http://www.loc.gov/mods/v3 http://www.loc.gov/standards/mods/v3/mods-3-2.xsd
low-copy component of the Pinus taeda genome
I have taken an alternative approach to characterize a large plant genome: sequence-based analysis of noncoding DNA. First, I have provided insight into the evolutionary processes occurring in noncoding DNA by experimentally testing the models of DNA turnover and fossil repeat contribution to low-copy DNA. Second, I have improved the basic understanding of the pine genome using a novel low-copy enrichment method. The pine genome's large size (> 20,000 Mb/1C) and conserved karyotype make it a model for basic genome organization in higher plants. Its low-copy kinetic component is in great excess to the DNA amount required for gene expression. The original Pinus strobus C₀T curve was reanalyzed using a new P. strobus genome size estimate, indicating that previous estimates of the excess low-copy component were upwardly biased. P. taeda low-copy sequences were sampled, revealing that diverged retroelements contribute to the excess low-copy DNA. Fossil repeats in the low-copy component of the pine genome were identified using a sequence-based approach. The pine genome's large (> 75%) repetitive DNA fraction impedes molecular approaches. Thus, a low-copy enrichment method was developed to facilitate efforts to characterize low-copy DNA and develop markers. The low-copy enrichment method, based on reassociation kinetics and hybrid capture, was shown to enrich for P. taeda low-copy sequences. The high proportion of repetitive DNA in the pine genome has hindered microsatellite marker development. Low-copy enrichment was tested as a method to improve marker recovery. Recovery of useful markers per sequence tested was higher from microsatellite-selected libraries constructed using P. taeda low-copy enriched DNA fragments than from total-genome microsatellite-selected libraries. A survey of the entire P. taeda range showed that the low-copy enrichment did not reduce allelism or polymorphic information content. The low-copy enrichment method provided a means to test nonrandom distribution of microsatellites within the genome. Nonrandom association of microsatellites with low-copy DNA was tested by comparing the number of microsatellite motifs in a low-copy enriched library with a total-genome library. (AC)[] motifs were overabundant among the low-copy enriched clones, but not the total-genome clones, suggesting that (AC)[] is preferentially associated with low-copy DNA.
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Includes bibliographical references (leaves 81-89).