textThe plastid genomes of land plants are generally highly conserved in gene content and order, ... more textThe plastid genomes of land plants are generally highly conserved in gene content and order, genome organization, and rates of sequence evolution; however, a few groups have experienced genomic change. The previously published sequence of Pelargonium X hortorum (Geraniaceae) reveals the largest, most rearranged plastid genome among land plants, and rate heterogeneity and genomic change have been documented in the monocot family Poaceae. Three initiatives were taken to characterize plastid genome evolution better in these groups. First, I estimate and compare genome-wide rates of sequence evolution in Geraniaceae genes relative to other angiosperms. An analysis of nucleotide substitutions for 72 plastid genes from 47 angiosperms, including nine Geraniaceae, shows that values of dN are accelerated in ribosomal protein and RNA polymerase genes. dN/dS, an indicator of selection, is significantly elevated in the same two classes of genes and ATPase genes. Second, I sequenced three additional Geraniaceae plastid genomes (Erodium texanum, Geranium palmatum, and Monsonia speciosa) and compare these sequences to each other, P. X hortorum, and other rosids. Geraniaceae plastid genomes are highly variable in size, gene content and order, and base composition. The genome of M. speciosa is among the smallest land plant plastid genomes, and one copy of the IR region in E. texanum has been lost. Gene/intron loss and gene duplication are rampant in Geraniaceae plastid genomes, and a number of losses are phylogenetically inconsistent. To explain the unusual rates and patterns of genome evolution in Geraniaceae, I propose a model of aberrant DNA repair coupled with altered gene expression. Lastly, I characterize genome evolution in the family Poaceae and order Poales. There has been a recent surge in the availability of Poaceae sequences, but a comprehensive analysis of genome evolution had not been performed that included any non-grass Poales taxa. I present the sequence of Typha latifolia (Typhaceae), the first non-grass Poales sequenced to date, and I show that Poaceae plastid genomes exhibit increased genomic rearrangements and nucleotide substitutions. These analyses show the extent of lineage-specific rate acceleration on the branch leading to Poaceae and deceleration during the diversification of the family.Biological Sciences, School o
Proceedings of the National Academy of Sciences, 2008
Angiosperm plastid genomes are generally conserved in gene content and order with rates of nucleo... more Angiosperm plastid genomes are generally conserved in gene content and order with rates of nucleotide substitutions for protein-coding genes lower than for nuclear protein-coding genes. A few groups have experienced genomic change, and extreme changes in gene content and order are found within the flowering plant family Geraniaceae. The complete plastid genome sequence of Pelargonium X hortorum (Geraniaceae) reveals the largest and most rearranged plastid genome identified to date. Highly elevated rates of sequence evolution in Geraniaceae mitochondrial genomes have been reported, but rates in Geraniaceae plastid genomes have not been characterized. Analysis of nucleotide substitution rates for 72 plastid genes for 47 angiosperm taxa, including nine Geraniaceae, show that values of dN are highly accelerated in ribosomal protein and RNA polymerase genes throughout the family. Furthermore, dN/dS is significantly elevated in the same two classes of plastid genes as well as in ATPase ge...
The ultrastructure of root cap columella cells was studied by morphometric analysis in wild-type,... more The ultrastructure of root cap columella cells was studied by morphometric analysis in wild-type, a reduced-starch mutant, and a starchless mutant of Arabidopsis grown in microgravity (F-microgravity) and compared to ground 1g (G-1g) and flight 1g (F-1g) controls. Seedlings of the wild-type and reduced-starch mutant that developed during an experiment on the Space Shuttle (both the F-microgravity samples and the F-lg control) exhibited a decreased starch content in comparison to the G-1g control. These results suggest that some factor associated with spaceflight (and not microgravity per se) affects starch metabolism. Elevated levels of ethylene were found during the experiments on the Space Shuttle, and analysis of ground controls with added ethylene demonstrated that this gas was responsible for decreased starch levels in the columella cells. This is the first study to use an on-board centrifuge as a control when quantifying starch in spaceflight-grown plants. Furthermore, our results show that ethylene levels must be carefully considered and controlled when designing experiments with plants for the International Space Station.
The brittleness of sedimentary rocks is a critical aspect of their potential to form hydraulicall... more The brittleness of sedimentary rocks is a critical aspect of their potential to form hydraulically stimulated fractures, resist embedment after stimulation, and thereby produce hydrocarbons over economically significant periods more efficiently. As such it is important to understand how brittle versus non-brittle rocks are organized within a play to improve the recovery of petroleum reserves by identifying higher potential stimulation intervals. The goal of this study is to document the link between the sequence stratigraphic hierarchy and its control on the evolution of mineralogy by FEI's QEMSCAN system, unconfined compressive rock strength, and dipole sonic derived brittleness for the Niobrara Formation. The Niobrara ultimately consists of a combination of sharply to diffusely bedded rocks composed of chalks to claystones with variable organic matter. It is mainly calcium carbonate rich with changing concentrations of detrital quartz, clay, and organic matter that function as...
textThe plastid genomes of land plants are generally highly conserved in gene content and order, ... more textThe plastid genomes of land plants are generally highly conserved in gene content and order, genome organization, and rates of sequence evolution; however, a few groups have experienced genomic change. The previously published sequence of Pelargonium X hortorum (Geraniaceae) reveals the largest, most rearranged plastid genome among land plants, and rate heterogeneity and genomic change have been documented in the monocot family Poaceae. Three initiatives were taken to characterize plastid genome evolution better in these groups. First, I estimate and compare genome-wide rates of sequence evolution in Geraniaceae genes relative to other angiosperms. An analysis of nucleotide substitutions for 72 plastid genes from 47 angiosperms, including nine Geraniaceae, shows that values of dN are accelerated in ribosomal protein and RNA polymerase genes. dN/dS, an indicator of selection, is significantly elevated in the same two classes of genes and ATPase genes. Second, I sequenced three additional Geraniaceae plastid genomes (Erodium texanum, Geranium palmatum, and Monsonia speciosa) and compare these sequences to each other, P. X hortorum, and other rosids. Geraniaceae plastid genomes are highly variable in size, gene content and order, and base composition. The genome of M. speciosa is among the smallest land plant plastid genomes, and one copy of the IR region in E. texanum has been lost. Gene/intron loss and gene duplication are rampant in Geraniaceae plastid genomes, and a number of losses are phylogenetically inconsistent. To explain the unusual rates and patterns of genome evolution in Geraniaceae, I propose a model of aberrant DNA repair coupled with altered gene expression. Lastly, I characterize genome evolution in the family Poaceae and order Poales. There has been a recent surge in the availability of Poaceae sequences, but a comprehensive analysis of genome evolution had not been performed that included any non-grass Poales taxa. I present the sequence of Typha latifolia (Typhaceae), the first non-grass Poales sequenced to date, and I show that Poaceae plastid genomes exhibit increased genomic rearrangements and nucleotide substitutions. These analyses show the extent of lineage-specific rate acceleration on the branch leading to Poaceae and deceleration during the diversification of the family.Biological Sciences, School o
Proceedings of the National Academy of Sciences, 2008
Angiosperm plastid genomes are generally conserved in gene content and order with rates of nucleo... more Angiosperm plastid genomes are generally conserved in gene content and order with rates of nucleotide substitutions for protein-coding genes lower than for nuclear protein-coding genes. A few groups have experienced genomic change, and extreme changes in gene content and order are found within the flowering plant family Geraniaceae. The complete plastid genome sequence of Pelargonium X hortorum (Geraniaceae) reveals the largest and most rearranged plastid genome identified to date. Highly elevated rates of sequence evolution in Geraniaceae mitochondrial genomes have been reported, but rates in Geraniaceae plastid genomes have not been characterized. Analysis of nucleotide substitution rates for 72 plastid genes for 47 angiosperm taxa, including nine Geraniaceae, show that values of dN are highly accelerated in ribosomal protein and RNA polymerase genes throughout the family. Furthermore, dN/dS is significantly elevated in the same two classes of plastid genes as well as in ATPase ge...
The ultrastructure of root cap columella cells was studied by morphometric analysis in wild-type,... more The ultrastructure of root cap columella cells was studied by morphometric analysis in wild-type, a reduced-starch mutant, and a starchless mutant of Arabidopsis grown in microgravity (F-microgravity) and compared to ground 1g (G-1g) and flight 1g (F-1g) controls. Seedlings of the wild-type and reduced-starch mutant that developed during an experiment on the Space Shuttle (both the F-microgravity samples and the F-lg control) exhibited a decreased starch content in comparison to the G-1g control. These results suggest that some factor associated with spaceflight (and not microgravity per se) affects starch metabolism. Elevated levels of ethylene were found during the experiments on the Space Shuttle, and analysis of ground controls with added ethylene demonstrated that this gas was responsible for decreased starch levels in the columella cells. This is the first study to use an on-board centrifuge as a control when quantifying starch in spaceflight-grown plants. Furthermore, our results show that ethylene levels must be carefully considered and controlled when designing experiments with plants for the International Space Station.
The brittleness of sedimentary rocks is a critical aspect of their potential to form hydraulicall... more The brittleness of sedimentary rocks is a critical aspect of their potential to form hydraulically stimulated fractures, resist embedment after stimulation, and thereby produce hydrocarbons over economically significant periods more efficiently. As such it is important to understand how brittle versus non-brittle rocks are organized within a play to improve the recovery of petroleum reserves by identifying higher potential stimulation intervals. The goal of this study is to document the link between the sequence stratigraphic hierarchy and its control on the evolution of mineralogy by FEI's QEMSCAN system, unconfined compressive rock strength, and dipole sonic derived brittleness for the Niobrara Formation. The Niobrara ultimately consists of a combination of sharply to diffusely bedded rocks composed of chalks to claystones with variable organic matter. It is mainly calcium carbonate rich with changing concentrations of detrital quartz, clay, and organic matter that function as...
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