Date of Award

6-1-2012

Document Type

Campus Access Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Biomedical Engineering and Biotechnology

First Advisor

Richard Kesseli

Second Advisor

Kenneth Kleene

Third Advisor

Adán Colón-Carmona

Abstract

Little is known about the origins of spliceosomal introns, the role of intron changes in gene evolution, or the relative rates and mechanisms of intron loss and gain. In the present study, intron size changes were scored and the conservation of intron positions was determined for 144 single-copy orthologous genes from thirteen species belonging to four major subfamilies of the composite family of flowering plants. The gene markers, known as the conserved orthologous set, were identified from express sequence tags (ESTs) in the Compositae Genome Project (CGP) database (http://compgenomics.ucdavis.edu/). Because introns are less constrained and have higher rates of evolution than the coding sequences of a genome, intron changes might be expected to be correlated with various species characteristics, particularly if transposons drive genome expansion, and streamlining in polyploids drives genome reduction. This hypothesis was tested by comparing intron lengths in the diploid species, Lactuca sativa (lettuce, 2n = 18), a likely tetraploid, Helianthus annuus (sunflower, 2n = 34), and other composite species that represent the diverse characteristics of the family. Intron length polymorphisms were independent of genome size, ploidy level, population size, and generation time, but were closely correlated with phylogenetic relatedness. The results also indicated that Helianthus annuus is not an ancient polyploid, but the result of chromosome break, fusion, and rearrangement events. Nine intron losses and no intron gains were found in the Asteraceae. Intron loss rates were not related to the degree of diversification within the four composite subfamilies. The intron deletions were precise, without residual intronic nucleotides or lost exonic sequences, and most deletions were close to the 3' end of a gene. The missing introns were significantly shorter than average intron length, and occurred primarily within highly expressed genes. These results support the reverse transcription-mediated model of intron loss and demonstrate that putative intron-exon boundaries determined from multiple alignments of conserved orthologous sequences over extensive evolutionary distances are a useful predictor of introns. Overall, results of the research reported in this dissertation demonstrated that introns provide a useful tool for studying evolutionary processes in closely related species.

Comments

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