palmer - One of the best experts on this subject based on the ideXlab platform.
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Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or Monocots?
BMC Evolutionary Biology, 2004Co-Authors: Saša Stefanović, Danny W Rice, Jeffrey D. PalmerAbstract:Background Numerous studies, using in aggregate some 28 genes, have achieved a consensus in recognizing three groups of plants, including Amborella , as comprising the basal-most grade of all other angiosperms. A major exception is the recent study by Goremykin et al. (2003; Mol. Biol. Evol . 20:1499–1505), whose analyses of 61 genes from 13 sequenced chloroplast genomes of land plants nearly always found 100% support for Monocots as the deepest angiosperms relative to Amborella , Calycanthus , and eudicots. We hypothesized that this conflict reflects a misrooting of angiosperms resulting from inadequate taxon sampling, inappropriate phylogenetic methodology, and rapid evolution in the grass lineage used to represent Monocots. Results We used two main approaches to test this hypothesis. First, we sequenced a large number of chloroplast genes from the Monocot Acorus and added these plus previously sequenced Acorus genes to the Goremykin et al. (2003) dataset in order to explore the effects of altered Monocot sampling under the same analytical conditions used in their study. With Acorus alone representing Monocots, strongly supported Amborella -sister trees were obtained in all maximum likelihood and parsimony analyses, and in some distance-based analyses. Trees with both Acorus and grasses gave either a well-supported Amborella -sister topology or else a highly unlikely topology with 100% support for grasses-sister and paraphyly of Monocots (i.e., Acorus sister to "dicots" rather than to grasses). Second, we reanalyzed the Goremykin et al. (2003) dataset focusing on methods designed to account for rate heterogeneity. These analyses supported an Amborella -sister hypothesis, with bootstrap support values often conflicting strongly with cognate analyses performed without allowing for rate heterogeneity. In addition, we carried out a limited set of analyses that included the chloroplast genome of Nymphaea , whose position as a basal angiosperm was also, and very recently, challenged. Conclusions These analyses show that Amborella (or Amborella plus Nymphaea ), but not Monocots, is the sister group of all other angiosperms among this limited set of taxa and that the grasses-sister topology is a long-branch-attraction artifact leading to incorrect rooting of angiosperms. These results highlight the danger of having lots of characters but too few and, especially, molecularly divergent taxa, a situation long recognized as potentially producing strongly misleading molecular trees. They also emphasize the importance in phylogenetic analysis of using appropriate evolutionary models.
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long branch attraction taxon sampling and the earliest angiosperms amborella or Monocots
BMC Evolutionary Biology, 2004Co-Authors: Danny W Rice, Sasa Stefanovic, Jeffrey D. PalmerAbstract:Numerous studies, using in aggregate some 28 genes, have achieved a consensus in recognizing three groups of plants, including Amborella, as comprising the basal-most grade of all other angiosperms. A major exception is the recent study by Goremykin et al. (2003; Mol. Biol. Evol. 20:1499–1505), whose analyses of 61 genes from 13 sequenced chloroplast genomes of land plants nearly always found 100% support for Monocots as the deepest angiosperms relative to Amborella, Calycanthus, and eudicots. We hypothesized that this conflict reflects a misrooting of angiosperms resulting from inadequate taxon sampling, inappropriate phylogenetic methodology, and rapid evolution in the grass lineage used to represent Monocots. We used two main approaches to test this hypothesis. First, we sequenced a large number of chloroplast genes from the Monocot Acorus and added these plus previously sequenced Acorus genes to the Goremykin et al. (2003) dataset in order to explore the effects of altered Monocot sampling under the same analytical conditions used in their study. With Acorus alone representing Monocots, strongly supported Amborella-sister trees were obtained in all maximum likelihood and parsimony analyses, and in some distance-based analyses. Trees with both Acorus and grasses gave either a well-supported Amborella-sister topology or else a highly unlikely topology with 100% support for grasses-sister and paraphyly of Monocots (i.e., Acorus sister to "dicots" rather than to grasses). Second, we reanalyzed the Goremykin et al. (2003) dataset focusing on methods designed to account for rate heterogeneity. These analyses supported an Amborella-sister hypothesis, with bootstrap support values often conflicting strongly with cognate analyses performed without allowing for rate heterogeneity. In addition, we carried out a limited set of analyses that included the chloroplast genome of Nymphaea, whose position as a basal angiosperm was also, and very recently, challenged. These analyses show that Amborella (or Amborella plus Nymphaea), but not Monocots, is the sister group of all other angiosperms among this limited set of taxa and that the grasses-sister topology is a long-branch-attraction artifact leading to incorrect rooting of angiosperms. These results highlight the danger of having lots of characters but too few and, especially, molecularly divergent taxa, a situation long recognized as potentially producing strongly misleading molecular trees. They also emphasize the importance in phylogenetic analysis of using appropriate evolutionary models.
Rita Sharma - One of the best experts on this subject based on the ideXlab platform.
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no evidence for transient transformation via pollen magnetofection in several Monocot species
Nature plants, 2020Co-Authors: Zuzana Vejlupkova, Cedar Warman, Rita Sharma, Henrik Vibe Scheller, Jenny C MortimerAbstract:Author(s): Vejlupkova, Zuzana; Warman, Cedar; Sharma, Rita; Scheller, Henrik Vibe; Mortimer, Jenny; Fowler, John | Abstract: ABSTRACT The development of rapid and efficient transformation methods for many plant species remains an obstacle in both the basic and applied plant sciences. A novel method described by Zhao et al. (2017) used magnetic nanoparticles to deliver DNA into pollen grains of several dicot species, and one Monocot (lily), to achieve transformation (“pollen magnetofection”). Using the published protocol, extensive trials by two independent research groups showed no indication of transient transformation success with pollen from two Monocots, maize and sorghum. To further address the feasibility of magnetofection, lily pollen was used for side-by-side trials of magnetofection with a proven methodology for transient transformation, biolistics. Using a Green Fluorescent Protein reporter plasmid, transformation efficiency with the biolistic approach averaged 0.7% over three trials. However, the same plasmid produced no recognizable transformants via magnetofection, despite screening g3500 individual pollen grains. We conclude that pollen magnetofection is not effective for transient transformation of pollen for at least three species of Monocots, and suggest that efforts to replicate the magnetofection protocol in dicot species would be useful to fully assess its potential. ARISING FROM Zhao et al. Nature Plants https://doi.org/10.1038/s41477-017-0063-z (2017)
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construction of a rice glycoside hydrolase phylogenomic database and identification of targets for biofuel research
Frontiers in Plant Science, 2013Co-Authors: Pamela C. Ronald, Rita Sharma, Kihong Jung, Manoj K SharmaAbstract:Glycoside hydrolases (GH) catalyze the hydrolysis of glycosidic bonds in cell wall polymers and can have major effects on cell wall architecture. Taking advantage of the massive datasets available in public databases, we have constructed a rice phylogenomic database of GHs (http://ricephylogenomics.ucdavis.edu/cellwalls/gh/). This database integrates multiple data types including the structural features, orthologous relationships, mutant availability, and gene expression patterns for each GH family in a phylogenomic context. The rice genome encodes 437 GH genes classified into 34 families. Based on pairwise comparison with eight dicot and four Monocot genomes, we identified 138 GH genes that are highly diverged between Monocots and dicots, 57 of which have diverged further in rice as compared with four Monocot genomes scanned in this study. Chromosomal localization and expression analysis suggest a role for both whole-genome and localized gene duplications in expansion and diversification of GH families in rice. We examined the meta-profiles of expression patterns of GH genes in twenty different anatomical tissues of rice. Transcripts of 51 genes exhibit tissue or developmental stage-preferential expression, whereas, seventeen other genes preferentially accumulate in actively growing tissues. When queried in RiceNet, a probabilistic functional gene network that facilitates functional gene predictions, nine out of seventeen genes form a regulatory network with the well-characterized genes involved in biosynthesis of cell wall polymers including cellulose synthase and cellulose synthase-like genes of rice. Two-thirds of the GH genes in rice are up regulated in response to biotic and abiotic stress treatments indicating a role in stress adaptation. Our analyses identify potential GH targets for cell wall modification.
Sasa Stefanovic - One of the best experts on this subject based on the ideXlab platform.
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long branch attraction taxon sampling and the earliest angiosperms amborella or Monocots
BMC Evolutionary Biology, 2004Co-Authors: Danny W Rice, Sasa Stefanovic, Jeffrey D. PalmerAbstract:Numerous studies, using in aggregate some 28 genes, have achieved a consensus in recognizing three groups of plants, including Amborella, as comprising the basal-most grade of all other angiosperms. A major exception is the recent study by Goremykin et al. (2003; Mol. Biol. Evol. 20:1499–1505), whose analyses of 61 genes from 13 sequenced chloroplast genomes of land plants nearly always found 100% support for Monocots as the deepest angiosperms relative to Amborella, Calycanthus, and eudicots. We hypothesized that this conflict reflects a misrooting of angiosperms resulting from inadequate taxon sampling, inappropriate phylogenetic methodology, and rapid evolution in the grass lineage used to represent Monocots. We used two main approaches to test this hypothesis. First, we sequenced a large number of chloroplast genes from the Monocot Acorus and added these plus previously sequenced Acorus genes to the Goremykin et al. (2003) dataset in order to explore the effects of altered Monocot sampling under the same analytical conditions used in their study. With Acorus alone representing Monocots, strongly supported Amborella-sister trees were obtained in all maximum likelihood and parsimony analyses, and in some distance-based analyses. Trees with both Acorus and grasses gave either a well-supported Amborella-sister topology or else a highly unlikely topology with 100% support for grasses-sister and paraphyly of Monocots (i.e., Acorus sister to "dicots" rather than to grasses). Second, we reanalyzed the Goremykin et al. (2003) dataset focusing on methods designed to account for rate heterogeneity. These analyses supported an Amborella-sister hypothesis, with bootstrap support values often conflicting strongly with cognate analyses performed without allowing for rate heterogeneity. In addition, we carried out a limited set of analyses that included the chloroplast genome of Nymphaea, whose position as a basal angiosperm was also, and very recently, challenged. These analyses show that Amborella (or Amborella plus Nymphaea), but not Monocots, is the sister group of all other angiosperms among this limited set of taxa and that the grasses-sister topology is a long-branch-attraction artifact leading to incorrect rooting of angiosperms. These results highlight the danger of having lots of characters but too few and, especially, molecularly divergent taxa, a situation long recognized as potentially producing strongly misleading molecular trees. They also emphasize the importance in phylogenetic analysis of using appropriate evolutionary models.
Jenny C Mortimer - One of the best experts on this subject based on the ideXlab platform.
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no evidence for transient transformation via pollen magnetofection in several Monocot species
Nature plants, 2020Co-Authors: Zuzana Vejlupkova, Cedar Warman, Rita Sharma, Henrik Vibe Scheller, Jenny C MortimerAbstract:Author(s): Vejlupkova, Zuzana; Warman, Cedar; Sharma, Rita; Scheller, Henrik Vibe; Mortimer, Jenny; Fowler, John | Abstract: ABSTRACT The development of rapid and efficient transformation methods for many plant species remains an obstacle in both the basic and applied plant sciences. A novel method described by Zhao et al. (2017) used magnetic nanoparticles to deliver DNA into pollen grains of several dicot species, and one Monocot (lily), to achieve transformation (“pollen magnetofection”). Using the published protocol, extensive trials by two independent research groups showed no indication of transient transformation success with pollen from two Monocots, maize and sorghum. To further address the feasibility of magnetofection, lily pollen was used for side-by-side trials of magnetofection with a proven methodology for transient transformation, biolistics. Using a Green Fluorescent Protein reporter plasmid, transformation efficiency with the biolistic approach averaged 0.7% over three trials. However, the same plasmid produced no recognizable transformants via magnetofection, despite screening g3500 individual pollen grains. We conclude that pollen magnetofection is not effective for transient transformation of pollen for at least three species of Monocots, and suggest that efforts to replicate the magnetofection protocol in dicot species would be useful to fully assess its potential. ARISING FROM Zhao et al. Nature Plants https://doi.org/10.1038/s41477-017-0063-z (2017)
Danny W Rice - One of the best experts on this subject based on the ideXlab platform.
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Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or Monocots?
BMC Evolutionary Biology, 2004Co-Authors: Saša Stefanović, Danny W Rice, Jeffrey D. PalmerAbstract:Background Numerous studies, using in aggregate some 28 genes, have achieved a consensus in recognizing three groups of plants, including Amborella , as comprising the basal-most grade of all other angiosperms. A major exception is the recent study by Goremykin et al. (2003; Mol. Biol. Evol . 20:1499–1505), whose analyses of 61 genes from 13 sequenced chloroplast genomes of land plants nearly always found 100% support for Monocots as the deepest angiosperms relative to Amborella , Calycanthus , and eudicots. We hypothesized that this conflict reflects a misrooting of angiosperms resulting from inadequate taxon sampling, inappropriate phylogenetic methodology, and rapid evolution in the grass lineage used to represent Monocots. Results We used two main approaches to test this hypothesis. First, we sequenced a large number of chloroplast genes from the Monocot Acorus and added these plus previously sequenced Acorus genes to the Goremykin et al. (2003) dataset in order to explore the effects of altered Monocot sampling under the same analytical conditions used in their study. With Acorus alone representing Monocots, strongly supported Amborella -sister trees were obtained in all maximum likelihood and parsimony analyses, and in some distance-based analyses. Trees with both Acorus and grasses gave either a well-supported Amborella -sister topology or else a highly unlikely topology with 100% support for grasses-sister and paraphyly of Monocots (i.e., Acorus sister to "dicots" rather than to grasses). Second, we reanalyzed the Goremykin et al. (2003) dataset focusing on methods designed to account for rate heterogeneity. These analyses supported an Amborella -sister hypothesis, with bootstrap support values often conflicting strongly with cognate analyses performed without allowing for rate heterogeneity. In addition, we carried out a limited set of analyses that included the chloroplast genome of Nymphaea , whose position as a basal angiosperm was also, and very recently, challenged. Conclusions These analyses show that Amborella (or Amborella plus Nymphaea ), but not Monocots, is the sister group of all other angiosperms among this limited set of taxa and that the grasses-sister topology is a long-branch-attraction artifact leading to incorrect rooting of angiosperms. These results highlight the danger of having lots of characters but too few and, especially, molecularly divergent taxa, a situation long recognized as potentially producing strongly misleading molecular trees. They also emphasize the importance in phylogenetic analysis of using appropriate evolutionary models.
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long branch attraction taxon sampling and the earliest angiosperms amborella or Monocots
BMC Evolutionary Biology, 2004Co-Authors: Danny W Rice, Sasa Stefanovic, Jeffrey D. PalmerAbstract:Numerous studies, using in aggregate some 28 genes, have achieved a consensus in recognizing three groups of plants, including Amborella, as comprising the basal-most grade of all other angiosperms. A major exception is the recent study by Goremykin et al. (2003; Mol. Biol. Evol. 20:1499–1505), whose analyses of 61 genes from 13 sequenced chloroplast genomes of land plants nearly always found 100% support for Monocots as the deepest angiosperms relative to Amborella, Calycanthus, and eudicots. We hypothesized that this conflict reflects a misrooting of angiosperms resulting from inadequate taxon sampling, inappropriate phylogenetic methodology, and rapid evolution in the grass lineage used to represent Monocots. We used two main approaches to test this hypothesis. First, we sequenced a large number of chloroplast genes from the Monocot Acorus and added these plus previously sequenced Acorus genes to the Goremykin et al. (2003) dataset in order to explore the effects of altered Monocot sampling under the same analytical conditions used in their study. With Acorus alone representing Monocots, strongly supported Amborella-sister trees were obtained in all maximum likelihood and parsimony analyses, and in some distance-based analyses. Trees with both Acorus and grasses gave either a well-supported Amborella-sister topology or else a highly unlikely topology with 100% support for grasses-sister and paraphyly of Monocots (i.e., Acorus sister to "dicots" rather than to grasses). Second, we reanalyzed the Goremykin et al. (2003) dataset focusing on methods designed to account for rate heterogeneity. These analyses supported an Amborella-sister hypothesis, with bootstrap support values often conflicting strongly with cognate analyses performed without allowing for rate heterogeneity. In addition, we carried out a limited set of analyses that included the chloroplast genome of Nymphaea, whose position as a basal angiosperm was also, and very recently, challenged. These analyses show that Amborella (or Amborella plus Nymphaea), but not Monocots, is the sister group of all other angiosperms among this limited set of taxa and that the grasses-sister topology is a long-branch-attraction artifact leading to incorrect rooting of angiosperms. These results highlight the danger of having lots of characters but too few and, especially, molecularly divergent taxa, a situation long recognized as potentially producing strongly misleading molecular trees. They also emphasize the importance in phylogenetic analysis of using appropriate evolutionary models.