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Genomic Perspectives on Evolution in Bracken Fern

Genomic Perspectives on Evolution in Bracken Fern

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Published by Joshua Der
The fern genus Pteridium comprises a number of closely related species distributed throughout the world. Collectively they are called bracken ferns and have historically been treated as a single species, Pteridium aquilinum. Bracken is notorious as a toxic weed that colonizes open fields and poisons livestock. Bracken is also easily cultured and has become one of the most intensively studied ferns. Bracken has been used as a model system for the study of the fern life cycle, fern gametophyte development, the pheromonal mechanism of sex determination, toxicology, invasion ecology, and climate change. This dissertation places bracken within a global evolutionary perspective and establishes bracken as an emerging system for evolutionary genomics in ferns. Bracken samples from around the world were examined for chloroplast DNA variation to infer historical phylogenetic and biogeographic evolutionary events. New high-throughput DNA sequencing technologies and bioinformatic approaches were used to determine the complete chloroplast genome sequence in bracken, to identify novel RNA editing sites in chloroplast transcripts, and to identify gene sequences that are expressed in the gametophyte stage of the fern life cycle. These data represent an important genomic resource in ferns and were examined within a functional and evolutionary perspective. Several novel approaches and analyses were developed in the course of this research. Results presented in this dissertation provide novel insights into fern biology and land plant evolution.
The fern genus Pteridium comprises a number of closely related species distributed throughout the world. Collectively they are called bracken ferns and have historically been treated as a single species, Pteridium aquilinum. Bracken is notorious as a toxic weed that colonizes open fields and poisons livestock. Bracken is also easily cultured and has become one of the most intensively studied ferns. Bracken has been used as a model system for the study of the fern life cycle, fern gametophyte development, the pheromonal mechanism of sex determination, toxicology, invasion ecology, and climate change. This dissertation places bracken within a global evolutionary perspective and establishes bracken as an emerging system for evolutionary genomics in ferns. Bracken samples from around the world were examined for chloroplast DNA variation to infer historical phylogenetic and biogeographic evolutionary events. New high-throughput DNA sequencing technologies and bioinformatic approaches were used to determine the complete chloroplast genome sequence in bracken, to identify novel RNA editing sites in chloroplast transcripts, and to identify gene sequences that are expressed in the gametophyte stage of the fern life cycle. These data represent an important genomic resource in ferns and were examined within a functional and evolutionary perspective. Several novel approaches and analyses were developed in the course of this research. Results presented in this dissertation provide novel insights into fern biology and land plant evolution.

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Categories:Types, Research, Science
Published by: Joshua Der on Jun 14, 2010
Copyright:Attribution Non-commercial

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01/26/2013

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GENOMIC PERSPECTIVES ON EVOLUTION IN BRACKEN FERNbyJoshua P. DerA dissertation submitted in partial fulfillmentof the requirements for the degreeofDOCTOR OF PHILOSOPHYinBiologyApproved:
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Paul G. Wolf
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Michael E. PfrenderMajor Professor
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Committee Member
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Carol D. VonDohlen
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Karen MockCommittee Member
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Committee Member
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Paul Cliften
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Byron BurnhamCommittee Member
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Dean of Graduate StudiesUTAH STATE UNIVERSITYLogan, Utah2010
 
ABSTRACTGenomic Perspectives on Evolution in Bracken FernbyJoshua P. Der, Doctor of PhilosophyUtah State University, 2010Major Professor: Paul G. WolfDepartment: BiologyThe fern genus
Pteridium 
comprises a number of closely related speciesdistributed throughout the world. Collectively they are called bracken ferns and havehistorically been treated as a single species,
Pteridium aquilinum 
. Bracken is notoriousas a toxic weed that colonizes open fields and poisons livestock. Bracken is also easilycultured and has become one of the most intensively studied ferns. Bracken has beenused as a model system for the study of the fern life cycle, fern gametophytedevelopment, the pheromonal mechanism of sex determination, toxicology, invasionecology, and climate change. This dissertation places bracken within a globalevolutionary perspective and establishes bracken as an emerging system forevolutionary genomics in ferns. Bracken samples from around the world were examinedfor chloroplast DNA variation to infer historical phylogenetic and biogeographicevolutionary events. New high-throughput DNA sequencing technologies andbioinformatic approaches were used to determine the complete chloroplast genomesequence in bracken, to identify novel RNA editing sites in chloroplast transcripts, and toidentify gene sequences that are expressed in the gametophyte stage of the fern lifeii
 
cycle. These data represent an important genomic resource in ferns and were examinedwithin a functional and evolutionary perspective. Several novel approaches and analyseswere developed in the course of this research. Results presented in this dissertationprovide novel insights into fern biology and land plant evolution.(105 pages)iii

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